GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in DLBC-TP
Lymphoid Neoplasm Diffuse Large B-cell Lymphoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C189158P
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in DLBC-TP. Broad Institute of MIT and Harvard. doi:10.7908/C189158P
Overview
Introduction

This pipeline performs Gene Set Enrichment Analysis (GSEA) using The Broad Institute GSEA tool with MSigDB - Class2: Canonical Pathways gene sets. For a given phenotype subtype, it shows what pathways are significantly enriched in each subtype by comparing gene expression profiles between subtypes. Here, the phenotype is mRNAseq_cNMF subtypes having more than three samples and the input expression file "DLBC-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt" is generated in the pipeline mRNAseq_Preprocess in the stddata run. This pipeline has the following features:

  1. For each subtype, calculates enrichment scores (ES) using signal to noise (S2N) that checks similarity between subtypes in expression level then calculates p values through permutation test.

  2. Lists pathways significantly enriched in each phenotype subtype and their enrichment scores (ES).

  3. Lists top 20 core genes enriched in each significant gene set and their enrichment scores (ES).

  4. Checks if the top core genes are up-regulated or down-regulated.

  5. Checks if the top core genes are high expressed or low expressed.

  6. Checks if the top core genes are significantly differently expressed genes.

Summary

Table 1.  Get Full Table basic data info

basic data info
Number of Gene Sets: 708
Number of samples: 48
Original number of Gene Sets: 1320
Maximum gene set size: 933

Table 2.  Get Full Table pheno data info

phenotype info
pheno.type: 1 - 6 :[ clus1 ] 10
pheno.type: 2 - 6 :[ clus2 ] 12
pheno.type: 3 - 6 :[ clus3 ] 9
pheno.type: 4 - 6 :[ clus4 ] 3
pheno.type: 5 - 6 :[ clus5 ] 8
pheno.type: 6 - 6 :[ clus6 ] 6

For the expression subtypes of 17683 genes in 49 samples, GSEA found enriched gene sets in each cluster using 48 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

  • clus1

    • Top enriched gene sets are KEGG OXIDATIVE PHOSPHORYLATION, KEGG PYRIMIDINE METABOLISM, KEGG ARGININE AND PROLINE METABOLISM, KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM, KEGG PYRUVATE METABOLISM, PID INTEGRIN3 PATHWAY, PID AVB3 INTEGRIN PATHWAY, PID SYNDECAN 1 PATHWAY, PID INTEGRIN A4B1 PATHWAY, REACTOME ANTIGEN PROCESSING CROSS PRESENTATION

    • And common core enriched genes are ALDH1B1, ALDH2, ABP1, ACY1, ADC, AGMAT, ALDH7A1, ARG2, ASL, ASS1

  • clus2

    • Top enriched gene sets are KEGG NOTCH SIGNALING PATHWAY, KEGG T CELL RECEPTOR SIGNALING PATHWAY, KEGG THYROID CANCER, KEGG PRIMARY IMMUNODEFICIENCY, BIOCARTA DEATH PATHWAY, BIOCARTA VIP PATHWAY, BIOCARTA TCR PATHWAY, ST T CELL SIGNAL TRANSDUCTION, PID TCR PATHWAY, PID CD8TCRPATHWAY

    • And common core enriched genes are CD3D, ZAP70, CD3E, CD28, GRAP2, ITK, LAT, LCP2, NCK1, RASGRP1

  • clus3

    • Top enriched gene sets are PID AURORA B PATHWAY, PID ATR PATHWAY, PID CDC42 REG PATHWAY, PID ATM PATHWAY, PID BARD1PATHWAY, REACTOME METABOLISM OF NON CODING RNA, REACTOME TRANSPORT OF MATURE TRANSCRIPT TO CYTOPLASM, REACTOME RNA POL II TRANSCRIPTION, REACTOME CELL CYCLE MITOTIC, REACTOME RECRUITMENT OF MITOTIC CENTROSOME PROTEINS AND COMPLEXES

    • And common core enriched genes are ATM, BRCA1, CDC25A, CDC25C, FANCD2, MRE11A, RAD50, RBBP8, NCBP1, NUP107

  • clus4

    • Top enriched gene sets are KEGG BASAL TRANSCRIPTION FACTORS, BIOCARTA CARM ER PATHWAY, BIOCARTA CREB PATHWAY, BIOCARTA VEGF PATHWAY, SIG BCR SIGNALING PATHWAY, PID FANCONI PATHWAY, PID E2F PATHWAY, PID ATM PATHWAY, PID HDAC CLASSI PATHWAY, PID PLK1 PATHWAY

    • And common core enriched genes are CDK2, CREBBP, EP300, KAT2B, ATM, CSNK1G3, MAPK8, MAPK9, RBL2, SIRT1

  • clus5

    • Top enriched gene sets are KEGG OXIDATIVE PHOSPHORYLATION, KEGG RIBOSOME, KEGG PARKINSONS DISEASE, KEGG HUNTINGTONS DISEASE, REACTOME TRANSLATION, REACTOME FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX, REACTOME TCA CYCLE AND RESPIRATORY ELECTRON TRANSPORT, REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE, REACTOME ACTIVATION OF NF KAPPAB IN B CELLS, REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S

    • And common core enriched genes are ATP5D, ATP5E, ATP5G1, ATP5H, ATP5J, ATP5O, COX4I1, COX5A, COX5B, COX6A1

  • clus6

    • Top enriched gene sets are KEGG LYSOSOME, KEGG TOLL LIKE RECEPTOR SIGNALING PATHWAY, KEGG NOD LIKE RECEPTOR SIGNALING PATHWAY, KEGG THYROID CANCER, ST TUMOR NECROSIS FACTOR PATHWAY, ST G ALPHA I PATHWAY, ST GAQ PATHWAY, PID ERBB2ERBB3PATHWAY, REACTOME ANTIVIRAL MECHANISM BY IFN STIMULATED GENES, REACTOME TRIGLYCERIDE BIOSYNTHESIS

    • And common core enriched genes are DDX58, HERC5, ISG15, UBE2L6, IFNB1, IRF1, IRF7, TNFAIP3, NFKB2, ADAR

Results
Subtype clus1 enriched pathways

Table 3.  Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus1. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
KEGG OXIDATIVE PHOSPHORYLATION 111 genes.ES.table 0.54 1.5 0.087 0.88 0.96 0.74 0.35 0.48 0.59 0.28
KEGG PYRIMIDINE METABOLISM 98 genes.ES.table 0.34 1.6 0.017 1 0.93 0.49 0.32 0.34 0.6 0.32
KEGG ARGININE AND PROLINE METABOLISM 53 genes.ES.table 0.63 1.8 0 1 0.45 0.49 0.18 0.4 0 0.31
KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM 44 genes.ES.table 0.45 1.7 0.021 1 0.68 0.43 0.27 0.32 0.65 0.38
KEGG PYRUVATE METABOLISM 38 genes.ES.table 0.52 1.7 0.018 1 0.72 0.5 0.26 0.37 0.52 0.32
PID INTEGRIN3 PATHWAY 42 genes.ES.table 0.65 1.6 0.031 0.96 0.96 0.55 0.15 0.47 0.59 0.3
PID AVB3 INTEGRIN PATHWAY 74 genes.ES.table 0.58 1.5 0.055 0.84 0.96 0.45 0.15 0.38 0.57 0.27
PID SYNDECAN 1 PATHWAY 46 genes.ES.table 0.71 1.7 0.013 1 0.82 0.63 0.15 0.54 0.59 0.34
PID INTEGRIN A4B1 PATHWAY 32 genes.ES.table 0.51 1.6 0.043 1 0.91 0.31 0.17 0.26 0.64 0.34
REACTOME ANTIGEN PROCESSING CROSS PRESENTATION 72 genes.ES.table 0.41 1.6 0.076 1 0.94 0.64 0.36 0.41 0.62 0.33
genes ES table in pathway: KEGG OXIDATIVE PHOSPHORYLATION

Table S1.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 P4HA3 P4HA3 P4HA3 3 0.86 0.11 YES
2 MAOA MAOA MAOA 248 0.46 0.15 YES
3 CKM CKM CKM 334 0.42 0.2 YES
4 NAGS NAGS NAGS 488 0.37 0.24 YES
5 CKB CKB CKB 492 0.37 0.28 YES
6 ADC ADC ADC 758 0.31 0.31 YES
7 AGMAT AGMAT AGMAT 848 0.3 0.34 YES
8 ABP1 ABP1 ABP1 896 0.29 0.37 YES
9 ASL ASL ASL 932 0.28 0.41 YES
10 CPS1 CPS1 CPS1 970 0.28 0.44 YES
11 ASS1 ASS1 ASS1 1017 0.27 0.47 YES
12 P4HA2 P4HA2 P4HA2 1036 0.27 0.5 YES
13 PYCR1 PYCR1 PYCR1 1233 0.24 0.52 YES
14 ALDH2 ALDH2 ALDH2 1612 0.2 0.52 YES
15 GAMT GAMT GAMT 1884 0.18 0.53 YES
16 ALDH1B1 ALDH1B1 ALDH1B1 2287 0.15 0.53 YES
17 SAT2 SAT2 SAT2 2301 0.15 0.55 YES
18 DAO DAO DAO 2342 0.15 0.56 YES
19 SAT1 SAT1 SAT1 2358 0.15 0.58 YES
20 ACY1 ACY1 ACY1 2606 0.13 0.58 YES
21 CKMT1A CKMT1A CKMT1A 2900 0.12 0.58 YES
22 PRODH PRODH PRODH 2998 0.12 0.59 YES
23 P4HA1 P4HA1 P4HA1 3052 0.12 0.6 YES
24 PYCRL PYCRL PYCRL 3073 0.11 0.61 YES
25 ARG2 ARG2 ARG2 3078 0.11 0.63 YES
26 CKMT2 CKMT2 CKMT2 3275 0.11 0.63 YES
27 ALDH7A1 ALDH7A1 ALDH7A1 4495 0.076 0.57 NO
28 GOT1 GOT1 GOT1 4577 0.074 0.57 NO
29 CKMT1B CKMT1B CKMT1B 5661 0.051 0.52 NO
30 AMD1 AMD1 AMD1 6275 0.039 0.49 NO
31 SRM SRM SRM 6451 0.036 0.48 NO
32 ALDH18A1 ALDH18A1 ALDH18A1 6500 0.035 0.48 NO
33 SMS SMS SMS 6829 0.029 0.47 NO
34 PYCR2 PYCR2 PYCR2 6904 0.028 0.47 NO
35 LAP3 LAP3 LAP3 7166 0.023 0.46 NO
36 OAT OAT OAT 7236 0.022 0.46 NO
37 GLUL GLUL GLUL 7427 0.018 0.45 NO
38 ALDH3A2 ALDH3A2 ALDH3A2 7659 0.013 0.44 NO
39 ALDH9A1 ALDH9A1 ALDH9A1 8294 0.0016 0.4 NO
40 MAOB MAOB MAOB 8392 -0.00017 0.4 NO
41 GLUD1 GLUD1 GLUD1 8395 -0.00022 0.4 NO
42 ALDH4A1 ALDH4A1 ALDH4A1 8824 -0.0084 0.37 NO
43 ODC1 ODC1 ODC1 9082 -0.014 0.36 NO
44 GOT2 GOT2 GOT2 9438 -0.021 0.34 NO
45 GLS GLS GLS 9806 -0.028 0.32 NO
46 NOS3 NOS3 NOS3 10006 -0.032 0.32 NO
47 NOS2 NOS2 NOS2 10462 -0.041 0.3 NO
48 GLUD2 GLUD2 GLUD2 11175 -0.057 0.26 NO
49 GATM GATM GATM 11844 -0.073 0.23 NO
50 ARG1 ARG1 ARG1 12421 -0.089 0.21 NO
51 NOS1 NOS1 NOS1 13004 -0.1 0.19 NO
52 GLS2 GLS2 GLS2 16355 -0.28 0.037 NO
53 PRODH2 PRODH2 PRODH2 16543 -0.3 0.064 NO

Figure S1.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG OXIDATIVE PHOSPHORYLATION.

Figure S2.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG OXIDATIVE PHOSPHORYLATION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG PYRIMIDINE METABOLISM

Table S2.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 GFPT2 GFPT2 GFPT2 478 0.38 0.072 YES
2 CHIA CHIA CHIA 1346 0.23 0.083 YES
3 HK3 HK3 HK3 1538 0.21 0.13 YES
4 CHIT1 CHIT1 CHIT1 1628 0.2 0.17 YES
5 GALK1 GALK1 GALK1 1914 0.17 0.2 YES
6 PGM1 PGM1 PGM1 2112 0.16 0.23 YES
7 GALE GALE GALE 2403 0.14 0.26 YES
8 PMM1 PMM1 PMM1 2498 0.14 0.29 YES
9 NANS NANS NANS 2503 0.14 0.32 YES
10 RENBP RENBP RENBP 2839 0.12 0.34 YES
11 HEXB HEXB HEXB 2840 0.12 0.37 YES
12 AMDHD2 AMDHD2 AMDHD2 2983 0.12 0.39 YES
13 TSTA3 TSTA3 TSTA3 3643 0.097 0.38 YES
14 GMPPB GMPPB GMPPB 3692 0.096 0.4 YES
15 GMPPA GMPPA GMPPA 3923 0.089 0.41 YES
16 PGM3 PGM3 PGM3 4090 0.085 0.42 YES
17 NPL NPL NPL 4309 0.08 0.43 YES
18 HEXA HEXA HEXA 4614 0.073 0.44 YES
19 MPI MPI MPI 4694 0.071 0.45 YES
20 HK1 HK1 HK1 5377 0.057 0.43 NO
21 UGP2 UGP2 UGP2 6136 0.042 0.39 NO
22 PGM2 PGM2 PGM2 6738 0.03 0.37 NO
23 UAP1 UAP1 UAP1 6922 0.028 0.36 NO
24 CYB5R1 CYB5R1 CYB5R1 6964 0.027 0.37 NO
25 FPGT FPGT FPGT 7141 0.023 0.36 NO
26 CMAS CMAS CMAS 7629 0.014 0.34 NO
27 GPI GPI GPI 7647 0.013 0.34 NO
28 PMM2 PMM2 PMM2 7691 0.012 0.34 NO
29 UGDH UGDH UGDH 7819 0.0099 0.34 NO
30 GMDS GMDS GMDS 7942 0.0078 0.34 NO
31 GNPNAT1 GNPNAT1 GNPNAT1 8004 0.0069 0.33 NO
32 CYB5R3 CYB5R3 CYB5R3 8228 0.0027 0.32 NO
33 UXS1 UXS1 UXS1 8771 -0.0075 0.29 NO
34 GALK2 GALK2 GALK2 9281 -0.018 0.27 NO
35 NAGK NAGK NAGK 9439 -0.021 0.26 NO
36 GALT GALT GALT 9551 -0.023 0.26 NO
37 GNPDA2 GNPDA2 GNPDA2 11199 -0.058 0.19 NO
38 GNPDA1 GNPDA1 GNPDA1 11301 -0.06 0.2 NO
39 GFPT1 GFPT1 GFPT1 11447 -0.064 0.2 NO
40 HK2 HK2 HK2 11728 -0.07 0.21 NO
41 FUK FUK FUK 11753 -0.071 0.22 NO
42 GNE GNE GNE 11972 -0.077 0.23 NO
43 NANP NANP NANP 14572 -0.16 0.13 NO
44 GCK GCK GCK 14919 -0.18 0.16 NO

Figure S3.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PYRIMIDINE METABOLISM.

Figure S4.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PYRIMIDINE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG ARGININE AND PROLINE METABOLISM

Table S3.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 LDHD LDHD LDHD 460 0.38 0.066 YES
2 HAGHL HAGHL HAGHL 612 0.34 0.14 YES
3 ME3 ME3 ME3 644 0.34 0.22 YES
4 ME1 ME1 ME1 1018 0.27 0.27 YES
5 PKLR PKLR PKLR 1292 0.24 0.31 YES
6 ALDH2 ALDH2 ALDH2 1612 0.2 0.34 YES
7 AKR1B1 AKR1B1 AKR1B1 1977 0.17 0.36 YES
8 PCK2 PCK2 PCK2 1986 0.17 0.4 YES
9 ALDH1B1 ALDH1B1 ALDH1B1 2287 0.15 0.42 YES
10 ACAT2 ACAT2 ACAT2 2550 0.14 0.44 YES
11 PKM2 PKM2 PKM2 3005 0.12 0.44 YES
12 PCK1 PCK1 PCK1 3225 0.11 0.45 YES
13 ACYP1 ACYP1 ACYP1 3553 0.099 0.46 YES
14 PDHB PDHB PDHB 3701 0.095 0.47 YES
15 MDH2 MDH2 MDH2 3897 0.09 0.48 YES
16 HAGH HAGH HAGH 4414 0.077 0.47 YES
17 ACSS2 ACSS2 ACSS2 4482 0.076 0.49 YES
18 ALDH7A1 ALDH7A1 ALDH7A1 4495 0.076 0.5 YES
19 LDHB LDHB LDHB 4569 0.074 0.52 YES
20 LDHA LDHA LDHA 4922 0.066 0.52 NO
21 PC PC PC 5198 0.06 0.51 NO
22 DLD DLD DLD 6363 0.038 0.46 NO
23 ACACB ACACB ACACB 7105 0.024 0.42 NO
24 ACSS1 ACSS1 ACSS1 7415 0.018 0.41 NO
25 ACAT1 ACAT1 ACAT1 7560 0.015 0.4 NO
26 ALDH3A2 ALDH3A2 ALDH3A2 7659 0.013 0.4 NO
27 LDHC LDHC LDHC 7994 0.0071 0.38 NO
28 ALDH9A1 ALDH9A1 ALDH9A1 8294 0.0016 0.37 NO
29 MDH1 MDH1 MDH1 8302 0.0015 0.37 NO
30 DLAT DLAT DLAT 8570 -0.0035 0.35 NO
31 LDHAL6B LDHAL6B LDHAL6B 8769 -0.0074 0.34 NO
32 ACYP2 ACYP2 ACYP2 8881 -0.0095 0.34 NO
33 PDHA1 PDHA1 PDHA1 9891 -0.029 0.29 NO
34 ME2 ME2 ME2 10876 -0.05 0.25 NO
35 GLO1 GLO1 GLO1 11647 -0.069 0.22 NO
36 GRHPR GRHPR GRHPR 11962 -0.077 0.22 NO
37 ACACA ACACA ACACA 12298 -0.086 0.22 NO
38 LDHAL6A LDHAL6A LDHAL6A 16865 -0.34 0.045 NO

Figure S5.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG ARGININE AND PROLINE METABOLISM.

Figure S6.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ARGININE AND PROLINE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM

Table S4.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 NME1-NME2 NME1-NME2 NME1-NME2 379 0.4 0.035 YES
2 UPP1 UPP1 UPP1 513 0.37 0.078 YES
3 AK5 AK5 AK5 564 0.36 0.12 YES
4 CDA CDA CDA 574 0.35 0.17 YES
5 NT5E NT5E NT5E 1130 0.26 0.18 YES
6 GDA GDA GDA 1450 0.22 0.19 YES
7 GPX1 GPX1 GPX1 1969 0.17 0.18 YES
8 TYMP TYMP TYMP 1971 0.17 0.21 YES
9 TK1 TK1 TK1 1991 0.17 0.23 YES
10 TYMS TYMS TYMS 2288 0.15 0.23 YES
11 GMPR GMPR GMPR 2375 0.14 0.25 YES
12 UCK2 UCK2 UCK2 2437 0.14 0.26 YES
13 DTYMK DTYMK DTYMK 2502 0.14 0.28 YES
14 NT5C NT5C NT5C 2538 0.14 0.3 YES
15 HPRT1 HPRT1 HPRT1 2669 0.13 0.31 YES
16 NME1 NME1 NME1 2763 0.12 0.32 YES
17 APRT APRT APRT 2867 0.12 0.33 YES
18 GUK1 GUK1 GUK1 2919 0.12 0.34 YES
19 DUT DUT DUT 2988 0.12 0.36 YES
20 PNP PNP PNP 3066 0.12 0.37 YES
21 AK1 AK1 AK1 3288 0.11 0.37 YES
22 RRM2 RRM2 RRM2 3297 0.11 0.38 YES
23 GLRX GLRX GLRX 3308 0.11 0.4 YES
24 IMPDH2 IMPDH2 IMPDH2 3361 0.1 0.41 YES
25 XDH XDH XDH 3489 0.1 0.42 YES
26 GMPR2 GMPR2 GMPR2 3874 0.091 0.41 YES
27 IMPDH1 IMPDH1 IMPDH1 3925 0.089 0.42 YES
28 NME2 NME2 NME2 4175 0.083 0.42 YES
29 ADAL ADAL ADAL 4535 0.075 0.4 YES
30 AK2 AK2 AK2 4738 0.07 0.4 YES
31 ADA ADA ADA 4793 0.069 0.41 YES
32 GSR GSR GSR 4815 0.068 0.42 YES
33 DHODH DHODH DHODH 5046 0.064 0.41 YES
34 TXN TXN TXN 5142 0.062 0.42 YES
35 TK2 TK2 TK2 5145 0.062 0.43 YES
36 UMPS UMPS UMPS 5330 0.058 0.42 YES
37 ADSL ADSL ADSL 5401 0.056 0.43 YES
38 CTPS CTPS CTPS 5476 0.055 0.43 YES
39 UCK1 UCK1 UCK1 6266 0.04 0.39 NO
40 NME4 NME4 NME4 6302 0.039 0.39 NO
41 DGUOK DGUOK DGUOK 6326 0.038 0.4 NO
42 PAICS PAICS PAICS 6443 0.036 0.4 NO
43 ADK ADK ADK 6665 0.032 0.39 NO
44 RRM1 RRM1 RRM1 6703 0.031 0.39 NO
45 CMPK1 CMPK1 CMPK1 6727 0.031 0.39 NO
46 DPYD DPYD DPYD 6784 0.03 0.4 NO
47 DCK DCK DCK 6822 0.029 0.4 NO
48 GMPS GMPS GMPS 7096 0.024 0.38 NO
49 NT5C3 NT5C3 NT5C3 7953 0.0077 0.34 NO
50 ATIC ATIC ATIC 8140 0.0041 0.33 NO
51 RRM2B RRM2B RRM2B 8841 -0.0088 0.29 NO
52 GART GART GART 9197 -0.016 0.27 NO
53 NT5C1A NT5C1A NT5C1A 9549 -0.023 0.25 NO
54 CAT CAT CAT 9598 -0.024 0.25 NO
55 PFAS PFAS PFAS 9780 -0.027 0.25 NO
56 AMPD3 AMPD3 AMPD3 10085 -0.034 0.24 NO
57 ADSSL1 ADSSL1 ADSSL1 10459 -0.041 0.22 NO
58 TXNRD1 TXNRD1 TXNRD1 10662 -0.045 0.22 NO
59 CTPS2 CTPS2 CTPS2 10700 -0.046 0.22 NO
60 AMPD2 AMPD2 AMPD2 10850 -0.05 0.22 NO
61 DCTD DCTD DCTD 10971 -0.052 0.22 NO
62 PPAT PPAT PPAT 11132 -0.056 0.22 NO
63 DPYS DPYS DPYS 11417 -0.063 0.21 NO
64 ADSS ADSS ADSS 11987 -0.077 0.19 NO
65 NT5C2 NT5C2 NT5C2 12078 -0.08 0.19 NO
66 CAD CAD CAD 12107 -0.08 0.2 NO
67 NT5C1B NT5C1B NT5C1B 12528 -0.092 0.19 NO
68 UPP2 UPP2 UPP2 12704 -0.096 0.2 NO
69 AMPD1 AMPD1 AMPD1 13848 -0.13 0.15 NO
70 NT5M NT5M NT5M 15861 -0.24 0.068 NO
71 UPB1 UPB1 UPB1 16021 -0.25 0.094 NO

Figure S7.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM.

Figure S8.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG PYRUVATE METABOLISM

Table S5.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 SDC1 SDC1 SDC1 83 0.6 0.049 YES
2 COL11A1 COL11A1 COL11A1 90 0.58 0.1 YES
3 COL10A1 COL10A1 COL10A1 94 0.58 0.15 YES
4 COL8A1 COL8A1 COL8A1 116 0.56 0.2 YES
5 COL7A1 COL7A1 COL7A1 152 0.52 0.24 YES
6 COL16A1 COL16A1 COL16A1 213 0.48 0.28 YES
7 COL12A1 COL12A1 COL12A1 247 0.46 0.32 YES
8 COL2A1 COL2A1 COL2A1 272 0.45 0.36 YES
9 COL13A1 COL13A1 COL13A1 280 0.44 0.4 YES
10 MET MET MET 442 0.38 0.43 YES
11 COL3A1 COL3A1 COL3A1 521 0.36 0.45 YES
12 MMP1 MMP1 MMP1 586 0.35 0.48 YES
13 COL5A1 COL5A1 COL5A1 599 0.35 0.51 YES
14 COL5A2 COL5A2 COL5A2 621 0.34 0.54 YES
15 COL1A1 COL1A1 COL1A1 713 0.32 0.56 YES
16 MMP7 MMP7 MMP7 872 0.3 0.58 YES
17 COL1A2 COL1A2 COL1A2 899 0.29 0.61 YES
18 COL4A6 COL4A6 COL4A6 904 0.29 0.63 YES
19 COL17A1 COL17A1 COL17A1 982 0.28 0.65 YES
20 MMP9 MMP9 MMP9 1326 0.23 0.66 YES
21 COL6A2 COL6A2 COL6A2 1504 0.21 0.66 YES
22 COL4A3 COL4A3 COL4A3 1518 0.21 0.68 YES
23 COL15A1 COL15A1 COL15A1 1925 0.17 0.67 YES
24 COL8A2 COL8A2 COL8A2 1935 0.17 0.69 YES
25 COL11A2 COL11A2 COL11A2 2027 0.17 0.7 YES
26 COL4A4 COL4A4 COL4A4 2360 0.15 0.69 YES
27 COL14A1 COL14A1 COL14A1 2478 0.14 0.7 YES
28 COL9A2 COL9A2 COL9A2 2512 0.14 0.71 YES
29 COL6A1 COL6A1 COL6A1 2630 0.13 0.71 YES
30 COL6A3 COL6A3 COL6A3 3018 0.12 0.7 NO
31 COL4A5 COL4A5 COL4A5 3077 0.11 0.71 NO
32 CCL5 CCL5 CCL5 3360 0.1 0.7 NO
33 SDCBP SDCBP SDCBP 3894 0.09 0.68 NO
34 PPIB PPIB PPIB 4728 0.07 0.64 NO
35 COL4A1 COL4A1 COL4A1 4785 0.069 0.64 NO
36 BSG BSG BSG 6537 0.034 0.55 NO
37 TGFB1 TGFB1 TGFB1 6768 0.03 0.54 NO
38 MAPK3 MAPK3 MAPK3 8502 -0.0022 0.44 NO
39 LAMA5 LAMA5 LAMA5 9952 -0.031 0.36 NO
40 HGF HGF HGF 11982 -0.077 0.25 NO
41 MAPK1 MAPK1 MAPK1 12489 -0.091 0.23 NO
42 HPSE HPSE HPSE 12815 -0.099 0.22 NO
43 PRKACA PRKACA PRKACA 13292 -0.11 0.2 NO
44 COL9A1 COL9A1 COL9A1 13620 -0.12 0.2 NO
45 CASK CASK CASK 14384 -0.15 0.17 NO
46 COL9A3 COL9A3 COL9A3 15754 -0.23 0.11 NO

Figure S9.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PYRUVATE METABOLISM.

Figure S10.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PYRUVATE METABOLISM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID INTEGRIN3 PATHWAY

Table S6.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 GPC6 GPC6 GPC6 49 0.65 0.075 YES
2 SDC1 SDC1 SDC1 83 0.6 0.14 YES
3 GXYLT2 GXYLT2 GXYLT2 132 0.53 0.21 YES
4 DCN DCN DCN 161 0.51 0.27 YES
5 HYAL1 HYAL1 HYAL1 510 0.37 0.29 YES
6 CSPG4 CSPG4 CSPG4 520 0.36 0.33 YES
7 GPC3 GPC3 GPC3 910 0.29 0.34 YES
8 BCAN BCAN BCAN 1024 0.27 0.37 YES
9 GPC4 GPC4 GPC4 1039 0.27 0.4 YES
10 VCAN VCAN VCAN 1151 0.25 0.43 YES
11 BGN BGN BGN 1260 0.24 0.45 YES
12 CHPF CHPF CHPF 1288 0.24 0.48 YES
13 GPC1 GPC1 GPC1 1331 0.23 0.5 YES
14 CHSY3 CHSY3 CHSY3 1501 0.21 0.52 YES
15 SDC2 SDC2 SDC2 1707 0.19 0.53 YES
16 CHST3 CHST3 CHST3 1922 0.17 0.54 YES
17 CHST13 CHST13 CHST13 2078 0.16 0.55 YES
18 CHST11 CHST11 CHST11 2312 0.15 0.55 YES
19 CSGALNACT1 CSGALNACT1 CSGALNACT1 2395 0.14 0.57 YES
20 AGRN AGRN AGRN 2480 0.14 0.58 YES
21 SDC4 SDC4 SDC4 2581 0.13 0.59 YES
22 HEXB HEXB HEXB 2840 0.12 0.59 NO
23 B3GAT3 B3GAT3 B3GAT3 3196 0.11 0.58 NO
24 B4GALT7 B4GALT7 B4GALT7 3711 0.095 0.56 NO
25 CHST9 CHST9 CHST9 3797 0.093 0.57 NO
26 HSPG2 HSPG2 HSPG2 4100 0.085 0.56 NO
27 HEXA HEXA HEXA 4614 0.073 0.54 NO
28 DSE DSE DSE 5856 0.048 0.48 NO
29 IDUA IDUA IDUA 6493 0.035 0.45 NO
30 ARSB ARSB ARSB 6582 0.034 0.44 NO
31 CHPF2 CHPF2 CHPF2 6626 0.033 0.45 NO
32 GPC2 GPC2 GPC2 8170 0.0037 0.36 NO
33 IDS IDS IDS 8525 -0.0028 0.34 NO
34 B3GALT6 B3GALT6 B3GALT6 9200 -0.016 0.3 NO
35 CHST14 CHST14 CHST14 9865 -0.029 0.27 NO
36 CSGALNACT2 CSGALNACT2 CSGALNACT2 10556 -0.043 0.24 NO
37 NCAN NCAN NCAN 11068 -0.055 0.21 NO
38 CHST12 CHST12 CHST12 11488 -0.065 0.2 NO
39 GXYLT1 GXYLT1 GXYLT1 12479 -0.091 0.15 NO
40 CHSY1 CHSY1 CHSY1 12520 -0.091 0.16 NO
41 UST UST UST 13549 -0.12 0.12 NO
42 SDC3 SDC3 SDC3 14038 -0.14 0.1 NO
43 CHST7 CHST7 CHST7 14281 -0.15 0.11 NO
44 CHST15 CHST15 CHST15 14553 -0.16 0.11 NO
45 B3GAT1 B3GAT1 B3GAT1 14847 -0.18 0.12 NO
46 GPC5 GPC5 GPC5 14870 -0.18 0.14 NO
47 B3GAT2 B3GAT2 B3GAT2 14876 -0.18 0.16 NO

Figure S11.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID INTEGRIN3 PATHWAY.

Figure S12.  Get High-res Image For the top 5 core enriched genes in the pathway: PID INTEGRIN3 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID AVB3 INTEGRIN PATHWAY

Table S7.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 COL11A1 COL11A1 COL11A1 90 0.58 0.024 YES
2 COL10A1 COL10A1 COL10A1 94 0.58 0.054 YES
3 COL8A1 COL8A1 COL8A1 116 0.56 0.08 YES
4 MMP2 MMP2 MMP2 142 0.53 0.11 YES
5 COL7A1 COL7A1 COL7A1 152 0.52 0.13 YES
6 LEPREL2 LEPREL2 LEPREL2 180 0.5 0.16 YES
7 COL16A1 COL16A1 COL16A1 213 0.48 0.18 YES
8 COL12A1 COL12A1 COL12A1 247 0.46 0.2 YES
9 MMP8 MMP8 MMP8 254 0.46 0.22 YES
10 COL2A1 COL2A1 COL2A1 272 0.45 0.24 YES
11 COL13A1 COL13A1 COL13A1 280 0.44 0.26 YES
12 MMP13 MMP13 MMP13 336 0.42 0.28 YES
13 PLOD2 PLOD2 PLOD2 352 0.42 0.3 YES
14 MMP11 MMP11 MMP11 374 0.4 0.32 YES
15 COL3A1 COL3A1 COL3A1 521 0.36 0.33 YES
16 COL5A3 COL5A3 COL5A3 555 0.36 0.35 YES
17 MMP1 MMP1 MMP1 586 0.35 0.36 YES
18 COL5A1 COL5A1 COL5A1 599 0.35 0.38 YES
19 COL5A2 COL5A2 COL5A2 621 0.34 0.4 YES
20 COL1A1 COL1A1 COL1A1 713 0.32 0.41 YES
21 BMP1 BMP1 BMP1 748 0.32 0.42 YES
22 MMP14 MMP14 MMP14 753 0.32 0.44 YES
23 MMP7 MMP7 MMP7 872 0.3 0.45 YES
24 COL1A2 COL1A2 COL1A2 899 0.29 0.46 YES
25 COL4A6 COL4A6 COL4A6 904 0.29 0.48 YES
26 MMP3 MMP3 MMP3 921 0.29 0.49 YES
27 COL17A1 COL17A1 COL17A1 982 0.28 0.5 YES
28 PCOLCE PCOLCE PCOLCE 1004 0.27 0.51 YES
29 ADAMTS2 ADAMTS2 ADAMTS2 1084 0.26 0.52 YES
30 MMP15 MMP15 MMP15 1158 0.25 0.53 YES
31 MMP17 MMP17 MMP17 1176 0.25 0.54 YES
32 MMP9 MMP9 MMP9 1326 0.23 0.54 YES
33 COL6A2 COL6A2 COL6A2 1504 0.21 0.55 YES
34 COL4A3 COL4A3 COL4A3 1518 0.21 0.55 YES
35 KLK2 KLK2 KLK2 1778 0.18 0.55 YES
36 COL23A1 COL23A1 COL23A1 1871 0.18 0.55 YES
37 COL15A1 COL15A1 COL15A1 1925 0.17 0.56 YES
38 COL8A2 COL8A2 COL8A2 1935 0.17 0.57 YES
39 TPSAB1 TPSAB1 TPSAB1 1960 0.17 0.57 YES
40 SERPINH1 SERPINH1 SERPINH1 2009 0.17 0.58 YES
41 ELANE ELANE ELANE 2014 0.17 0.59 YES
42 COL11A2 COL11A2 COL11A2 2027 0.17 0.6 YES
43 COL28A1 COL28A1 COL28A1 2047 0.16 0.6 YES
44 MMP24 MMP24 MMP24 2100 0.16 0.61 YES
45 TIMP2 TIMP2 TIMP2 2208 0.16 0.61 YES
46 ADAMTS14 ADAMTS14 ADAMTS14 2235 0.15 0.62 YES
47 COL4A4 COL4A4 COL4A4 2360 0.15 0.62 YES
48 COL22A1 COL22A1 COL22A1 2429 0.14 0.62 YES
49 COL14A1 COL14A1 COL14A1 2478 0.14 0.62 YES
50 COL9A2 COL9A2 COL9A2 2512 0.14 0.63 YES
51 PRSS1 PRSS1 PRSS1 2518 0.14 0.64 YES
52 TIMP1 TIMP1 TIMP1 2613 0.13 0.64 YES
53 COL6A1 COL6A1 COL6A1 2630 0.13 0.64 YES
54 PLOD1 PLOD1 PLOD1 2854 0.12 0.64 NO
55 COL6A3 COL6A3 COL6A3 3018 0.12 0.63 NO
56 COL21A1 COL21A1 COL21A1 3061 0.12 0.64 NO
57 COL4A5 COL4A5 COL4A5 3077 0.11 0.64 NO
58 ADAMTS3 ADAMTS3 ADAMTS3 3541 0.1 0.62 NO
59 MMP16 MMP16 MMP16 3673 0.096 0.62 NO
60 CRTAP CRTAP CRTAP 4139 0.084 0.6 NO
61 COL4A2 COL4A2 COL4A2 4195 0.082 0.6 NO
62 COL24A1 COL24A1 COL24A1 4718 0.07 0.57 NO
63 PPIB PPIB PPIB 4728 0.07 0.57 NO
64 COL4A1 COL4A1 COL4A1 4785 0.069 0.57 NO
65 P4HB P4HB P4HB 5450 0.055 0.54 NO
66 FURIN FURIN FURIN 5503 0.054 0.54 NO
67 PLOD3 PLOD3 PLOD3 5970 0.045 0.51 NO
68 GLT25D1 GLT25D1 GLT25D1 6260 0.04 0.5 NO
69 COL27A1 COL27A1 COL27A1 7053 0.025 0.46 NO
70 MMP25 MMP25 MMP25 9840 -0.028 0.3 NO
71 LEPREL1 LEPREL1 LEPREL1 10678 -0.046 0.25 NO
72 CMA1 CMA1 CMA1 10875 -0.05 0.24 NO
73 CTSG CTSG CTSG 11496 -0.065 0.21 NO
74 KLKB1 KLKB1 KLKB1 11625 -0.068 0.21 NO
75 CTRB1 CTRB1 CTRB1 12665 -0.095 0.15 NO
76 TLL2 TLL2 TLL2 13401 -0.12 0.12 NO
77 COL9A1 COL9A1 COL9A1 13620 -0.12 0.11 NO
78 MMP10 MMP10 MMP10 14597 -0.16 0.065 NO
79 TLL1 TLL1 TLL1 15574 -0.22 0.02 NO
80 COL9A3 COL9A3 COL9A3 15754 -0.23 0.022 NO
81 CTRB2 CTRB2 CTRB2 16365 -0.28 0.0016 NO
82 COL19A1 COL19A1 COL19A1 16458 -0.29 0.011 NO
83 GLT25D2 GLT25D2 GLT25D2 16778 -0.33 0.0096 NO
84 COL25A1 COL25A1 COL25A1 17043 -0.38 0.014 NO
85 PCOLCE2 PCOLCE2 PCOLCE2 17268 -0.43 0.023 NO

Figure S13.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID AVB3 INTEGRIN PATHWAY.

Figure S14.  Get High-res Image For the top 5 core enriched genes in the pathway: PID AVB3 INTEGRIN PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID SYNDECAN 1 PATHWAY

Table S8.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 GPC6 GPC6 GPC6 49 0.65 0.078 YES
2 SDC1 SDC1 SDC1 83 0.6 0.15 YES
3 GXYLT2 GXYLT2 GXYLT2 132 0.53 0.21 YES
4 DCN DCN DCN 161 0.51 0.27 YES
5 HS6ST3 HS6ST3 HS6ST3 450 0.38 0.3 YES
6 CSPG4 CSPG4 CSPG4 520 0.36 0.35 YES
7 HS3ST2 HS3ST2 HS3ST2 710 0.32 0.38 YES
8 GPC3 GPC3 GPC3 910 0.29 0.4 YES
9 BCAN BCAN BCAN 1024 0.27 0.43 YES
10 HS6ST2 HS6ST2 HS6ST2 1028 0.27 0.46 YES
11 GPC4 GPC4 GPC4 1039 0.27 0.49 YES
12 VCAN VCAN VCAN 1151 0.25 0.52 YES
13 BGN BGN BGN 1260 0.24 0.54 YES
14 GPC1 GPC1 GPC1 1331 0.23 0.57 YES
15 SDC2 SDC2 SDC2 1707 0.19 0.57 YES
16 HS3ST4 HS3ST4 HS3ST4 2094 0.16 0.57 YES
17 AGRN AGRN AGRN 2480 0.14 0.56 YES
18 SDC4 SDC4 SDC4 2581 0.13 0.57 YES
19 NAGLU NAGLU NAGLU 3130 0.11 0.56 NO
20 B3GAT3 B3GAT3 B3GAT3 3196 0.11 0.57 NO
21 NDST3 NDST3 NDST3 3363 0.1 0.57 NO
22 B4GALT7 B4GALT7 B4GALT7 3711 0.095 0.56 NO
23 HSPG2 HSPG2 HSPG2 4100 0.085 0.55 NO
24 IDUA IDUA IDUA 6493 0.035 0.42 NO
25 GUSB GUSB GUSB 6945 0.027 0.4 NO
26 GLB1 GLB1 GLB1 7507 0.016 0.37 NO
27 EXT1 EXT1 EXT1 7830 0.0098 0.35 NO
28 GPC2 GPC2 GPC2 8170 0.0037 0.33 NO
29 HPSE2 HPSE2 HPSE2 8247 0.0024 0.33 NO
30 GLCE GLCE GLCE 8360 0.00053 0.32 NO
31 IDS IDS IDS 8525 -0.0028 0.31 NO
32 HS2ST1 HS2ST1 HS2ST1 8730 -0.0068 0.3 NO
33 SGSH SGSH SGSH 9037 -0.013 0.28 NO
34 B3GALT6 B3GALT6 B3GALT6 9200 -0.016 0.28 NO
35 EXT2 EXT2 EXT2 10435 -0.04 0.21 NO
36 NCAN NCAN NCAN 11068 -0.055 0.18 NO
37 NDST1 NDST1 NDST1 11296 -0.06 0.18 NO
38 HS3ST1 HS3ST1 HS3ST1 11329 -0.06 0.18 NO
39 HS3ST3A1 HS3ST3A1 HS3ST3A1 11522 -0.065 0.18 NO
40 GXYLT1 GXYLT1 GXYLT1 12479 -0.091 0.14 NO
41 HPSE HPSE HPSE 12815 -0.099 0.13 NO
42 HS6ST1 HS6ST1 HS6ST1 13305 -0.11 0.12 NO
43 NDST2 NDST2 NDST2 13725 -0.13 0.11 NO
44 SDC3 SDC3 SDC3 14038 -0.14 0.11 NO
45 B3GAT1 B3GAT1 B3GAT1 14847 -0.18 0.084 NO
46 GPC5 GPC5 GPC5 14870 -0.18 0.1 NO
47 B3GAT2 B3GAT2 B3GAT2 14876 -0.18 0.13 NO
48 HS3ST3B1 HS3ST3B1 HS3ST3B1 16092 -0.26 0.089 NO

Figure S15.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID SYNDECAN 1 PATHWAY.

Figure S16.  Get High-res Image For the top 5 core enriched genes in the pathway: PID SYNDECAN 1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID INTEGRIN A4B1 PATHWAY

Table S9.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 SPP1 SPP1 SPP1 129 0.54 0.13 YES
2 THBS2 THBS2 THBS2 222 0.48 0.25 YES
3 FN1 FN1 FN1 597 0.35 0.31 YES
4 ADAM28 ADAM28 ADAM28 980 0.28 0.36 YES
5 THBS1 THBS1 THBS1 1167 0.25 0.42 YES
6 BCAR1 BCAR1 BCAR1 1651 0.2 0.44 YES
7 PRKAR1B PRKAR1B PRKAR1B 1883 0.18 0.47 YES
8 CD14 CD14 CD14 2304 0.15 0.48 YES
9 MDK MDK MDK 2684 0.13 0.5 YES
10 RAC1 RAC1 RAC1 3042 0.12 0.5 YES
11 CD81 CD81 CD81 4011 0.087 0.47 NO
12 JAM2 JAM2 JAM2 4314 0.08 0.48 NO
13 ITGB1 ITGB1 ITGB1 5411 0.056 0.43 NO
14 PTK2 PTK2 PTK2 6087 0.043 0.4 NO
15 IGSF8 IGSF8 IGSF8 6235 0.04 0.4 NO
16 AMICA1 AMICA1 AMICA1 6593 0.033 0.39 NO
17 DOCK1 DOCK1 DOCK1 6823 0.029 0.38 NO
18 ARF6 ARF6 ARF6 7454 0.017 0.35 NO
19 CRK CRK CRK 7582 0.014 0.35 NO
20 PTPRA PTPRA PTPRA 9198 -0.016 0.26 NO
21 PXN PXN PXN 9225 -0.016 0.27 NO
22 YWHAZ YWHAZ YWHAZ 9431 -0.02 0.26 NO
23 PRKAR1A PRKAR1A PRKAR1A 9562 -0.023 0.26 NO
24 PRKACB PRKACB PRKACB 9968 -0.031 0.24 NO
25 SRC SRC SRC 10582 -0.044 0.22 NO
26 VCAM1 VCAM1 VCAM1 10596 -0.044 0.23 NO
27 GIT1 GIT1 GIT1 10598 -0.044 0.24 NO
28 PTK2B PTK2B PTK2B 11290 -0.06 0.22 NO
29 ABI1 ABI1 ABI1 11996 -0.078 0.2 NO
30 TLN1 TLN1 TLN1 12690 -0.096 0.18 NO
31 PRKACA PRKACA PRKACA 13292 -0.11 0.18 NO
32 ITGA4 ITGA4 ITGA4 16322 -0.28 0.076 NO

Figure S17.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID INTEGRIN A4B1 PATHWAY.

Figure S18.  Get High-res Image For the top 5 core enriched genes in the pathway: PID INTEGRIN A4B1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: REACTOME ANTIGEN PROCESSING CROSS PRESENTATION

Table S10.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 MMP2 MMP2 MMP2 142 0.53 0.083 YES
2 MMP8 MMP8 MMP8 254 0.46 0.16 YES
3 MMP13 MMP13 MMP13 336 0.42 0.22 YES
4 MMP11 MMP11 MMP11 374 0.4 0.29 YES
5 MMP1 MMP1 MMP1 586 0.35 0.34 YES
6 MMP14 MMP14 MMP14 753 0.32 0.38 YES
7 MMP7 MMP7 MMP7 872 0.3 0.43 YES
8 MMP3 MMP3 MMP3 921 0.29 0.48 YES
9 MMP15 MMP15 MMP15 1158 0.25 0.5 YES
10 MMP17 MMP17 MMP17 1176 0.25 0.55 YES
11 MMP9 MMP9 MMP9 1326 0.23 0.58 YES
12 KLK2 KLK2 KLK2 1778 0.18 0.58 YES
13 TPSAB1 TPSAB1 TPSAB1 1960 0.17 0.6 YES
14 ELANE ELANE ELANE 2014 0.17 0.63 YES
15 MMP24 MMP24 MMP24 2100 0.16 0.65 YES
16 TIMP2 TIMP2 TIMP2 2208 0.16 0.67 YES
17 PRSS1 PRSS1 PRSS1 2518 0.14 0.68 YES
18 TIMP1 TIMP1 TIMP1 2613 0.13 0.7 YES
19 MMP16 MMP16 MMP16 3673 0.096 0.65 NO
20 FURIN FURIN FURIN 5503 0.054 0.56 NO
21 MMP25 MMP25 MMP25 9840 -0.028 0.32 NO
22 CMA1 CMA1 CMA1 10875 -0.05 0.27 NO
23 CTSG CTSG CTSG 11496 -0.065 0.24 NO
24 KLKB1 KLKB1 KLKB1 11625 -0.068 0.25 NO
25 CTRB1 CTRB1 CTRB1 12665 -0.095 0.21 NO
26 MMP10 MMP10 MMP10 14597 -0.16 0.12 NO
27 CTRB2 CTRB2 CTRB2 16365 -0.28 0.074 NO

Figure S19.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME ANTIGEN PROCESSING CROSS PRESENTATION.

Figure S20.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME ANTIGEN PROCESSING CROSS PRESENTATION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Fold change

For the top enriched genes, if you want to check whether they are

Expression level

For the top enriched genes, if you want to check whether they are

An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap

Significant gene list

For the top enriched genes, if you want to check whether they are

Subtype clus2 enriched pathways

Table 4.  Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus2. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
KEGG NOTCH SIGNALING PATHWAY 47 genes.ES.table 0.44 1.6 0.016 0.91 0.95 0.53 0.41 0.32 0.52 0.28
KEGG T CELL RECEPTOR SIGNALING PATHWAY 105 genes.ES.table 0.56 1.7 0.0065 1 0.67 0.36 0.25 0.27 0.35 0.24
KEGG THYROID CANCER 29 genes.ES.table 0.65 1.9 0.0061 1 0.31 0.21 0.06 0.2 0 0.25
KEGG PRIMARY IMMUNODEFICIENCY 34 genes.ES.table 0.65 1.8 0.0082 1 0.57 0.32 0.1 0.29 0.5 0.36
BIOCARTA DEATH PATHWAY 33 genes.ES.table 0.48 1.7 0.017 1 0.72 0.21 0.2 0.17 0.35 0.24
BIOCARTA VIP PATHWAY 25 genes.ES.table 0.53 1.6 0.0061 0.9 0.91 0.28 0.21 0.22 0.47 0.25
BIOCARTA TCR PATHWAY 44 genes.ES.table 0.52 1.7 0.016 1 0.79 0.27 0.18 0.22 0.4 0.25
ST T CELL SIGNAL TRANSDUCTION 43 genes.ES.table 0.59 1.7 0.0086 1 0.65 0.4 0.2 0.32 0.41 0.27
PID TCR PATHWAY 66 genes.ES.table 0.57 1.7 0.0062 1 0.64 0.33 0.21 0.27 0.54 0.35
PID CD8TCRPATHWAY 53 genes.ES.table 0.58 1.6 0.036 0.94 0.94 0.28 0.14 0.24 0.51 0.29
genes ES table in pathway: KEGG NOTCH SIGNALING PATHWAY

Table S11.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 TCF7 TCF7 TCF7 155 0.68 0.15 YES
2 CDH1 CDH1 CDH1 268 0.6 0.29 YES
3 LEF1 LEF1 LEF1 479 0.51 0.4 YES
4 RET RET RET 668 0.45 0.5 YES
5 NTRK1 NTRK1 NTRK1 1011 0.38 0.57 YES
6 TCF7L1 TCF7L1 TCF7L1 1058 0.37 0.65 YES
7 TCF7L2 TCF7L2 TCF7L2 2754 0.21 0.61 NO
8 RXRG RXRG RXRG 4297 0.13 0.55 NO
9 BRAF BRAF BRAF 4932 0.11 0.54 NO
10 TFG TFG TFG 6824 0.065 0.45 NO
11 TPR TPR TPR 7613 0.049 0.42 NO
12 PPARG PPARG PPARG 7751 0.047 0.42 NO
13 NCOA4 NCOA4 NCOA4 7783 0.046 0.43 NO
14 MYC MYC MYC 8279 0.037 0.41 NO
15 RXRB RXRB RXRB 8355 0.036 0.42 NO
16 MAPK1 MAPK1 MAPK1 8468 0.034 0.42 NO
17 PAX8 PAX8 PAX8 8685 0.03 0.41 NO
18 CTNNB1 CTNNB1 CTNNB1 9192 0.022 0.39 NO
19 RXRA RXRA RXRA 9705 0.014 0.36 NO
20 CCND1 CCND1 CCND1 10059 0.0071 0.34 NO
21 TPM3 TPM3 TPM3 10722 -0.0039 0.31 NO
22 KRAS KRAS KRAS 11266 -0.013 0.28 NO
23 MAPK3 MAPK3 MAPK3 11930 -0.023 0.25 NO
24 CCDC6 CCDC6 CCDC6 12099 -0.026 0.24 NO
25 NRAS NRAS NRAS 12193 -0.027 0.24 NO
26 MAP2K1 MAP2K1 MAP2K1 13053 -0.042 0.21 NO
27 TP53 TP53 TP53 13471 -0.051 0.2 NO
28 MAP2K2 MAP2K2 MAP2K2 13955 -0.061 0.18 NO
29 HRAS HRAS HRAS 15727 -0.12 0.11 NO

Figure S21.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG NOTCH SIGNALING PATHWAY.

Figure S22.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG NOTCH SIGNALING PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG T CELL RECEPTOR SIGNALING PATHWAY

Table S12.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CD40LG CD40LG CD40LG 8 1.1 0.16 YES
2 AIRE AIRE AIRE 83 0.78 0.26 YES
3 ICOS ICOS ICOS 114 0.73 0.36 YES
4 CD3E CD3E CD3E 641 0.46 0.4 YES
5 CD3D CD3D CD3D 997 0.38 0.43 YES
6 ZAP70 ZAP70 ZAP70 1002 0.38 0.48 YES
7 CD8B CD8B CD8B 1449 0.32 0.5 YES
8 CD8A CD8A CD8A 1526 0.31 0.54 YES
9 AICDA AICDA AICDA 1660 0.3 0.57 YES
10 IL7R IL7R IL7R 1738 0.29 0.61 YES
11 TNFRSF13B TNFRSF13B TNFRSF13B 1804 0.28 0.65 YES
12 IGLL1 IGLL1 IGLL1 3371 0.17 0.58 NO
13 RAG1 RAG1 RAG1 3408 0.17 0.6 NO
14 CD4 CD4 CD4 3441 0.17 0.63 NO
15 RFXAP RFXAP RFXAP 4282 0.14 0.6 NO
16 LCK LCK LCK 4686 0.12 0.59 NO
17 TNFRSF13C TNFRSF13C TNFRSF13C 6288 0.076 0.51 NO
18 JAK3 JAK3 JAK3 6567 0.07 0.5 NO
19 PTPRC PTPRC PTPRC 6889 0.063 0.5 NO
20 CD79A CD79A CD79A 6958 0.062 0.5 NO
21 IL2RG IL2RG IL2RG 7444 0.052 0.48 NO
22 RFX5 RFX5 RFX5 7829 0.045 0.46 NO
23 TAP2 TAP2 TAP2 8779 0.028 0.42 NO
24 BLNK BLNK BLNK 9521 0.016 0.38 NO
25 IKBKG IKBKG IKBKG 10038 0.0074 0.35 NO
26 TAP1 TAP1 TAP1 10144 0.0058 0.34 NO
27 BTK BTK BTK 10738 -0.0042 0.31 NO
28 CIITA CIITA CIITA 10806 -0.0054 0.31 NO
29 DCLRE1C DCLRE1C DCLRE1C 12137 -0.026 0.23 NO
30 CD19 CD19 CD19 13163 -0.044 0.18 NO
31 UNG UNG UNG 15005 -0.088 0.09 NO
32 CD40 CD40 CD40 15144 -0.093 0.096 NO
33 RFXANK RFXANK RFXANK 15475 -0.11 0.092 NO
34 ADA ADA ADA 16835 -0.23 0.047 NO

Figure S23.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG T CELL RECEPTOR SIGNALING PATHWAY.

Figure S24.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG T CELL RECEPTOR SIGNALING PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG THYROID CANCER

Table S13.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CD28 CD28 CD28 206 0.64 0.056 YES
2 GRAP2 GRAP2 GRAP2 286 0.59 0.11 YES
3 PRKCQ PRKCQ PRKCQ 313 0.57 0.17 YES
4 ITK ITK ITK 341 0.56 0.23 YES
5 CD3G CD3G CD3G 467 0.51 0.28 YES
6 CD3E CD3E CD3E 641 0.46 0.31 YES
7 CD3D CD3D CD3D 997 0.38 0.33 YES
8 ZAP70 ZAP70 ZAP70 1002 0.38 0.37 YES
9 LAT LAT LAT 1072 0.37 0.41 YES
10 CD247 CD247 CD247 1360 0.33 0.43 YES
11 SLA2 SLA2 SLA2 1391 0.33 0.46 YES
12 FYB FYB FYB 1656 0.3 0.48 YES
13 RASGRP2 RASGRP2 RASGRP2 1887 0.27 0.49 YES
14 LCP2 LCP2 LCP2 2221 0.24 0.5 YES
15 PRKCA PRKCA PRKCA 2350 0.24 0.52 YES
16 FYN FYN FYN 2430 0.23 0.54 YES
17 PRKCB PRKCB PRKCB 2919 0.2 0.53 YES
18 NCK1 NCK1 NCK1 3363 0.17 0.52 YES
19 CD4 CD4 CD4 3441 0.17 0.53 YES
20 GAB2 GAB2 GAB2 3447 0.17 0.55 YES
21 RASGRP1 RASGRP1 RASGRP1 3473 0.17 0.57 YES
22 CARD11 CARD11 CARD11 3641 0.16 0.57 YES
23 RASSF5 RASSF5 RASSF5 4302 0.13 0.55 NO
24 LCK LCK LCK 4686 0.12 0.54 NO
25 TRAF6 TRAF6 TRAF6 5034 0.11 0.53 NO
26 IKBKB IKBKB IKBKB 5205 0.1 0.54 NO
27 PRKCE PRKCE PRKCE 5427 0.098 0.53 NO
28 PDPK1 PDPK1 PDPK1 5886 0.086 0.52 NO
29 PTPN6 PTPN6 PTPN6 6375 0.075 0.5 NO
30 FLNA FLNA FLNA 6550 0.07 0.49 NO
31 SH3BP2 SH3BP2 SH3BP2 6574 0.07 0.5 NO
32 PTPRC PTPRC PTPRC 6889 0.063 0.49 NO
33 MALT1 MALT1 MALT1 7016 0.061 0.49 NO
34 HLA-DRA HLA-DRA HLA-DRA 7216 0.057 0.48 NO
35 MAP3K14 MAP3K14 MAP3K14 7242 0.056 0.49 NO
36 PLCG1 PLCG1 PLCG1 7325 0.054 0.49 NO
37 SOS1 SOS1 SOS1 7405 0.053 0.49 NO
38 INPP5D INPP5D INPP5D 7696 0.048 0.48 NO
39 AKT1 AKT1 AKT1 7767 0.046 0.48 NO
40 STIM1 STIM1 STIM1 7774 0.046 0.48 NO
41 PTPN11 PTPN11 PTPN11 7833 0.045 0.48 NO
42 HLA-DRB1 HLA-DRB1 HLA-DRB1 8177 0.039 0.47 NO
43 CBL CBL CBL 8450 0.035 0.46 NO
44 RAP1A RAP1A RAP1A 8950 0.025 0.43 NO
45 PAG1 PAG1 PAG1 9199 0.022 0.42 NO
46 CHUK CHUK CHUK 9374 0.019 0.41 NO
47 TRPV6 TRPV6 TRPV6 9394 0.019 0.41 NO
48 SHC1 SHC1 SHC1 9836 0.011 0.39 NO
49 ORAI1 ORAI1 ORAI1 9996 0.0082 0.38 NO
50 IKBKG IKBKG IKBKG 10038 0.0074 0.38 NO
51 MAP3K8 MAP3K8 MAP3K8 10502 0.000048 0.35 NO
52 CDC42 CDC42 CDC42 10510 -0.000065 0.35 NO
53 CD80 CD80 CD80 10787 -0.0051 0.34 NO
54 CSK CSK CSK 11086 -0.01 0.32 NO
55 CD86 CD86 CD86 11126 -0.011 0.32 NO
56 DBNL DBNL DBNL 11216 -0.012 0.32 NO
57 KRAS KRAS KRAS 11266 -0.013 0.32 NO
58 GRB2 GRB2 GRB2 11774 -0.021 0.29 NO
59 PTEN PTEN PTEN 11843 -0.022 0.29 NO
60 BCL10 BCL10 BCL10 11889 -0.023 0.29 NO
61 MAP4K1 MAP4K1 MAP4K1 12177 -0.027 0.27 NO
62 NRAS NRAS NRAS 12193 -0.027 0.28 NO
63 WAS WAS WAS 13459 -0.05 0.21 NO
64 VAV1 VAV1 VAV1 14891 -0.085 0.14 NO
65 STK39 STK39 STK39 15035 -0.089 0.14 NO
66 HRAS HRAS HRAS 15727 -0.12 0.11 NO

Figure S25.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG THYROID CANCER.

Figure S26.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG THYROID CANCER, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG PRIMARY IMMUNODEFICIENCY

Table S14.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CD28 CD28 CD28 206 0.64 0.078 YES
2 GRAP2 GRAP2 GRAP2 286 0.59 0.16 YES
3 ITK ITK ITK 341 0.56 0.23 YES
4 CTLA4 CTLA4 CTLA4 471 0.51 0.3 YES
5 CD3D CD3D CD3D 997 0.38 0.32 YES
6 ZAP70 ZAP70 ZAP70 1002 0.38 0.37 YES
7 LAT LAT LAT 1072 0.37 0.42 YES
8 ITPKA ITPKA ITPKA 1725 0.29 0.42 YES
9 RASGRP4 RASGRP4 RASGRP4 1867 0.28 0.45 YES
10 RASGRP2 RASGRP2 RASGRP2 1887 0.27 0.49 YES
11 PAK6 PAK6 PAK6 2062 0.26 0.52 YES
12 LCP2 LCP2 LCP2 2221 0.24 0.54 YES
13 EPHB2 EPHB2 EPHB2 2278 0.24 0.57 YES
14 NCK1 NCK1 NCK1 3363 0.17 0.54 YES
15 RASGRP1 RASGRP1 RASGRP1 3473 0.17 0.55 YES
16 PAK3 PAK3 PAK3 3506 0.17 0.57 YES
17 DAG1 DAG1 DAG1 3578 0.16 0.59 YES
18 NFAT5 NFAT5 NFAT5 4377 0.13 0.56 NO
19 LCK LCK LCK 4686 0.12 0.56 NO
20 SOS2 SOS2 SOS2 6052 0.082 0.5 NO
21 PAK4 PAK4 PAK4 6180 0.079 0.5 NO
22 PAK2 PAK2 PAK2 6502 0.072 0.49 NO
23 PTPRC PTPRC PTPRC 6889 0.063 0.48 NO
24 RAF1 RAF1 RAF1 6931 0.063 0.49 NO
25 PLCG1 PLCG1 PLCG1 7325 0.054 0.47 NO
26 SOS1 SOS1 SOS1 7405 0.053 0.48 NO
27 RASGRP3 RASGRP3 RASGRP3 8093 0.041 0.44 NO
28 FBXW7 FBXW7 FBXW7 8285 0.037 0.44 NO
29 CBL CBL CBL 8450 0.035 0.43 NO
30 MAPK1 MAPK1 MAPK1 8468 0.034 0.44 NO
31 PAK1 PAK1 PAK1 8668 0.03 0.43 NO
32 CSK CSK CSK 11086 -0.01 0.29 NO
33 NFKBIA NFKBIA NFKBIA 11383 -0.015 0.28 NO
34 NFKB1 NFKB1 NFKB1 11447 -0.016 0.28 NO
35 NFKBIE NFKBIE NFKBIE 11705 -0.02 0.26 NO
36 GRB2 GRB2 GRB2 11774 -0.021 0.26 NO
37 ITPKB ITPKB ITPKB 11834 -0.022 0.26 NO
38 NFKB2 NFKB2 NFKB2 12764 -0.037 0.22 NO
39 NFKBIB NFKBIB NFKBIB 13517 -0.052 0.18 NO
40 NFKBIL1 NFKBIL1 NFKBIL1 14446 -0.072 0.14 NO
41 VAV1 VAV1 VAV1 14891 -0.085 0.12 NO
42 PRDX1 PRDX1 PRDX1 15198 -0.095 0.12 NO
43 DTYMK DTYMK DTYMK 16003 -0.14 0.094 NO

Figure S27.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PRIMARY IMMUNODEFICIENCY.

Figure S28.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PRIMARY IMMUNODEFICIENCY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA DEATH PATHWAY

Table S15.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CD40LG CD40LG CD40LG 8 1.1 0.069 YES
2 ICOS ICOS ICOS 114 0.73 0.11 YES
3 IL2 IL2 IL2 181 0.66 0.14 YES
4 CD28 CD28 CD28 206 0.64 0.18 YES
5 GRAP2 GRAP2 GRAP2 286 0.59 0.22 YES
6 PRKCQ PRKCQ PRKCQ 313 0.57 0.25 YES
7 ITK ITK ITK 341 0.56 0.28 YES
8 CD3G CD3G CD3G 467 0.51 0.31 YES
9 CTLA4 CTLA4 CTLA4 471 0.51 0.34 YES
10 CD3E CD3E CD3E 641 0.46 0.36 YES
11 PIK3R5 PIK3R5 PIK3R5 882 0.41 0.37 YES
12 CD3D CD3D CD3D 997 0.38 0.39 YES
13 ZAP70 ZAP70 ZAP70 1002 0.38 0.41 YES
14 LAT LAT LAT 1072 0.37 0.43 YES
15 PDCD1 PDCD1 PDCD1 1261 0.34 0.44 YES
16 CD247 CD247 CD247 1360 0.33 0.46 YES
17 CD8B CD8B CD8B 1449 0.32 0.47 YES
18 CD8A CD8A CD8A 1526 0.31 0.49 YES
19 PAK6 PAK6 PAK6 2062 0.26 0.47 YES
20 CBLB CBLB CBLB 2117 0.25 0.48 YES
21 LCP2 LCP2 LCP2 2221 0.24 0.49 YES
22 IFNG IFNG IFNG 2260 0.24 0.51 YES
23 FYN FYN FYN 2430 0.23 0.51 YES
24 IL4 IL4 IL4 2646 0.22 0.51 YES
25 CSF2 CSF2 CSF2 2839 0.2 0.51 YES
26 VAV3 VAV3 VAV3 3097 0.19 0.51 YES
27 NFATC2 NFATC2 NFATC2 3109 0.19 0.52 YES
28 NFATC1 NFATC1 NFATC1 3210 0.18 0.53 YES
29 NCK1 NCK1 NCK1 3363 0.17 0.53 YES
30 CD4 CD4 CD4 3441 0.17 0.54 YES
31 RASGRP1 RASGRP1 RASGRP1 3473 0.17 0.54 YES
32 PAK3 PAK3 PAK3 3506 0.17 0.55 YES
33 CARD11 CARD11 CARD11 3641 0.16 0.56 YES
34 PIK3CA PIK3CA PIK3CA 3787 0.15 0.56 YES
35 NCK2 NCK2 NCK2 4117 0.14 0.55 YES
36 PPP3R2 PPP3R2 PPP3R2 4212 0.14 0.55 YES
37 AKT3 AKT3 AKT3 4255 0.14 0.56 YES
38 NFAT5 NFAT5 NFAT5 4377 0.13 0.56 YES
39 LCK LCK LCK 4686 0.12 0.55 NO
40 IKBKB IKBKB IKBKB 5205 0.1 0.52 NO
41 PIK3R3 PIK3R3 PIK3R3 5451 0.097 0.52 NO
42 PIK3CB PIK3CB PIK3CB 6037 0.082 0.49 NO
43 SOS2 SOS2 SOS2 6052 0.082 0.49 NO
44 PAK4 PAK4 PAK4 6180 0.079 0.49 NO
45 NFATC3 NFATC3 NFATC3 6209 0.078 0.49 NO
46 PTPN6 PTPN6 PTPN6 6375 0.075 0.49 NO
47 PAK2 PAK2 PAK2 6502 0.072 0.48 NO
48 DLG1 DLG1 DLG1 6587 0.07 0.48 NO
49 PTPRC PTPRC PTPRC 6889 0.063 0.47 NO
50 PIK3CD PIK3CD PIK3CD 6895 0.063 0.48 NO
51 RAF1 RAF1 RAF1 6931 0.063 0.48 NO
52 MALT1 MALT1 MALT1 7016 0.061 0.48 NO
53 MAP3K14 MAP3K14 MAP3K14 7242 0.056 0.47 NO
54 TNF TNF TNF 7293 0.055 0.47 NO
55 PLCG1 PLCG1 PLCG1 7325 0.054 0.47 NO
56 SOS1 SOS1 SOS1 7405 0.053 0.47 NO
57 AKT1 AKT1 AKT1 7767 0.046 0.45 NO
58 PPP3CA PPP3CA PPP3CA 7929 0.044 0.44 NO
59 JUN JUN JUN 8034 0.042 0.44 NO
60 VAV2 VAV2 VAV2 8294 0.037 0.43 NO
61 CBL CBL CBL 8450 0.035 0.42 NO
62 MAPK1 MAPK1 MAPK1 8468 0.034 0.42 NO
63 PAK1 PAK1 PAK1 8668 0.03 0.41 NO
64 GSK3B GSK3B GSK3B 8917 0.026 0.4 NO
65 CHP CHP CHP 8929 0.026 0.4 NO
66 PIK3CG PIK3CG PIK3CG 9121 0.023 0.39 NO
67 MAPK13 MAPK13 MAPK13 9196 0.022 0.39 NO
68 MAPK9 MAPK9 MAPK9 9208 0.021 0.39 NO
69 PIK3R1 PIK3R1 PIK3R1 9278 0.02 0.39 NO
70 RELA RELA RELA 9280 0.02 0.39 NO
71 CHUK CHUK CHUK 9374 0.019 0.38 NO
72 PPP3CB PPP3CB PPP3CB 9524 0.016 0.38 NO
73 MAP2K7 MAP2K7 MAP2K7 9547 0.016 0.38 NO
74 RHOA RHOA RHOA 9893 0.01 0.36 NO
75 IKBKG IKBKG IKBKG 10038 0.0074 0.35 NO
76 MAPK12 MAPK12 MAPK12 10221 0.0046 0.34 NO
77 MAP3K8 MAP3K8 MAP3K8 10502 0.000048 0.32 NO
78 CDC42 CDC42 CDC42 10510 -0.000065 0.32 NO
79 AKT2 AKT2 AKT2 11156 -0.011 0.29 NO
80 KRAS KRAS KRAS 11266 -0.013 0.28 NO
81 PIK3R2 PIK3R2 PIK3R2 11301 -0.013 0.28 NO
82 PPP3CC PPP3CC PPP3CC 11339 -0.014 0.28 NO
83 PPP3R1 PPP3R1 PPP3R1 11369 -0.014 0.28 NO
84 NFKBIA NFKBIA NFKBIA 11383 -0.015 0.28 NO
85 NFATC4 NFATC4 NFATC4 11422 -0.015 0.28 NO
86 NFKB1 NFKB1 NFKB1 11447 -0.016 0.28 NO
87 MAPK14 MAPK14 MAPK14 11658 -0.019 0.27 NO
88 NFKBIE NFKBIE NFKBIE 11705 -0.02 0.26 NO
89 GRB2 GRB2 GRB2 11774 -0.021 0.26 NO
90 BCL10 BCL10 BCL10 11889 -0.023 0.26 NO
91 MAPK3 MAPK3 MAPK3 11930 -0.023 0.26 NO
92 NRAS NRAS NRAS 12193 -0.027 0.24 NO
93 MAP3K7 MAP3K7 MAP3K7 12836 -0.039 0.21 NO
94 MAPK11 MAPK11 MAPK11 12975 -0.041 0.2 NO
95 MAP2K1 MAP2K1 MAP2K1 13053 -0.042 0.2 NO
96 NFKBIB NFKBIB NFKBIB 13517 -0.052 0.18 NO
97 FOS FOS FOS 13543 -0.052 0.18 NO
98 MAP2K2 MAP2K2 MAP2K2 13955 -0.061 0.16 NO
99 PDK1 PDK1 PDK1 14026 -0.062 0.16 NO
100 CDK4 CDK4 CDK4 14442 -0.072 0.14 NO
101 VAV1 VAV1 VAV1 14891 -0.085 0.12 NO
102 HRAS HRAS HRAS 15727 -0.12 0.081 NO
103 TEC TEC TEC 16202 -0.15 0.064 NO
104 IL10 IL10 IL10 16240 -0.16 0.071 NO
105 CBLC CBLC CBLC 16256 -0.16 0.08 NO

Figure S29.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA DEATH PATHWAY.

Figure S30.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA DEATH PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA VIP PATHWAY

Table S16.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 TNFRSF25 TNFRSF25 TNFRSF25 152 0.69 0.21 YES
2 GAS2 GAS2 GAS2 860 0.41 0.3 YES
3 BCL2 BCL2 BCL2 1819 0.28 0.34 YES
4 CASP10 CASP10 CASP10 2181 0.25 0.4 YES
5 DFFB DFFB DFFB 3507 0.17 0.38 YES
6 TNFSF12 TNFSF12 TNFSF12 3546 0.16 0.43 YES
7 CASP8 CASP8 CASP8 3577 0.16 0.48 YES
8 TNFSF10 TNFSF10 TNFSF10 6769 0.066 0.32 NO
9 RIPK1 RIPK1 RIPK1 6954 0.062 0.33 NO
10 MAP3K14 MAP3K14 MAP3K14 7242 0.056 0.33 NO
11 CASP6 CASP6 CASP6 7252 0.056 0.35 NO
12 TNFRSF10B TNFRSF10B TNFRSF10B 7742 0.047 0.34 NO
13 CFLAR CFLAR CFLAR 7907 0.044 0.34 NO
14 CASP7 CASP7 CASP7 8853 0.027 0.3 NO
15 CASP9 CASP9 CASP9 8991 0.025 0.3 NO
16 XIAP XIAP XIAP 9239 0.021 0.29 NO
17 RELA RELA RELA 9280 0.02 0.29 NO
18 CHUK CHUK CHUK 9374 0.019 0.29 NO
19 TRADD TRADD TRADD 9581 0.015 0.29 NO
20 CYCS CYCS CYCS 9797 0.012 0.28 NO
21 CASP3 CASP3 CASP3 9840 0.011 0.28 NO
22 TNFRSF10A TNFRSF10A TNFRSF10A 9941 0.0092 0.28 NO
23 SPTAN1 SPTAN1 SPTAN1 10433 0.00097 0.25 NO
24 NFKBIA NFKBIA NFKBIA 11383 -0.015 0.2 NO
25 NFKB1 NFKB1 NFKB1 11447 -0.016 0.2 NO
26 TRAF2 TRAF2 TRAF2 13022 -0.042 0.13 NO
27 LMNA LMNA LMNA 13253 -0.046 0.13 NO
28 APAF1 APAF1 APAF1 13560 -0.052 0.13 NO
29 BIRC3 BIRC3 BIRC3 13660 -0.055 0.14 NO
30 FADD FADD FADD 13744 -0.056 0.15 NO
31 BIRC2 BIRC2 BIRC2 13768 -0.057 0.17 NO
32 DFFA DFFA DFFA 13987 -0.061 0.18 NO
33 BID BID BID 15334 -0.1 0.13 NO

Figure S31.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA VIP PATHWAY.

Figure S32.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA VIP PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA TCR PATHWAY

Table S17.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 VIPR2 VIPR2 VIPR2 16 0.99 0.18 YES
2 VIPR1 VIPR1 VIPR1 70 0.81 0.32 YES
3 GNG4 GNG4 GNG4 81 0.78 0.46 YES
4 GCGR GCGR GCGR 298 0.58 0.55 YES
5 GNG7 GNG7 GNG7 570 0.48 0.62 YES
6 GIPR GIPR GIPR 1280 0.34 0.64 YES
7 ADCYAP1 ADCYAP1 ADCYAP1 1686 0.29 0.68 YES
8 SCT SCT SCT 2768 0.21 0.65 NO
9 GNG12 GNG12 GNG12 5916 0.085 0.49 NO
10 GNG2 GNG2 GNG2 7084 0.06 0.43 NO
11 GNB5 GNB5 GNB5 8087 0.041 0.38 NO
12 GNB3 GNB3 GNB3 9392 0.019 0.31 NO
13 GNG3 GNG3 GNG3 9493 0.017 0.31 NO
14 GNAS GNAS GNAS 9553 0.016 0.31 NO
15 GNB4 GNB4 GNB4 11500 -0.016 0.2 NO
16 GNB1 GNB1 GNB1 12548 -0.033 0.15 NO
17 GNG13 GNG13 GNG13 12680 -0.036 0.15 NO
18 GNG10 GNG10 GNG10 12936 -0.04 0.14 NO
19 GNG11 GNG11 GNG11 13228 -0.045 0.13 NO
20 GNB2 GNB2 GNB2 13288 -0.047 0.14 NO
21 GNGT2 GNGT2 GNGT2 13779 -0.057 0.12 NO
22 GNG5 GNG5 GNG5 14070 -0.063 0.12 NO
23 VIP VIP VIP 14184 -0.065 0.12 NO
24 GLP1R GLP1R GLP1R 15318 -0.1 0.074 NO
25 GNG8 GNG8 GNG8 15447 -0.1 0.085 NO
26 SCTR SCTR SCTR 16801 -0.22 0.049 NO

Figure S33.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA TCR PATHWAY.

Figure S34.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA TCR PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: ST T CELL SIGNAL TRANSDUCTION

Table S18.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CD3G CD3G CD3G 467 0.51 0.07 YES
2 CD3E CD3E CD3E 641 0.46 0.15 YES
3 CD3D CD3D CD3D 997 0.38 0.2 YES
4 ZAP70 ZAP70 ZAP70 1002 0.38 0.27 YES
5 LAT LAT LAT 1072 0.37 0.34 YES
6 CD247 CD247 CD247 1360 0.33 0.38 YES
7 PRKCA PRKCA PRKCA 2350 0.24 0.37 YES
8 FYN FYN FYN 2430 0.23 0.41 YES
9 MAP3K1 MAP3K1 MAP3K1 2659 0.21 0.44 YES
10 PRKCB PRKCB PRKCB 2919 0.2 0.46 YES
11 NFATC2 NFATC2 NFATC2 3109 0.19 0.49 YES
12 NFATC1 NFATC1 NFATC1 3210 0.18 0.52 YES
13 PIK3CA PIK3CA PIK3CA 3787 0.15 0.51 NO
14 LCK LCK LCK 4686 0.12 0.48 NO
15 PTPN7 PTPN7 PTPN7 4952 0.11 0.49 NO
16 MAPK8 MAPK8 MAPK8 4993 0.11 0.51 NO
17 RASA1 RASA1 RASA1 5290 0.1 0.51 NO
18 NFATC3 NFATC3 NFATC3 6209 0.078 0.47 NO
19 RAF1 RAF1 RAF1 6931 0.063 0.44 NO
20 PLCG1 PLCG1 PLCG1 7325 0.054 0.43 NO
21 SOS1 SOS1 SOS1 7405 0.053 0.44 NO
22 PPP3CA PPP3CA PPP3CA 7929 0.044 0.42 NO
23 JUN JUN JUN 8034 0.042 0.42 NO
24 CALM1 CALM1 CALM1 8736 0.029 0.38 NO
25 PIK3CG PIK3CG PIK3CG 9121 0.023 0.37 NO
26 PIK3R1 PIK3R1 PIK3R1 9278 0.02 0.36 NO
27 RELA RELA RELA 9280 0.02 0.37 NO
28 PPP3CB PPP3CB PPP3CB 9524 0.016 0.36 NO
29 ELK1 ELK1 ELK1 9635 0.014 0.35 NO
30 SHC1 SHC1 SHC1 9836 0.011 0.34 NO
31 MAP2K4 MAP2K4 MAP2K4 10459 0.00064 0.31 NO
32 RAC1 RAC1 RAC1 11232 -0.012 0.27 NO
33 PPP3CC PPP3CC PPP3CC 11339 -0.014 0.26 NO
34 NFKBIA NFKBIA NFKBIA 11383 -0.015 0.26 NO
35 NFATC4 NFATC4 NFATC4 11422 -0.015 0.26 NO
36 NFKB1 NFKB1 NFKB1 11447 -0.016 0.27 NO
37 GRB2 GRB2 GRB2 11774 -0.021 0.25 NO
38 MAPK3 MAPK3 MAPK3 11930 -0.023 0.25 NO
39 CALM2 CALM2 CALM2 13001 -0.041 0.19 NO
40 MAP2K1 MAP2K1 MAP2K1 13053 -0.042 0.2 NO
41 FOS FOS FOS 13543 -0.052 0.18 NO
42 CALM3 CALM3 CALM3 14574 -0.075 0.14 NO
43 VAV1 VAV1 VAV1 14891 -0.085 0.14 NO
44 HRAS HRAS HRAS 15727 -0.12 0.11 NO

Figure S35.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: ST T CELL SIGNAL TRANSDUCTION.

Figure S36.  Get High-res Image For the top 5 core enriched genes in the pathway: ST T CELL SIGNAL TRANSDUCTION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID TCR PATHWAY

Table S19.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 ADCY5 ADCY5 ADCY5 14 0.99 0.17 YES
2 GNG4 GNG4 GNG4 81 0.78 0.29 YES
3 MYO5B MYO5B MYO5B 555 0.48 0.35 YES
4 GNG7 GNG7 GNG7 570 0.48 0.43 YES
5 ADCY1 ADCY1 ADCY1 1394 0.33 0.44 YES
6 AVPR2 AVPR2 AVPR2 1756 0.29 0.46 YES
7 PRKAR2B PRKAR2B PRKAR2B 2116 0.25 0.49 YES
8 ADCY6 ADCY6 ADCY6 2425 0.23 0.51 YES
9 AQP1 AQP1 AQP1 2836 0.2 0.52 YES
10 AQP3 AQP3 AQP3 3386 0.17 0.52 YES
11 ADCY7 ADCY7 ADCY7 3681 0.16 0.53 YES
12 ADCY4 ADCY4 ADCY4 3755 0.16 0.55 YES
13 PRKACB PRKACB PRKACB 3785 0.15 0.57 YES
14 RAB11FIP2 RAB11FIP2 RAB11FIP2 4455 0.13 0.56 NO
15 ADCY9 ADCY9 ADCY9 4640 0.12 0.57 NO
16 GNG12 GNG12 GNG12 5916 0.085 0.51 NO
17 PRKAR2A PRKAR2A PRKAR2A 6267 0.077 0.5 NO
18 GNG2 GNG2 GNG2 7084 0.06 0.46 NO
19 PRKACA PRKACA PRKACA 7784 0.046 0.43 NO
20 GNB5 GNB5 GNB5 8087 0.041 0.42 NO
21 PRKAR1A PRKAR1A PRKAR1A 9030 0.024 0.37 NO
22 GNB3 GNB3 GNB3 9392 0.019 0.36 NO
23 GNG3 GNG3 GNG3 9493 0.017 0.35 NO
24 GNAS GNAS GNAS 9553 0.016 0.35 NO
25 GNB4 GNB4 GNB4 11500 -0.016 0.24 NO
26 AQP4 AQP4 AQP4 11632 -0.019 0.24 NO
27 ADCY2 ADCY2 ADCY2 12287 -0.029 0.21 NO
28 PRKAR1B PRKAR1B PRKAR1B 12501 -0.032 0.2 NO
29 GNB1 GNB1 GNB1 12548 -0.033 0.2 NO
30 RAB11A RAB11A RAB11A 12641 -0.035 0.2 NO
31 GNG13 GNG13 GNG13 12680 -0.036 0.21 NO
32 GNG10 GNG10 GNG10 12936 -0.04 0.2 NO
33 GNG11 GNG11 GNG11 13228 -0.045 0.19 NO
34 GNB2 GNB2 GNB2 13288 -0.047 0.2 NO
35 GNGT2 GNGT2 GNGT2 13779 -0.057 0.18 NO
36 GNG5 GNG5 GNG5 14070 -0.063 0.17 NO
37 ADCY3 ADCY3 ADCY3 14827 -0.083 0.14 NO
38 GNG8 GNG8 GNG8 15447 -0.1 0.13 NO

Figure S37.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID TCR PATHWAY.

Figure S38.  Get High-res Image For the top 5 core enriched genes in the pathway: PID TCR PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID CD8TCRPATHWAY

Table S20.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 ADCY5 ADCY5 ADCY5 14 0.99 0.13 YES
2 GNG4 GNG4 GNG4 81 0.78 0.23 YES
3 ADRA2A ADRA2A ADRA2A 279 0.59 0.3 YES
4 PRKCQ PRKCQ PRKCQ 313 0.57 0.37 YES
5 GNG7 GNG7 GNG7 570 0.48 0.42 YES
6 RGS4 RGS4 RGS4 680 0.45 0.47 YES
7 ADCY1 ADCY1 ADCY1 1394 0.33 0.47 YES
8 PRKCH PRKCH PRKCH 1929 0.27 0.48 YES
9 GNAZ GNAZ GNAZ 2110 0.25 0.5 YES
10 PRKCA PRKCA PRKCA 2350 0.24 0.52 YES
11 ADCY6 ADCY6 ADCY6 2425 0.23 0.55 YES
12 GNAI1 GNAI1 GNAI1 2567 0.22 0.57 YES
13 RGS17 RGS17 RGS17 2892 0.2 0.57 YES
14 PRKCB PRKCB PRKCB 2919 0.2 0.6 YES
15 ADCY7 ADCY7 ADCY7 3681 0.16 0.58 NO
16 ADCY4 ADCY4 ADCY4 3755 0.16 0.59 NO
17 ADCY9 ADCY9 ADCY9 4640 0.12 0.56 NO
18 PRKCE PRKCE PRKCE 5427 0.098 0.53 NO
19 GNG12 GNG12 GNG12 5916 0.085 0.51 NO
20 ADRA2B ADRA2B ADRA2B 6200 0.079 0.5 NO
21 GNG2 GNG2 GNG2 7084 0.06 0.46 NO
22 PRKCG PRKCG PRKCG 7761 0.046 0.43 NO
23 GNB5 GNB5 GNB5 8087 0.041 0.42 NO
24 GNAI2 GNAI2 GNAI2 8565 0.033 0.39 NO
25 RGS19 RGS19 RGS19 8894 0.026 0.38 NO
26 GNB3 GNB3 GNB3 9392 0.019 0.35 NO
27 GNG3 GNG3 GNG3 9493 0.017 0.35 NO
28 GNAS GNAS GNAS 9553 0.016 0.35 NO
29 PRKCD PRKCD PRKCD 10801 -0.0053 0.28 NO
30 GNB4 GNB4 GNB4 11500 -0.016 0.24 NO
31 ADCY2 ADCY2 ADCY2 12287 -0.029 0.2 NO
32 GNB1 GNB1 GNB1 12548 -0.033 0.19 NO
33 GNG13 GNG13 GNG13 12680 -0.036 0.19 NO
34 GNG10 GNG10 GNG10 12936 -0.04 0.18 NO
35 GNG11 GNG11 GNG11 13228 -0.045 0.17 NO
36 GNB2 GNB2 GNB2 13288 -0.047 0.17 NO
37 GNGT2 GNGT2 GNGT2 13779 -0.057 0.15 NO
38 GNG5 GNG5 GNG5 14070 -0.063 0.14 NO
39 GNAI3 GNAI3 GNAI3 14781 -0.081 0.11 NO
40 ADCY3 ADCY3 ADCY3 14827 -0.083 0.12 NO
41 GNG8 GNG8 GNG8 15447 -0.1 0.098 NO
42 RGS20 RGS20 RGS20 16690 -0.21 0.055 NO

Figure S39.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID CD8TCRPATHWAY.

Figure S40.  Get High-res Image For the top 5 core enriched genes in the pathway: PID CD8TCRPATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Fold change

For the top enriched genes, if you want to check whether they are

Expression level

For the top enriched genes, if you want to check whether they are

An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap

Significant gene list

For the top enriched genes, if you want to check whether they are

Subtype clus3 enriched pathways

Table 5.  Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus3. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
PID AURORA B PATHWAY 39 genes.ES.table 0.55 1.7 0.045 0.28 0.73 0.56 0.27 0.41 0.11 0.062
PID ATR PATHWAY 39 genes.ES.table 0.57 1.8 0.023 0.36 0.65 0.49 0.2 0.39 0.12 0.085
PID CDC42 REG PATHWAY 29 genes.ES.table 0.66 1.8 0.002 0.41 0.56 0.38 0.16 0.32 0.11 0.088
PID ATM PATHWAY 34 genes.ES.table 0.59 2 0.0019 0.4 0.12 0.56 0.26 0.42 0 0.081
PID BARD1PATHWAY 29 genes.ES.table 0.67 1.8 0.0038 0.57 0.4 0.62 0.22 0.48 0 0.12
REACTOME METABOLISM OF NON CODING RNA 47 genes.ES.table 0.54 1.9 0.028 0.8 0.38 0.62 0.33 0.42 0 0.15
REACTOME TRANSPORT OF MATURE TRANSCRIPT TO CYTOPLASM 44 genes.ES.table 0.56 1.8 0.019 0.54 0.47 0.68 0.37 0.43 0 0.11
REACTOME RNA POL II TRANSCRIPTION 93 genes.ES.table 0.39 1.7 0.053 0.36 0.68 0.41 0.32 0.28 0.12 0.089
REACTOME CELL CYCLE MITOTIC 297 genes.ES.table 0.45 1.8 0.056 0.39 0.63 0.46 0.28 0.34 0.12 0.089
REACTOME RECRUITMENT OF MITOTIC CENTROSOME PROTEINS AND COMPLEXES 59 genes.ES.table 0.44 1.8 0.03 0.38 0.58 0.51 0.3 0.36 0.11 0.084
genes ES table in pathway: PID AURORA B PATHWAY

Table S21.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 RBBP8 RBBP8 RBBP8 1232 0.24 0.009 YES
2 BLM BLM BLM 1306 0.23 0.081 YES
3 BRCA1 BRCA1 BRCA1 1830 0.19 0.12 YES
4 ABL1 ABL1 ABL1 1886 0.19 0.17 YES
5 SMC3 SMC3 SMC3 2150 0.17 0.22 YES
6 MRE11A MRE11A MRE11A 2511 0.15 0.24 YES
7 FANCD2 FANCD2 FANCD2 3059 0.13 0.26 YES
8 UBE2N UBE2N UBE2N 3131 0.13 0.3 YES
9 BID BID BID 3302 0.12 0.33 YES
10 CDC25A CDC25A CDC25A 3313 0.12 0.37 YES
11 TP53BP1 TP53BP1 TP53BP1 3398 0.12 0.4 YES
12 RAD50 RAD50 RAD50 3727 0.11 0.42 YES
13 ATM ATM ATM 3740 0.11 0.45 YES
14 FAM175A FAM175A FAM175A 3957 0.1 0.47 YES
15 UIMC1 UIMC1 UIMC1 3963 0.1 0.5 YES
16 SMC1A SMC1A SMC1A 4019 0.098 0.53 YES
17 TOP3A TOP3A TOP3A 4160 0.094 0.56 YES
18 MDC1 MDC1 MDC1 4331 0.089 0.58 YES
19 CDC25C CDC25C CDC25C 4536 0.084 0.59 YES
20 TRIM28 TRIM28 TRIM28 6207 0.041 0.51 NO
21 CHEK2 CHEK2 CHEK2 7077 0.02 0.47 NO
22 RNF8 RNF8 RNF8 7213 0.017 0.47 NO
23 H2AFX H2AFX H2AFX 7256 0.016 0.47 NO
24 RAD9A RAD9A RAD9A 7617 0.0075 0.45 NO
25 NBN NBN NBN 7675 0.0062 0.45 NO
26 DCLRE1C DCLRE1C DCLRE1C 7947 0.00021 0.44 NO
27 CTBP1 CTBP1 CTBP1 8829 -0.02 0.39 NO
28 RAD17 RAD17 RAD17 8879 -0.021 0.4 NO
29 KAT5 KAT5 KAT5 8979 -0.023 0.4 NO
30 XRCC4 XRCC4 XRCC4 9069 -0.025 0.4 NO
31 MDM2 MDM2 MDM2 9372 -0.032 0.4 NO
32 YWHAB YWHAB YWHAB 10212 -0.052 0.36 NO
33 RFWD2 RFWD2 RFWD2 11383 -0.084 0.33 NO
34 TERF2 TERF2 TERF2 11651 -0.092 0.34 NO

Figure S41.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID AURORA B PATHWAY.

Figure S42.  Get High-res Image For the top 5 core enriched genes in the pathway: PID AURORA B PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID ATR PATHWAY

Table S22.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 NUP153 NUP153 NUP153 1937 0.18 -0.058 YES
2 NUP205 NUP205 NUP205 2200 0.17 -0.026 YES
3 NUP155 NUP155 NUP155 2210 0.17 0.021 YES
4 NUPL1 NUPL1 NUPL1 2229 0.17 0.067 YES
5 TGS1 TGS1 TGS1 2359 0.16 0.1 YES
6 GEMIN5 GEMIN5 GEMIN5 2452 0.16 0.14 YES
7 NUP107 NUP107 NUP107 2585 0.15 0.18 YES
8 NUP188 NUP188 NUP188 2627 0.15 0.22 YES
9 NUPL2 NUPL2 NUPL2 3358 0.12 0.21 YES
10 NUP54 NUP54 NUP54 3540 0.11 0.23 YES
11 NUP210 NUP210 NUP210 3614 0.11 0.26 YES
12 SEH1L SEH1L SEH1L 3638 0.11 0.29 YES
13 PRMT5 PRMT5 PRMT5 3704 0.11 0.32 YES
14 POM121 POM121 POM121 3910 0.1 0.33 YES
15 TPR TPR TPR 3958 0.1 0.36 YES
16 NUP37 NUP37 NUP37 4051 0.098 0.38 YES
17 NUP50 NUP50 NUP50 4084 0.096 0.4 YES
18 SMN1 SMN1 SMN1 4198 0.093 0.42 YES
19 NUP35 NUP35 NUP35 4283 0.091 0.44 YES
20 SMN2 SMN2 SMN2 4754 0.078 0.44 YES
21 NCBP1 NCBP1 NCBP1 4755 0.078 0.46 YES
22 DDX20 DDX20 DDX20 4762 0.078 0.48 YES
23 GEMIN4 GEMIN4 GEMIN4 4897 0.074 0.5 YES
24 SNRPF SNRPF SNRPF 4937 0.073 0.52 YES
25 NUP85 NUP85 NUP85 5100 0.069 0.52 YES
26 NUP88 NUP88 NUP88 5604 0.056 0.51 YES
27 PHAX PHAX PHAX 5715 0.053 0.52 YES
28 WDR77 WDR77 WDR77 5738 0.052 0.53 YES
29 NUP214 NUP214 NUP214 5814 0.05 0.54 YES
30 NUP62 NUP62 NUP62 6143 0.042 0.54 NO
31 AAAS AAAS AAAS 6464 0.034 0.53 NO
32 SNRPD1 SNRPD1 SNRPD1 6519 0.033 0.53 NO
33 SNRPG SNRPG SNRPG 6609 0.031 0.54 NO
34 RAE1 RAE1 RAE1 6799 0.026 0.53 NO
35 NCBP2 NCBP2 NCBP2 7291 0.015 0.51 NO
36 CLNS1A CLNS1A CLNS1A 7500 0.01 0.5 NO
37 RANBP2 RANBP2 RANBP2 7636 0.0071 0.5 NO
38 SNUPN SNUPN SNUPN 7744 0.0046 0.49 NO
39 NUP133 NUP133 NUP133 7789 0.0036 0.49 NO
40 SNRPB SNRPB SNRPB 8280 -0.0072 0.46 NO
41 NUP93 NUP93 NUP93 8348 -0.0087 0.46 NO
42 SNRPD3 SNRPD3 SNRPD3 8533 -0.013 0.46 NO
43 NUP43 NUP43 NUP43 8706 -0.017 0.45 NO
44 SNRPE SNRPE SNRPE 8710 -0.017 0.46 NO
45 SNRPD2 SNRPD2 SNRPD2 9410 -0.033 0.42 NO
46 GEMIN6 GEMIN6 GEMIN6 9837 -0.043 0.41 NO
47 GEMIN7 GEMIN7 GEMIN7 12306 -0.11 0.3 NO

Figure S43.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID ATR PATHWAY.

Figure S44.  Get High-res Image For the top 5 core enriched genes in the pathway: PID ATR PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID CDC42 REG PATHWAY

Table S23.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 BARD1 BARD1 BARD1 248 0.42 0.12 YES
2 RBBP8 RBBP8 RBBP8 1232 0.24 0.14 YES
3 CDK2 CDK2 CDK2 1687 0.2 0.17 YES
4 BRCA1 BRCA1 BRCA1 1830 0.19 0.22 YES
5 TOPBP1 TOPBP1 TOPBP1 2056 0.18 0.26 YES
6 ATR ATR ATR 2350 0.16 0.3 YES
7 MRE11A MRE11A MRE11A 2511 0.15 0.34 YES
8 FANCF FANCF FANCF 2868 0.14 0.36 YES
9 FANCC FANCC FANCC 2892 0.14 0.4 YES
10 RAD51 RAD51 RAD51 3021 0.13 0.44 YES
11 FANCD2 FANCD2 FANCD2 3059 0.13 0.47 YES
12 PRKDC PRKDC PRKDC 3061 0.13 0.52 YES
13 FANCA FANCA FANCA 3151 0.13 0.55 YES
14 CCNE1 CCNE1 CCNE1 3414 0.12 0.57 YES
15 FANCG FANCG FANCG 3628 0.11 0.59 YES
16 RAD50 RAD50 RAD50 3727 0.11 0.62 YES
17 ATM ATM ATM 3740 0.11 0.65 YES
18 TP53 TP53 TP53 3938 0.1 0.67 YES
19 NPM1 NPM1 NPM1 5534 0.057 0.6 NO
20 FANCE FANCE FANCE 5767 0.052 0.6 NO
21 PCNA PCNA PCNA 6202 0.041 0.59 NO
22 EWSR1 EWSR1 EWSR1 6426 0.035 0.59 NO
23 XRCC5 XRCC5 XRCC5 6495 0.033 0.6 NO
24 FANCL FANCL FANCL 6546 0.032 0.6 NO
25 CSTF1 CSTF1 CSTF1 7011 0.022 0.58 NO
26 NBN NBN NBN 7675 0.0062 0.55 NO
27 XRCC6 XRCC6 XRCC6 8132 -0.0035 0.52 NO
28 UBE2D3 UBE2D3 UBE2D3 8191 -0.0047 0.52 NO
29 UBE2L3 UBE2L3 UBE2L3 10038 -0.048 0.43 NO

Figure S45.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID CDC42 REG PATHWAY.

Figure S46.  Get High-res Image For the top 5 core enriched genes in the pathway: PID CDC42 REG PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID ATM PATHWAY

Table S24.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 NUP153 NUP153 NUP153 1937 0.18 -0.052 YES
2 NUP205 NUP205 NUP205 2200 0.17 -0.014 YES
3 NUP155 NUP155 NUP155 2210 0.17 0.038 YES
4 NUPL1 NUPL1 NUPL1 2229 0.17 0.09 YES
5 NUP107 NUP107 NUP107 2585 0.15 0.12 YES
6 NUP188 NUP188 NUP188 2627 0.15 0.16 YES
7 U2AF2 U2AF2 U2AF2 2994 0.13 0.18 YES
8 SRRM1 SRRM1 SRRM1 3200 0.13 0.21 YES
9 NUPL2 NUPL2 NUPL2 3358 0.12 0.24 YES
10 NUP54 NUP54 NUP54 3540 0.11 0.26 YES
11 NUP210 NUP210 NUP210 3614 0.11 0.3 YES
12 SEH1L SEH1L SEH1L 3638 0.11 0.33 YES
13 NFX1 NFX1 NFX1 3836 0.1 0.35 YES
14 POM121 POM121 POM121 3910 0.1 0.38 YES
15 TPR TPR TPR 3958 0.1 0.41 YES
16 NUP37 NUP37 NUP37 4051 0.098 0.43 YES
17 NUP50 NUP50 NUP50 4084 0.096 0.46 YES
18 NUP35 NUP35 NUP35 4283 0.091 0.48 YES
19 NCBP1 NCBP1 NCBP1 4755 0.078 0.48 YES
20 CPSF2 CPSF2 CPSF2 4976 0.072 0.49 YES
21 SLBP SLBP SLBP 5016 0.071 0.51 YES
22 NUP85 NUP85 NUP85 5100 0.069 0.52 YES
23 UPF3B UPF3B UPF3B 5540 0.057 0.52 YES
24 NUP88 NUP88 NUP88 5604 0.056 0.53 YES
25 NUP214 NUP214 NUP214 5814 0.05 0.53 YES
26 NUP62 NUP62 NUP62 6143 0.042 0.53 YES
27 RNPS1 RNPS1 RNPS1 6324 0.038 0.53 YES
28 EIF4E EIF4E EIF4E 6341 0.037 0.54 YES
29 CDC40 CDC40 CDC40 6458 0.034 0.55 YES
30 AAAS AAAS AAAS 6464 0.034 0.56 YES
31 RAE1 RAE1 RAE1 6799 0.026 0.55 NO
32 MAGOH MAGOH MAGOH 6831 0.025 0.55 NO
33 DHX38 DHX38 DHX38 7094 0.02 0.54 NO
34 NCBP2 NCBP2 NCBP2 7291 0.015 0.54 NO
35 NXF1 NXF1 NXF1 7371 0.013 0.54 NO
36 THOC4 THOC4 THOC4 7460 0.011 0.53 NO
37 RANBP2 RANBP2 RANBP2 7636 0.0071 0.53 NO
38 NUP133 NUP133 NUP133 7789 0.0036 0.52 NO
39 U2AF1 U2AF1 U2AF1 8030 -0.0015 0.51 NO
40 NUP93 NUP93 NUP93 8348 -0.0087 0.49 NO
41 NUP43 NUP43 NUP43 8706 -0.017 0.48 NO
42 RBM8A RBM8A RBM8A 9175 -0.028 0.46 NO
43 CPSF1 CPSF1 CPSF1 9309 -0.031 0.46 NO
44 CPSF3 CPSF3 CPSF3 9918 -0.045 0.44 NO

Figure S47.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID ATM PATHWAY.

Figure S48.  Get High-res Image For the top 5 core enriched genes in the pathway: PID ATM PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID BARD1PATHWAY

Table S25.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CEP70 CEP70 CEP70 388 0.38 0.026 YES
2 PLK4 PLK4 PLK4 702 0.31 0.047 YES
3 CEP72 CEP72 CEP72 965 0.27 0.066 YES
4 CEP76 CEP76 CEP76 1203 0.24 0.084 YES
5 CEP290 CEP290 CEP290 1464 0.22 0.096 YES
6 CDK2 CDK2 CDK2 1687 0.2 0.11 YES
7 CENPJ CENPJ CENPJ 1690 0.2 0.14 YES
8 TUBGCP5 TUBGCP5 TUBGCP5 1745 0.2 0.16 YES
9 NEDD1 NEDD1 NEDD1 1770 0.2 0.18 YES
10 TUBGCP3 TUBGCP3 TUBGCP3 1872 0.19 0.2 YES
11 HAUS2 HAUS2 HAUS2 2073 0.18 0.21 YES
12 PLK1 PLK1 PLK1 2076 0.18 0.23 YES
13 CEP164 CEP164 CEP164 2105 0.18 0.25 YES
14 E2F3 E2F3 E2F3 2122 0.17 0.27 YES
15 CKAP5 CKAP5 CKAP5 2181 0.17 0.29 YES
16 FGFR1OP FGFR1OP FGFR1OP 2301 0.16 0.3 YES
17 CEP192 CEP192 CEP192 2455 0.16 0.32 YES
18 AKAP9 AKAP9 AKAP9 2664 0.15 0.32 YES
19 NEK2 NEK2 NEK2 2817 0.14 0.33 YES
20 CCNA2 CCNA2 CCNA2 2941 0.14 0.34 YES
21 PCNT PCNT PCNT 3071 0.13 0.35 YES
22 CLASP1 CLASP1 CLASP1 3137 0.13 0.36 YES
23 CDC25A CDC25A CDC25A 3313 0.12 0.37 YES
24 CSNK1E CSNK1E CSNK1E 3319 0.12 0.38 YES
25 TUBGCP6 TUBGCP6 TUBGCP6 3476 0.12 0.39 YES
26 CCNB2 CCNB2 CCNB2 3624 0.11 0.4 YES
27 ALMS1 ALMS1 ALMS1 3948 0.1 0.39 YES
28 WEE1 WEE1 WEE1 3965 0.1 0.4 YES
29 TUBG1 TUBG1 TUBG1 4009 0.099 0.41 YES
30 CDK1 CDK1 CDK1 4363 0.088 0.4 YES
31 YWHAG YWHAG YWHAG 4423 0.087 0.41 YES
32 XPO1 XPO1 XPO1 4477 0.086 0.42 YES
33 CEP57 CEP57 CEP57 4507 0.085 0.43 YES
34 CDC25C CDC25C CDC25C 4536 0.084 0.44 YES
35 CCNB1 CCNB1 CCNB1 4844 0.075 0.43 YES
36 E2F1 E2F1 E2F1 4874 0.075 0.44 YES
37 TUBG2 TUBG2 TUBG2 4950 0.073 0.44 YES
38 CEP135 CEP135 CEP135 5110 0.069 0.44 YES
39 NUMA1 NUMA1 NUMA1 5241 0.065 0.44 YES
40 PKMYT1 PKMYT1 PKMYT1 5532 0.057 0.43 NO
41 PRKACA PRKACA PRKACA 5583 0.056 0.44 NO
42 DYNC1I2 DYNC1I2 DYNC1I2 5793 0.051 0.43 NO
43 CDK5RAP2 CDK5RAP2 CDK5RAP2 6315 0.038 0.41 NO
44 TUBB TUBB TUBB 6322 0.038 0.41 NO
45 CEP63 CEP63 CEP63 6325 0.038 0.42 NO
46 PCM1 PCM1 PCM1 6975 0.022 0.38 NO
47 MAPRE1 MAPRE1 MAPRE1 7057 0.021 0.38 NO
48 NINL NINL NINL 7347 0.014 0.36 NO
49 DCTN1 DCTN1 DCTN1 7408 0.013 0.36 NO
50 CEP250 CEP250 CEP250 7424 0.012 0.36 NO
51 YWHAE YWHAE YWHAE 7585 0.0083 0.36 NO
52 DYNC1H1 DYNC1H1 DYNC1H1 7589 0.0082 0.36 NO
53 CDK7 CDK7 CDK7 7633 0.0072 0.36 NO
54 CDC25B CDC25B CDC25B 8007 -0.00092 0.33 NO
55 HSP90AA1 HSP90AA1 HSP90AA1 8014 -0.0011 0.33 NO
56 PAFAH1B1 PAFAH1B1 PAFAH1B1 8831 -0.02 0.29 NO
57 CCNH CCNH CCNH 9108 -0.026 0.28 NO
58 DCTN2 DCTN2 DCTN2 9154 -0.027 0.28 NO
59 TUBGCP2 TUBGCP2 TUBGCP2 9425 -0.033 0.27 NO
60 CSNK1D CSNK1D CSNK1D 9594 -0.037 0.26 NO
61 MNAT1 MNAT1 MNAT1 9799 -0.042 0.26 NO
62 PPP2R1A PPP2R1A PPP2R1A 10291 -0.055 0.24 NO
63 ACTR1A ACTR1A ACTR1A 10361 -0.056 0.24 NO
64 DYNLL1 DYNLL1 DYNLL1 11169 -0.079 0.2 NO
65 OFD1 OFD1 OFD1 11329 -0.083 0.2 NO
66 AZI1 AZI1 AZI1 11542 -0.089 0.2 NO
67 SSNA1 SSNA1 SSNA1 11827 -0.098 0.2 NO
68 TUBA1A TUBA1A TUBA1A 12345 -0.11 0.18 NO
69 CETN2 CETN2 CETN2 12620 -0.12 0.18 NO
70 DCTN3 DCTN3 DCTN3 12646 -0.12 0.2 NO
71 TUBA4A TUBA4A TUBA4A 13422 -0.16 0.17 NO
72 PRKAR2B PRKAR2B PRKAR2B 13454 -0.16 0.19 NO
73 SDCCAG8 SDCCAG8 SDCCAG8 13524 -0.16 0.21 NO
74 CCNA1 CCNA1 CCNA1 14502 -0.21 0.18 NO

Figure S49.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID BARD1PATHWAY.

Figure S50.  Get High-res Image For the top 5 core enriched genes in the pathway: PID BARD1PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: REACTOME METABOLISM OF NON CODING RNA

Table S26.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CASC5 CASC5 CASC5 63 0.55 0.05 YES
2 BUB1B BUB1B BUB1B 519 0.35 0.058 YES
3 INCENP INCENP INCENP 596 0.33 0.086 YES
4 STAG1 STAG1 STAG1 694 0.31 0.11 YES
5 CENPI CENPI CENPI 737 0.3 0.14 YES
6 SGOL1 SGOL1 SGOL1 787 0.3 0.16 YES
7 CENPK CENPK CENPK 841 0.29 0.19 YES
8 KIF18A KIF18A KIF18A 959 0.27 0.21 YES
9 KNTC1 KNTC1 KNTC1 974 0.27 0.23 YES
10 TAOK1 TAOK1 TAOK1 1073 0.26 0.25 YES
11 ZWINT ZWINT ZWINT 1262 0.24 0.27 YES
12 CENPQ CENPQ CENPQ 1319 0.23 0.28 YES
13 MAD2L1 MAD2L1 MAD2L1 1533 0.21 0.29 YES
14 ZWILCH ZWILCH ZWILCH 1554 0.21 0.31 YES
15 CDCA8 CDCA8 CDCA8 1727 0.2 0.32 YES
16 SPC24 SPC24 SPC24 1778 0.2 0.34 YES
17 SGOL2 SGOL2 SGOL2 1906 0.19 0.35 YES
18 PPP2R5E PPP2R5E PPP2R5E 1935 0.18 0.36 YES
19 CENPA CENPA CENPA 2058 0.18 0.38 YES
20 CCDC99 CCDC99 CCDC99 2069 0.18 0.39 YES
21 PLK1 PLK1 PLK1 2076 0.18 0.41 YES
22 ERCC6L ERCC6L ERCC6L 2102 0.18 0.42 YES
23 SMC3 SMC3 SMC3 2150 0.17 0.44 YES
24 CKAP5 CKAP5 CKAP5 2181 0.17 0.45 YES
25 NUF2 NUF2 NUF2 2208 0.17 0.47 YES
26 SKA1 SKA1 SKA1 2219 0.17 0.48 YES
27 CENPL CENPL CENPL 2278 0.16 0.5 YES
28 SPC25 SPC25 SPC25 2328 0.16 0.51 YES
29 AHCTF1 AHCTF1 AHCTF1 2494 0.15 0.52 YES
30 NUP107 NUP107 NUP107 2585 0.15 0.52 YES
31 CLIP1 CLIP1 CLIP1 2797 0.14 0.53 YES
32 CENPO CENPO CENPO 2882 0.14 0.54 YES
33 CENPC1 CENPC1 CENPC1 3040 0.13 0.54 YES
34 CLASP1 CLASP1 CLASP1 3137 0.13 0.55 YES
35 ZW10 ZW10 ZW10 3232 0.12 0.55 YES
36 BUB3 BUB3 BUB3 3239 0.12 0.56 YES
37 PPP2R1B PPP2R1B PPP2R1B 3425 0.12 0.56 YES
38 KIF2A KIF2A KIF2A 3582 0.11 0.57 YES
39 SEH1L SEH1L SEH1L 3638 0.11 0.57 YES
40 SMC1A SMC1A SMC1A 4019 0.098 0.56 YES
41 NUP37 NUP37 NUP37 4051 0.098 0.57 YES
42 KIF2C KIF2C KIF2C 4151 0.095 0.57 YES
43 BUB1 BUB1 BUB1 4178 0.094 0.58 YES
44 XPO1 XPO1 XPO1 4477 0.086 0.57 YES
45 APITD1 APITD1 APITD1 4541 0.084 0.58 YES
46 NSL1 NSL1 NSL1 4582 0.083 0.58 YES
47 PPP2R5B PPP2R5B PPP2R5B 4603 0.082 0.59 YES
48 NDC80 NDC80 NDC80 4787 0.077 0.59 NO
49 CENPN CENPN CENPN 4944 0.073 0.59 NO
50 NUP85 NUP85 NUP85 5100 0.069 0.58 NO
51 STAG2 STAG2 STAG2 5210 0.066 0.58 NO
52 RAD21 RAD21 RAD21 5516 0.058 0.57 NO
53 PPP2R5D PPP2R5D PPP2R5D 5741 0.052 0.56 NO
54 CDC20 CDC20 CDC20 5777 0.051 0.57 NO
55 MIS12 MIS12 MIS12 5824 0.05 0.57 NO
56 ITGB3BP ITGB3BP ITGB3BP 5844 0.05 0.57 NO
57 RCC2 RCC2 RCC2 5921 0.048 0.57 NO
58 AURKB AURKB AURKB 6932 0.023 0.52 NO
59 MAPRE1 MAPRE1 MAPRE1 7057 0.021 0.51 NO
60 PPP1CC PPP1CC PPP1CC 7181 0.018 0.51 NO
61 PPP2R5A PPP2R5A PPP2R5A 7355 0.014 0.5 NO
62 PPP2CB PPP2CB PPP2CB 7426 0.012 0.5 NO
63 DSN1 DSN1 DSN1 7435 0.012 0.5 NO
64 CENPH CENPH CENPH 7542 0.0094 0.49 NO
65 RANBP2 RANBP2 RANBP2 7636 0.0071 0.49 NO
66 NUP133 NUP133 NUP133 7789 0.0036 0.48 NO
67 CENPT CENPT CENPT 7929 0.00054 0.47 NO
68 PPP2R5C PPP2R5C PPP2R5C 8016 -0.0011 0.47 NO
69 SKA2 SKA2 SKA2 8169 -0.0043 0.46 NO
70 BIRC5 BIRC5 BIRC5 8327 -0.0082 0.45 NO
71 PPP2CA PPP2CA PPP2CA 8600 -0.014 0.44 NO
72 NDEL1 NDEL1 NDEL1 8702 -0.017 0.43 NO
73 NUP43 NUP43 NUP43 8706 -0.017 0.43 NO
74 PAFAH1B1 PAFAH1B1 PAFAH1B1 8831 -0.02 0.43 NO
75 SEC13 SEC13 SEC13 8894 -0.021 0.43 NO
76 MLF1IP MLF1IP MLF1IP 8915 -0.021 0.43 NO
77 PMF1 PMF1 PMF1 9272 -0.03 0.41 NO
78 CENPP CENPP CENPP 9381 -0.033 0.41 NO
79 RANGAP1 RANGAP1 RANGAP1 9833 -0.043 0.39 NO
80 NUDC NUDC NUDC 10185 -0.051 0.37 NO
81 PPP2R1A PPP2R1A PPP2R1A 10291 -0.055 0.37 NO
82 CENPM CENPM CENPM 10468 -0.059 0.37 NO
83 RPS27 RPS27 RPS27 12095 -0.11 0.28 NO
84 B9D2 B9D2 B9D2 13158 -0.14 0.24 NO
85 MAD1L1 MAD1L1 MAD1L1 14137 -0.19 0.2 NO

Figure S51.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME METABOLISM OF NON CODING RNA.

Figure S52.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME METABOLISM OF NON CODING RNA, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: REACTOME TRANSPORT OF MATURE TRANSCRIPT TO CYTOPLASM

Table S27.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 NGEF NGEF NGEF 377 0.38 0.1 YES
2 DNMBP DNMBP DNMBP 578 0.33 0.2 YES
3 DOCK10 DOCK10 DOCK10 599 0.33 0.31 YES
4 BCAR3 BCAR3 BCAR3 1317 0.23 0.35 YES
5 SPATA13 SPATA13 SPATA13 1355 0.23 0.42 YES
6 APC APC APC 1982 0.18 0.44 YES
7 VAV3 VAV3 VAV3 2114 0.17 0.49 YES
8 ARHGAP17 ARHGAP17 ARHGAP17 2192 0.17 0.55 YES
9 ITSN1 ITSN1 ITSN1 2280 0.16 0.6 YES
10 RACGAP1 RACGAP1 RACGAP1 2637 0.15 0.62 YES
11 MCF2 MCF2 MCF2 2795 0.14 0.66 YES
12 RALBP1 RALBP1 RALBP1 4149 0.095 0.62 NO
13 ARHGEF7 ARHGEF7 ARHGEF7 4907 0.074 0.6 NO
14 ITSN2 ITSN2 ITSN2 5610 0.056 0.58 NO
15 NME1 NME1 NME1 5756 0.052 0.58 NO
16 MCF2L MCF2L MCF2L 5893 0.049 0.59 NO
17 ARHGEF6 ARHGEF6 ARHGEF6 6432 0.035 0.57 NO
18 FARP2 FARP2 FARP2 7216 0.017 0.54 NO
19 ARHGAP1 ARHGAP1 ARHGAP1 7308 0.015 0.54 NO
20 ARHGDIA ARHGDIA ARHGDIA 7756 0.0044 0.51 NO
21 FGD1 FGD1 FGD1 7814 0.003 0.51 NO
22 DOCK11 DOCK11 DOCK11 7933 0.00043 0.5 NO
23 DOCK9 DOCK9 DOCK9 7982 -0.00033 0.5 NO
24 ARHGEF9 ARHGEF9 ARHGEF9 8424 -0.011 0.48 NO
25 CDC42 CDC42 CDC42 8646 -0.015 0.47 NO
26 GIT1 GIT1 GIT1 8867 -0.02 0.46 NO
27 VAV2 VAV2 VAV2 8884 -0.021 0.47 NO
28 PLCG1 PLCG1 PLCG1 9692 -0.04 0.44 NO
29 DOCK6 DOCK6 DOCK6 9842 -0.043 0.44 NO

Figure S53.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME TRANSPORT OF MATURE TRANSCRIPT TO CYTOPLASM.

Figure S54.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME TRANSPORT OF MATURE TRANSCRIPT TO CYTOPLASM, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: REACTOME RNA POL II TRANSCRIPTION

Table S28.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CEP70 CEP70 CEP70 388 0.38 0.036 YES
2 PLK4 PLK4 PLK4 702 0.31 0.066 YES
3 CEP72 CEP72 CEP72 965 0.27 0.093 YES
4 CEP76 CEP76 CEP76 1203 0.24 0.12 YES
5 CEP290 CEP290 CEP290 1464 0.22 0.14 YES
6 CENPJ CENPJ CENPJ 1690 0.2 0.15 YES
7 TUBGCP5 TUBGCP5 TUBGCP5 1745 0.2 0.18 YES
8 NEDD1 NEDD1 NEDD1 1770 0.2 0.21 YES
9 TUBGCP3 TUBGCP3 TUBGCP3 1872 0.19 0.23 YES
10 HAUS2 HAUS2 HAUS2 2073 0.18 0.25 YES
11 PLK1 PLK1 PLK1 2076 0.18 0.28 YES
12 CEP164 CEP164 CEP164 2105 0.18 0.3 YES
13 CKAP5 CKAP5 CKAP5 2181 0.17 0.32 YES
14 FGFR1OP FGFR1OP FGFR1OP 2301 0.16 0.34 YES
15 CEP192 CEP192 CEP192 2455 0.16 0.36 YES
16 AKAP9 AKAP9 AKAP9 2664 0.15 0.37 YES
17 NEK2 NEK2 NEK2 2817 0.14 0.38 YES
18 PCNT PCNT PCNT 3071 0.13 0.39 YES
19 CLASP1 CLASP1 CLASP1 3137 0.13 0.4 YES
20 CSNK1E CSNK1E CSNK1E 3319 0.12 0.41 YES
21 TUBGCP6 TUBGCP6 TUBGCP6 3476 0.12 0.42 YES
22 ALMS1 ALMS1 ALMS1 3948 0.1 0.41 YES
23 TUBG1 TUBG1 TUBG1 4009 0.099 0.42 YES
24 CDK1 CDK1 CDK1 4363 0.088 0.42 YES
25 YWHAG YWHAG YWHAG 4423 0.087 0.43 YES
26 CEP57 CEP57 CEP57 4507 0.085 0.44 YES
27 CCNB1 CCNB1 CCNB1 4844 0.075 0.43 YES
28 TUBG2 TUBG2 TUBG2 4950 0.073 0.43 YES
29 CEP135 CEP135 CEP135 5110 0.069 0.43 YES
30 NUMA1 NUMA1 NUMA1 5241 0.065 0.44 YES
31 PRKACA PRKACA PRKACA 5583 0.056 0.43 NO
32 DYNC1I2 DYNC1I2 DYNC1I2 5793 0.051 0.42 NO
33 CDK5RAP2 CDK5RAP2 CDK5RAP2 6315 0.038 0.4 NO
34 TUBB TUBB TUBB 6322 0.038 0.4 NO
35 CEP63 CEP63 CEP63 6325 0.038 0.41 NO
36 PCM1 PCM1 PCM1 6975 0.022 0.38 NO
37 MAPRE1 MAPRE1 MAPRE1 7057 0.021 0.38 NO
38 NINL NINL NINL 7347 0.014 0.36 NO
39 DCTN1 DCTN1 DCTN1 7408 0.013 0.36 NO
40 CEP250 CEP250 CEP250 7424 0.012 0.36 NO
41 YWHAE YWHAE YWHAE 7585 0.0083 0.35 NO
42 DYNC1H1 DYNC1H1 DYNC1H1 7589 0.0082 0.35 NO
43 HSP90AA1 HSP90AA1 HSP90AA1 8014 -0.0011 0.33 NO
44 PAFAH1B1 PAFAH1B1 PAFAH1B1 8831 -0.02 0.29 NO
45 DCTN2 DCTN2 DCTN2 9154 -0.027 0.27 NO
46 TUBGCP2 TUBGCP2 TUBGCP2 9425 -0.033 0.26 NO
47 CSNK1D CSNK1D CSNK1D 9594 -0.037 0.26 NO
48 PPP2R1A PPP2R1A PPP2R1A 10291 -0.055 0.23 NO
49 ACTR1A ACTR1A ACTR1A 10361 -0.056 0.23 NO
50 DYNLL1 DYNLL1 DYNLL1 11169 -0.079 0.2 NO
51 OFD1 OFD1 OFD1 11329 -0.083 0.2 NO
52 AZI1 AZI1 AZI1 11542 -0.089 0.2 NO
53 SSNA1 SSNA1 SSNA1 11827 -0.098 0.2 NO
54 TUBA1A TUBA1A TUBA1A 12345 -0.11 0.19 NO
55 CETN2 CETN2 CETN2 12620 -0.12 0.2 NO
56 DCTN3 DCTN3 DCTN3 12646 -0.12 0.21 NO
57 TUBA4A TUBA4A TUBA4A 13422 -0.16 0.19 NO
58 PRKAR2B PRKAR2B PRKAR2B 13454 -0.16 0.22 NO
59 SDCCAG8 SDCCAG8 SDCCAG8 13524 -0.16 0.24 NO

Figure S55.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME RNA POL II TRANSCRIPTION.

Figure S56.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME RNA POL II TRANSCRIPTION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: REACTOME CELL CYCLE MITOTIC

Table S29.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CASC5 CASC5 CASC5 63 0.55 0.013 YES
2 DNA2 DNA2 DNA2 132 0.48 0.024 YES
3 RBL1 RBL1 RBL1 168 0.46 0.036 YES
4 CEP70 CEP70 CEP70 388 0.38 0.034 YES
5 RB1 RB1 RB1 439 0.36 0.042 YES
6 BUB1B BUB1B BUB1B 519 0.35 0.048 YES
7 INCENP INCENP INCENP 596 0.33 0.054 YES
8 STAG1 STAG1 STAG1 694 0.31 0.058 YES
9 PLK4 PLK4 PLK4 702 0.31 0.067 YES
10 MCM8 MCM8 MCM8 709 0.31 0.076 YES
11 CENPI CENPI CENPI 737 0.3 0.083 YES
12 SGOL1 SGOL1 SGOL1 787 0.3 0.089 YES
13 POLE2 POLE2 POLE2 793 0.3 0.098 YES
14 CENPK CENPK CENPK 841 0.29 0.1 YES
15 MCM10 MCM10 MCM10 863 0.28 0.11 YES
16 CCND2 CCND2 CCND2 873 0.28 0.12 YES
17 ANAPC1 ANAPC1 ANAPC1 912 0.28 0.12 YES
18 KIF18A KIF18A KIF18A 959 0.27 0.13 YES
19 CEP72 CEP72 CEP72 965 0.27 0.14 YES
20 KNTC1 KNTC1 KNTC1 974 0.27 0.15 YES
21 KIF23 KIF23 KIF23 1032 0.26 0.15 YES
22 LIN52 LIN52 LIN52 1039 0.26 0.16 YES
23 TAOK1 TAOK1 TAOK1 1073 0.26 0.16 YES
24 RPA4 RPA4 RPA4 1076 0.26 0.17 YES
25 CEP76 CEP76 CEP76 1203 0.24 0.17 YES
26 ZWINT ZWINT ZWINT 1262 0.24 0.18 YES
27 GINS4 GINS4 GINS4 1295 0.23 0.18 YES
28 CENPQ CENPQ CENPQ 1319 0.23 0.19 YES
29 KIF20A KIF20A KIF20A 1357 0.23 0.19 YES
30 PSMD5 PSMD5 PSMD5 1416 0.22 0.2 YES
31 CEP290 CEP290 CEP290 1464 0.22 0.2 YES
32 E2F5 E2F5 E2F5 1473 0.22 0.2 YES
33 MYC MYC MYC 1529 0.21 0.21 YES
34 MAD2L1 MAD2L1 MAD2L1 1533 0.21 0.21 YES
35 MCM4 MCM4 MCM4 1546 0.21 0.22 YES
36 ZWILCH ZWILCH ZWILCH 1554 0.21 0.23 YES
37 SKP2 SKP2 SKP2 1633 0.2 0.23 YES
38 RFC3 RFC3 RFC3 1682 0.2 0.23 YES
39 CDK2 CDK2 CDK2 1687 0.2 0.24 YES
40 CENPJ CENPJ CENPJ 1690 0.2 0.24 YES
41 CDC6 CDC6 CDC6 1691 0.2 0.25 YES
42 LIN9 LIN9 LIN9 1711 0.2 0.25 YES
43 CDCA8 CDCA8 CDCA8 1727 0.2 0.26 YES
44 TUBGCP5 TUBGCP5 TUBGCP5 1745 0.2 0.26 YES
45 NEDD1 NEDD1 NEDD1 1770 0.2 0.27 YES
46 SPC24 SPC24 SPC24 1778 0.2 0.27 YES
47 CDC7 CDC7 CDC7 1825 0.19 0.28 YES
48 TFDP1 TFDP1 TFDP1 1863 0.19 0.28 YES
49 TUBGCP3 TUBGCP3 TUBGCP3 1872 0.19 0.28 YES
50 CCNE2 CCNE2 CCNE2 1876 0.19 0.29 YES
51 SGOL2 SGOL2 SGOL2 1906 0.19 0.3 YES
52 PPP2R5E PPP2R5E PPP2R5E 1935 0.18 0.3 YES
53 CENPA CENPA CENPA 2058 0.18 0.3 YES
54 CCDC99 CCDC99 CCDC99 2069 0.18 0.3 YES
55 HAUS2 HAUS2 HAUS2 2073 0.18 0.31 YES
56 PLK1 PLK1 PLK1 2076 0.18 0.31 YES
57 ERCC6L ERCC6L ERCC6L 2102 0.18 0.32 YES
58 CEP164 CEP164 CEP164 2105 0.18 0.32 YES
59 FBXO5 FBXO5 FBXO5 2115 0.17 0.33 YES
60 E2F3 E2F3 E2F3 2122 0.17 0.33 YES
61 SMC3 SMC3 SMC3 2150 0.17 0.33 YES
62 RFC5 RFC5 RFC5 2155 0.17 0.34 YES
63 POLE POLE POLE 2161 0.17 0.34 YES
64 CKAP5 CKAP5 CKAP5 2181 0.17 0.35 YES
65 GINS1 GINS1 GINS1 2206 0.17 0.35 YES
66 NUF2 NUF2 NUF2 2208 0.17 0.36 YES
67 SKA1 SKA1 SKA1 2219 0.17 0.36 YES
68 CDC45 CDC45 CDC45 2241 0.17 0.36 YES
69 CENPL CENPL CENPL 2278 0.16 0.37 YES
70 FGFR1OP FGFR1OP FGFR1OP 2301 0.16 0.37 YES
71 SPC25 SPC25 SPC25 2328 0.16 0.38 YES
72 AURKA AURKA AURKA 2372 0.16 0.38 YES
73 PRIM2 PRIM2 PRIM2 2385 0.16 0.38 YES
74 POLD3 POLD3 POLD3 2414 0.16 0.38 YES
75 CEP192 CEP192 CEP192 2455 0.16 0.39 YES
76 AHCTF1 AHCTF1 AHCTF1 2494 0.15 0.39 YES
77 NUP107 NUP107 NUP107 2585 0.15 0.39 YES
78 DHFR DHFR DHFR 2648 0.15 0.39 YES
79 AKAP9 AKAP9 AKAP9 2664 0.15 0.39 YES
80 POLA1 POLA1 POLA1 2690 0.15 0.4 YES
81 CDC23 CDC23 CDC23 2767 0.14 0.4 YES
82 CLIP1 CLIP1 CLIP1 2797 0.14 0.4 YES
83 LIN54 LIN54 LIN54 2815 0.14 0.4 YES
84 NEK2 NEK2 NEK2 2817 0.14 0.41 YES
85 CENPO CENPO CENPO 2882 0.14 0.41 YES
86 CCNA2 CCNA2 CCNA2 2941 0.14 0.41 YES
87 MYBL2 MYBL2 MYBL2 3033 0.13 0.41 YES
88 CENPC1 CENPC1 CENPC1 3040 0.13 0.41 YES
89 PCNT PCNT PCNT 3071 0.13 0.41 YES
90 CLASP1 CLASP1 CLASP1 3137 0.13 0.41 YES
91 PRIM1 PRIM1 PRIM1 3231 0.12 0.41 YES
92 ZW10 ZW10 ZW10 3232 0.12 0.41 YES
93 BUB3 BUB3 BUB3 3239 0.12 0.42 YES
94 CDC25A CDC25A CDC25A 3313 0.12 0.42 YES
95 CSNK1E CSNK1E CSNK1E 3319 0.12 0.42 YES
96 RRM2 RRM2 RRM2 3328 0.12 0.42 YES
97 RBBP4 RBBP4 RBBP4 3339 0.12 0.43 YES
98 TYMS TYMS TYMS 3368 0.12 0.43 YES
99 MCM2 MCM2 MCM2 3406 0.12 0.43 YES
100 CCNE1 CCNE1 CCNE1 3414 0.12 0.43 YES
101 PPP2R1B PPP2R1B PPP2R1B 3425 0.12 0.44 YES
102 TUBGCP6 TUBGCP6 TUBGCP6 3476 0.12 0.44 YES
103 PSMD12 PSMD12 PSMD12 3497 0.12 0.44 YES
104 RBL2 RBL2 RBL2 3510 0.12 0.44 YES
105 RPA1 RPA1 RPA1 3556 0.11 0.44 YES
106 POLD1 POLD1 POLD1 3566 0.11 0.44 YES
107 KIF2A KIF2A KIF2A 3582 0.11 0.45 YES
108 CCNB2 CCNB2 CCNB2 3624 0.11 0.45 YES
109 SEH1L SEH1L SEH1L 3638 0.11 0.45 YES
110 PSME4 PSME4 PSME4 3802 0.1 0.44 YES
111 ALMS1 ALMS1 ALMS1 3948 0.1 0.44 YES
112 WEE1 WEE1 WEE1 3965 0.1 0.44 YES
113 TUBG1 TUBG1 TUBG1 4009 0.099 0.44 YES
114 SMC1A SMC1A SMC1A 4019 0.098 0.44 YES
115 NUP37 NUP37 NUP37 4051 0.098 0.45 YES
116 KIF2C KIF2C KIF2C 4151 0.095 0.44 YES
117 BUB1 BUB1 BUB1 4178 0.094 0.44 YES
118 CDC27 CDC27 CDC27 4294 0.09 0.44 YES
119 CDK1 CDK1 CDK1 4363 0.088 0.44 YES
120 YWHAG YWHAG YWHAG 4423 0.087 0.44 YES
121 XPO1 XPO1 XPO1 4477 0.086 0.44 YES
122 CEP57 CEP57 CEP57 4507 0.085 0.44 YES
123 CDC25C CDC25C CDC25C 4536 0.084 0.44 YES
124 APITD1 APITD1 APITD1 4541 0.084 0.44 YES
125 MCM6 MCM6 MCM6 4544 0.084 0.44 YES
126 NSL1 NSL1 NSL1 4582 0.083 0.44 YES
127 UBE2C UBE2C UBE2C 4594 0.082 0.45 YES
128 PPP2R5B PPP2R5B PPP2R5B 4603 0.082 0.45 YES
129 E2F2 E2F2 E2F2 4677 0.08 0.45 YES
130 CUL1 CUL1 CUL1 4750 0.078 0.44 YES
131 NDC80 NDC80 NDC80 4787 0.077 0.45 YES
132 GMNN GMNN GMNN 4811 0.076 0.45 YES
133 CCNB1 CCNB1 CCNB1 4844 0.075 0.45 YES
134 PSMD3 PSMD3 PSMD3 4852 0.075 0.45 YES
135 CDC14A CDC14A CDC14A 4853 0.075 0.45 YES
136 E2F1 E2F1 E2F1 4874 0.075 0.45 YES
137 CENPN CENPN CENPN 4944 0.073 0.45 YES
138 TUBG2 TUBG2 TUBG2 4950 0.073 0.45 YES
139 RFC4 RFC4 RFC4 5056 0.07 0.45 NO
140 LIG1 LIG1 LIG1 5096 0.069 0.45 NO
141 NUP85 NUP85 NUP85 5100 0.069 0.45 NO
142 CEP135 CEP135 CEP135 5110 0.069 0.45 NO
143 MCM3 MCM3 MCM3 5201 0.066 0.45 NO
144 STAG2 STAG2 STAG2 5210 0.066 0.45 NO
145 NUMA1 NUMA1 NUMA1 5241 0.065 0.45 NO
146 DBF4 DBF4 DBF4 5349 0.062 0.45 NO
147 MCM5 MCM5 MCM5 5483 0.059 0.44 NO
148 RAD21 RAD21 RAD21 5516 0.058 0.44 NO
149 PKMYT1 PKMYT1 PKMYT1 5532 0.057 0.44 NO
150 FEN1 FEN1 FEN1 5563 0.057 0.44 NO
151 PRKACA PRKACA PRKACA 5583 0.056 0.44 NO
152 PSMA8 PSMA8 PSMA8 5618 0.055 0.44 NO
153 PPP2R5D PPP2R5D PPP2R5D 5741 0.052 0.44 NO
154 CDC20 CDC20 CDC20 5777 0.051 0.44 NO
155 DYNC1I2 DYNC1I2 DYNC1I2 5793 0.051 0.44 NO
156 ANAPC10 ANAPC10 ANAPC10 5810 0.05 0.44 NO
157 MIS12 MIS12 MIS12 5824 0.05 0.44 NO
158 ITGB3BP ITGB3BP ITGB3BP 5844 0.05 0.44 NO
159 PSMD11 PSMD11 PSMD11 5889 0.049 0.44 NO
160 RCC2 RCC2 RCC2 5921 0.048 0.44 NO
161 DYRK1A DYRK1A DYRK1A 6039 0.045 0.43 NO
162 CDK4 CDK4 CDK4 6052 0.045 0.43 NO
163 PCNA PCNA PCNA 6202 0.041 0.42 NO
164 CDK5RAP2 CDK5RAP2 CDK5RAP2 6315 0.038 0.42 NO
165 TUBB TUBB TUBB 6322 0.038 0.42 NO
166 CEP63 CEP63 CEP63 6325 0.038 0.42 NO
167 MCM7 MCM7 MCM7 6668 0.029 0.4 NO
168 PSMD14 PSMD14 PSMD14 6682 0.029 0.4 NO
169 ANAPC4 ANAPC4 ANAPC4 6782 0.026 0.4 NO
170 PSMA1 PSMA1 PSMA1 6801 0.026 0.4 NO
171 AURKB AURKB AURKB 6932 0.023 0.39 NO
172 PCM1 PCM1 PCM1 6975 0.022 0.39 NO
173 MAPRE1 MAPRE1 MAPRE1 7057 0.021 0.38 NO
174 POLA2 POLA2 POLA2 7093 0.02 0.38 NO
175 CDKN1B CDKN1B CDKN1B 7102 0.02 0.38 NO
176 PPP1CC PPP1CC PPP1CC 7181 0.018 0.38 NO
177 PSMC6 PSMC6 PSMC6 7218 0.017 0.38 NO
178 PSMA3 PSMA3 PSMA3 7220 0.017 0.38 NO
179 PSMD2 PSMD2 PSMD2 7254 0.016 0.38 NO
180 ANAPC5 ANAPC5 ANAPC5 7266 0.016 0.38 NO
181 CDC16 CDC16 CDC16 7269 0.016 0.38 NO
182 NINL NINL NINL 7347 0.014 0.37 NO
183 PPP2R5A PPP2R5A PPP2R5A 7355 0.014 0.37 NO
184 PSMB2 PSMB2 PSMB2 7365 0.014 0.37 NO
185 DCTN1 DCTN1 DCTN1 7408 0.013 0.37 NO
186 CEP250 CEP250 CEP250 7424 0.012 0.37 NO
187 PPP2CB PPP2CB PPP2CB 7426 0.012 0.37 NO
188 DSN1 DSN1 DSN1 7435 0.012 0.37 NO
189 ANAPC7 ANAPC7 ANAPC7 7526 0.0099 0.36 NO
190 CENPH CENPH CENPH 7542 0.0094 0.36 NO
191 E2F4 E2F4 E2F4 7543 0.0094 0.36 NO
192 YWHAE YWHAE YWHAE 7585 0.0083 0.36 NO
193 DYNC1H1 DYNC1H1 DYNC1H1 7589 0.0082 0.36 NO
194 CDK7 CDK7 CDK7 7633 0.0072 0.36 NO
195 RANBP2 RANBP2 RANBP2 7636 0.0071 0.36 NO
196 CKS1B CKS1B CKS1B 7642 0.0068 0.36 NO
197 NUP133 NUP133 NUP133 7789 0.0036 0.35 NO
198 UBE2D1 UBE2D1 UBE2D1 7800 0.0034 0.35 NO
199 BTRC BTRC BTRC 7821 0.0029 0.35 NO
200 PPP2R2A PPP2R2A PPP2R2A 7902 0.001 0.35 NO
201 CENPT CENPT CENPT 7929 0.00054 0.34 NO
202 MAX MAX MAX 7954 0.0001 0.34 NO
203 POLD2 POLD2 POLD2 7999 -0.00077 0.34 NO
204 PSMF1 PSMF1 PSMF1 8006 -0.0009 0.34 NO
205 CDC25B CDC25B CDC25B 8007 -0.00092 0.34 NO
206 HSP90AA1 HSP90AA1 HSP90AA1 8014 -0.0011 0.34 NO
207 PPP2R5C PPP2R5C PPP2R5C 8016 -0.0011 0.34 NO
208 PSMD1 PSMD1 PSMD1 8043 -0.0018 0.34 NO
209 PSMA4 PSMA4 PSMA4 8137 -0.0036 0.33 NO
210 SKA2 SKA2 SKA2 8169 -0.0043 0.33 NO
211 BIRC5 BIRC5 BIRC5 8327 -0.0082 0.32 NO
212 GINS2 GINS2 GINS2 8428 -0.011 0.32 NO
213 PSMD6 PSMD6 PSMD6 8462 -0.012 0.32 NO
214 PSMC4 PSMC4 PSMC4 8531 -0.013 0.31 NO
215 GORASP1 GORASP1 GORASP1 8594 -0.014 0.31 NO
216 PPP2CA PPP2CA PPP2CA 8600 -0.014 0.31 NO
217 NDEL1 NDEL1 NDEL1 8702 -0.017 0.3 NO
218 NUP43 NUP43 NUP43 8706 -0.017 0.3 NO
219 ANAPC2 ANAPC2 ANAPC2 8781 -0.018 0.3 NO
220 PAFAH1B1 PAFAH1B1 PAFAH1B1 8831 -0.02 0.3 NO
221 SEC13 SEC13 SEC13 8894 -0.021 0.3 NO
222 MLF1IP MLF1IP MLF1IP 8915 -0.021 0.3 NO
223 CCNH CCNH CCNH 9108 -0.026 0.28 NO
224 PSME1 PSME1 PSME1 9126 -0.026 0.28 NO
225 DCTN2 DCTN2 DCTN2 9154 -0.027 0.28 NO
226 RPA2 RPA2 RPA2 9157 -0.027 0.28 NO
227 PSMD8 PSMD8 PSMD8 9204 -0.029 0.28 NO
228 PSMD10 PSMD10 PSMD10 9241 -0.03 0.28 NO
229 PMF1 PMF1 PMF1 9272 -0.03 0.28 NO
230 PSMA6 PSMA6 PSMA6 9361 -0.032 0.28 NO
231 CENPP CENPP CENPP 9381 -0.033 0.28 NO
232 TUBGCP2 TUBGCP2 TUBGCP2 9425 -0.033 0.28 NO
233 PSMC3 PSMC3 PSMC3 9428 -0.034 0.28 NO
234 CDK6 CDK6 CDK6 9455 -0.034 0.28 NO
235 CDKN2D CDKN2D CDKN2D 9468 -0.034 0.28 NO
236 PSMC2 PSMC2 PSMC2 9475 -0.035 0.28 NO
237 PSMA5 PSMA5 PSMA5 9483 -0.035 0.28 NO
238 CDT1 CDT1 CDT1 9511 -0.035 0.28 NO
239 CSNK1D CSNK1D CSNK1D 9594 -0.037 0.27 NO
240 MNAT1 MNAT1 MNAT1 9799 -0.042 0.26 NO
241 RANGAP1 RANGAP1 RANGAP1 9833 -0.043 0.26 NO
242 HDAC1 HDAC1 HDAC1 9937 -0.046 0.26 NO
243 CDKN2C CDKN2C CDKN2C 10106 -0.049 0.25 NO
244 NUDC NUDC NUDC 10185 -0.051 0.25 NO
245 CDC26 CDC26 CDC26 10237 -0.053 0.24 NO
246 PSMA2 PSMA2 PSMA2 10281 -0.054 0.24 NO
247 PPP2R1A PPP2R1A PPP2R1A 10291 -0.055 0.25 NO
248 PSMB7 PSMB7 PSMB7 10348 -0.056 0.24 NO
249 ACTR1A ACTR1A ACTR1A 10361 -0.056 0.24 NO
250 PSME2 PSME2 PSME2 10395 -0.057 0.24 NO
251 PSMD7 PSMD7 PSMD7 10401 -0.058 0.25 NO
252 CENPM CENPM CENPM 10468 -0.059 0.24 NO
253 PSMD13 PSMD13 PSMD13 10524 -0.061 0.24 NO
254 PSMC5 PSMC5 PSMC5 10640 -0.064 0.24 NO
255 PSMB4 PSMB4 PSMB4 10654 -0.064 0.24 NO
256 PSMB8 PSMB8 PSMB8 10880 -0.071 0.23 NO
257 PSMA7 PSMA7 PSMA7 11165 -0.079 0.22 NO
258 DYNLL1 DYNLL1 DYNLL1 11169 -0.079 0.22 NO
259 RFC2 RFC2 RFC2 11284 -0.082 0.21 NO
260 PSMB5 PSMB5 PSMB5 11287 -0.082 0.22 NO
261 OFD1 OFD1 OFD1 11329 -0.083 0.22 NO
262 PPP2R3B PPP2R3B PPP2R3B 11364 -0.084 0.22 NO
263 SKP1 SKP1 SKP1 11367 -0.084 0.22 NO
264 UBE2E1 UBE2E1 UBE2E1 11491 -0.088 0.21 NO
265 PSMD9 PSMD9 PSMD9 11539 -0.089 0.21 NO
266 AZI1 AZI1 AZI1 11542 -0.089 0.22 NO
267 RPS27A RPS27A RPS27A 11679 -0.093 0.21 NO
268 RPA3 RPA3 RPA3 11772 -0.096 0.21 NO
269 SSNA1 SSNA1 SSNA1 11827 -0.098 0.21 NO
270 PSMD4 PSMD4 PSMD4 11940 -0.1 0.2 NO
271 PSMB6 PSMB6 PSMB6 11991 -0.1 0.2 NO
272 PSMB3 PSMB3 PSMB3 12094 -0.11 0.2 NO
273 RPS27 RPS27 RPS27 12095 -0.11 0.21 NO
274 UBA52 UBA52 UBA52 12149 -0.11 0.21 NO
275 PSMB10 PSMB10 PSMB10 12233 -0.11 0.2 NO
276 TUBA1A TUBA1A TUBA1A 12345 -0.11 0.2 NO
277 PSMB1 PSMB1 PSMB1 12434 -0.12 0.2 NO
278 CDKN1A CDKN1A CDKN1A 12530 -0.12 0.2 NO
279 CETN2 CETN2 CETN2 12620 -0.12 0.2 NO
280 DCTN3 DCTN3 DCTN3 12646 -0.12 0.2 NO
281 CCND1 CCND1 CCND1 12655 -0.12 0.2 NO
282 PSMB9 PSMB9 PSMB9 13034 -0.14 0.18 NO
283 PTTG1 PTTG1 PTTG1 13057 -0.14 0.19 NO
284 B9D2 B9D2 B9D2 13158 -0.14 0.19 NO
285 PSMC1 PSMC1 PSMC1 13176 -0.14 0.19 NO
286 CCND3 CCND3 CCND3 13276 -0.15 0.19 NO
287 CDKN2B CDKN2B CDKN2B 13326 -0.15 0.19 NO
288 ANAPC11 ANAPC11 ANAPC11 13403 -0.15 0.19 NO
289 TUBA4A TUBA4A TUBA4A 13422 -0.16 0.19 NO
290 PRKAR2B PRKAR2B PRKAR2B 13454 -0.16 0.2 NO
291 SDCCAG8 SDCCAG8 SDCCAG8 13524 -0.16 0.2 NO
292 TK2 TK2 TK2 13681 -0.17 0.19 NO
293 LIN37 LIN37 LIN37 13951 -0.18 0.18 NO
294 MAD1L1 MAD1L1 MAD1L1 14137 -0.19 0.18 NO
295 CCNA1 CCNA1 CCNA1 14502 -0.21 0.16 NO
296 POLD4 POLD4 POLD4 15128 -0.25 0.14 NO
297 CDKN2A CDKN2A CDKN2A 16095 -0.34 0.09 NO

Figure S57.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME CELL CYCLE MITOTIC.

Figure S58.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME CELL CYCLE MITOTIC, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: REACTOME RECRUITMENT OF MITOTIC CENTROSOME PROTEINS AND COMPLEXES

Table S30.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 BRCA2 BRCA2 BRCA2 82 0.53 0.11 YES
2 CLSPN CLSPN CLSPN 135 0.48 0.2 YES
3 RFC3 RFC3 RFC3 1682 0.2 0.16 YES
4 CDK2 CDK2 CDK2 1687 0.2 0.2 YES
5 CDC6 CDC6 CDC6 1691 0.2 0.24 YES
6 TOPBP1 TOPBP1 TOPBP1 2056 0.18 0.26 YES
7 PLK1 PLK1 PLK1 2076 0.18 0.29 YES
8 TIMELESS TIMELESS TIMELESS 2084 0.18 0.33 YES
9 CEP164 CEP164 CEP164 2105 0.18 0.36 YES
10 RFC5 RFC5 RFC5 2155 0.17 0.4 YES
11 ATR ATR ATR 2350 0.16 0.42 YES
12 CHEK1 CHEK1 CHEK1 2464 0.16 0.45 YES
13 CCNA2 CCNA2 CCNA2 2941 0.14 0.45 YES
14 RAD51 RAD51 RAD51 3021 0.13 0.47 YES
15 FANCD2 FANCD2 FANCD2 3059 0.13 0.5 YES
16 CDC25A CDC25A CDC25A 3313 0.12 0.51 YES
17 MCM2 MCM2 MCM2 3406 0.12 0.53 YES
18 TIPIN TIPIN TIPIN 3492 0.12 0.55 YES
19 RPA1 RPA1 RPA1 3556 0.11 0.57 YES
20 CDC25C CDC25C CDC25C 4536 0.084 0.53 NO
21 RAD1 RAD1 RAD1 4837 0.075 0.53 NO
22 RFC4 RFC4 RFC4 5056 0.07 0.53 NO
23 FBXW11 FBXW11 FBXW11 5779 0.051 0.5 NO
24 SMARCAL1 SMARCAL1 SMARCAL1 5884 0.049 0.5 NO
25 MCM7 MCM7 MCM7 6668 0.029 0.47 NO
26 HUS1 HUS1 HUS1 7232 0.016 0.44 NO
27 PPP2R2B PPP2R2B PPP2R2B 7327 0.014 0.44 NO
28 RAD9A RAD9A RAD9A 7617 0.0075 0.42 NO
29 NBN NBN NBN 7675 0.0062 0.42 NO
30 YWHAZ YWHAZ YWHAZ 8205 -0.0051 0.39 NO
31 PPP2CA PPP2CA PPP2CA 8600 -0.014 0.37 NO
32 RAD17 RAD17 RAD17 8879 -0.021 0.36 NO
33 RPA2 RPA2 RPA2 9157 -0.027 0.35 NO
34 MDM2 MDM2 MDM2 9372 -0.032 0.34 NO
35 YWHAB YWHAB YWHAB 10212 -0.052 0.31 NO
36 PPP2R1A PPP2R1A PPP2R1A 10291 -0.055 0.31 NO
37 ATRIP ATRIP ATRIP 10471 -0.059 0.32 NO
38 RFC2 RFC2 RFC2 11284 -0.082 0.29 NO
39 SSPO SSPO SSPO 16212 -0.36 0.082 NO

Figure S59.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME RECRUITMENT OF MITOTIC CENTROSOME PROTEINS AND COMPLEXES.

Figure S60.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME RECRUITMENT OF MITOTIC CENTROSOME PROTEINS AND COMPLEXES, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Fold change

For the top enriched genes, if you want to check whether they are

Expression level

For the top enriched genes, if you want to check whether they are

An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap

Significant gene list

For the top enriched genes, if you want to check whether they are

Subtype clus4 enriched pathways

Table 6.  Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus4. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
KEGG BASAL TRANSCRIPTION FACTORS 34 genes.ES.table 0.56 1.5 0.061 1 0.96 0.35 0.15 0.3 1 0.51
BIOCARTA CARM ER PATHWAY 34 genes.ES.table 0.38 1.5 0.068 1 0.98 0.35 0.25 0.27 1 0.55
BIOCARTA CREB PATHWAY 26 genes.ES.table 0.47 1.4 0.068 1 0.99 0.5 0.24 0.38 1 0.53
BIOCARTA VEGF PATHWAY 29 genes.ES.table 0.43 1.5 0.084 1 0.97 0.41 0.25 0.31 1 0.51
SIG BCR SIGNALING PATHWAY 46 genes.ES.table 0.46 1.8 0.022 1 0.62 0.39 0.23 0.3 1 0.52
PID FANCONI PATHWAY 46 genes.ES.table 0.53 1.6 0.035 1 0.86 0.5 0.25 0.38 0.94 0.48
PID E2F PATHWAY 69 genes.ES.table 0.48 1.6 0.079 1 0.91 0.55 0.3 0.39 1 0.53
PID ATM PATHWAY 34 genes.ES.table 0.45 1.5 0.098 1 0.96 0.62 0.36 0.4 1 0.51
PID HDAC CLASSI PATHWAY 65 genes.ES.table 0.29 1.5 0.086 1 0.98 0.28 0.24 0.21 1 0.52
PID PLK1 PATHWAY 45 genes.ES.table 0.55 1.6 0.059 1 0.92 0.64 0.32 0.44 0.94 0.48
genes ES table in pathway: KEGG BASAL TRANSCRIPTION FACTORS

Table S31.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 NFATC2 NFATC2 NFATC2 579 0.49 0.033 YES
2 CR2 CR2 CR2 691 0.46 0.088 YES
3 AKT3 AKT3 AKT3 782 0.44 0.14 YES
4 ITPR3 ITPR3 ITPR3 967 0.4 0.18 YES
5 PPP3CA PPP3CA PPP3CA 1187 0.36 0.22 YES
6 CD22 CD22 CD22 1248 0.35 0.26 YES
7 PIK3CA PIK3CA PIK3CA 1455 0.32 0.3 YES
8 ITPR1 ITPR1 ITPR1 1631 0.3 0.33 YES
9 PPP1R13B PPP1R13B PPP1R13B 1943 0.27 0.35 YES
10 PDK1 PDK1 PDK1 2139 0.26 0.37 YES
11 SOS2 SOS2 SOS2 2404 0.23 0.39 YES
12 BCL2 BCL2 BCL2 2503 0.23 0.41 YES
13 PTPRC PTPRC PTPRC 2646 0.22 0.43 YES
14 DAG1 DAG1 DAG1 3146 0.18 0.43 YES
15 SOS1 SOS1 SOS1 3231 0.18 0.45 YES
16 MAPK1 MAPK1 MAPK1 3817 0.15 0.44 YES
17 PIK3R1 PIK3R1 PIK3R1 3860 0.15 0.45 YES
18 BTK BTK BTK 4097 0.14 0.46 YES
19 BCR BCR BCR 4418 0.12 0.46 NO
20 NR0B2 NR0B2 NR0B2 5204 0.096 0.43 NO
21 ITPR2 ITPR2 ITPR2 5364 0.09 0.43 NO
22 SHC1 SHC1 SHC1 5806 0.075 0.42 NO
23 AKT1 AKT1 AKT1 6343 0.059 0.39 NO
24 PLCG2 PLCG2 PLCG2 6446 0.055 0.39 NO
25 LYN LYN LYN 6620 0.05 0.39 NO
26 AKT2 AKT2 AKT2 6704 0.048 0.39 NO
27 GSK3B GSK3B GSK3B 7214 0.034 0.37 NO
28 SYK SYK SYK 7228 0.034 0.37 NO
29 MAPK3 MAPK3 MAPK3 7325 0.031 0.37 NO
30 INPP5D INPP5D INPP5D 7509 0.025 0.36 NO
31 FLOT2 FLOT2 FLOT2 7562 0.024 0.36 NO
32 PPP3CB PPP3CB PPP3CB 7644 0.021 0.36 NO
33 RAF1 RAF1 RAF1 8671 -0.0073 0.3 NO
34 GSK3A GSK3A GSK3A 8985 -0.016 0.29 NO
35 VAV1 VAV1 VAV1 9375 -0.026 0.27 NO
36 NFATC1 NFATC1 NFATC1 10294 -0.054 0.23 NO
37 FLOT1 FLOT1 FLOT1 10657 -0.066 0.21 NO
38 PIK3CD PIK3CD PIK3CD 11309 -0.086 0.19 NO
39 GRB2 GRB2 GRB2 11755 -0.1 0.18 NO
40 CD19 CD19 CD19 12041 -0.11 0.18 NO
41 CD81 CD81 CD81 12179 -0.12 0.18 NO
42 PPP3CC PPP3CC PPP3CC 12400 -0.13 0.19 NO
43 MAP4K1 MAP4K1 MAP4K1 12508 -0.13 0.2 NO
44 CSK CSK CSK 12963 -0.15 0.2 NO
45 BAD BAD BAD 14232 -0.22 0.15 NO
46 BLNK BLNK BLNK 15173 -0.3 0.14 NO

Figure S61.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG BASAL TRANSCRIPTION FACTORS.

Figure S62.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG BASAL TRANSCRIPTION FACTORS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA CARM ER PATHWAY

Table S32.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 MAPK10 MAPK10 MAPK10 6 1.3 0.16 YES
2 G6PC G6PC G6PC 348 0.57 0.21 YES
3 MAPK8 MAPK8 MAPK8 593 0.48 0.25 YES
4 SKP2 SKP2 SKP2 1064 0.38 0.27 YES
5 EP300 EP300 EP300 1226 0.35 0.3 YES
6 SIRT1 SIRT1 SIRT1 1420 0.33 0.34 YES
7 BCL6 BCL6 BCL6 2044 0.26 0.33 YES
8 CSNK1G3 CSNK1G3 CSNK1G3 2067 0.26 0.36 YES
9 KAT2B KAT2B KAT2B 2458 0.23 0.37 YES
10 RBL2 RBL2 RBL2 2650 0.22 0.38 YES
11 FOXO1 FOXO1 FOXO1 3082 0.19 0.38 YES
12 FOXO3 FOXO3 FOXO3 3178 0.18 0.4 YES
13 CREBBP CREBBP CREBBP 3335 0.17 0.41 YES
14 YWHAG YWHAG YWHAG 3682 0.16 0.41 YES
15 MAPK9 MAPK9 MAPK9 3819 0.15 0.42 YES
16 CDK2 CDK2 CDK2 3853 0.15 0.44 YES
17 USP7 USP7 USP7 3997 0.14 0.45 YES
18 PLK1 PLK1 PLK1 4476 0.12 0.44 NO
19 IKBKB IKBKB IKBKB 4945 0.11 0.42 NO
20 CCNB1 CCNB1 CCNB1 5315 0.091 0.41 NO
21 FOXO4 FOXO4 FOXO4 5499 0.085 0.41 NO
22 XPO1 XPO1 XPO1 5528 0.084 0.42 NO
23 CAT CAT CAT 5745 0.077 0.42 NO
24 AKT1 AKT1 AKT1 6343 0.059 0.39 NO
25 YWHAH YWHAH YWHAH 6463 0.055 0.39 NO
26 CSNK1G2 CSNK1G2 CSNK1G2 6616 0.05 0.39 NO
27 SGK1 SGK1 SGK1 6881 0.042 0.38 NO
28 RAN RAN RAN 7489 0.026 0.35 NO
29 CSNK1D CSNK1D CSNK1D 7500 0.026 0.35 NO
30 CHUK CHUK CHUK 7629 0.022 0.35 NO
31 FBXO32 FBXO32 FBXO32 8006 0.011 0.33 NO
32 CSNK1A1 CSNK1A1 CSNK1A1 8174 0.0062 0.32 NO
33 RALA RALA RALA 8361 0.00063 0.31 NO
34 YWHAZ YWHAZ YWHAZ 8485 -0.0023 0.3 NO
35 CTNNB1 CTNNB1 CTNNB1 8685 -0.0078 0.29 NO
36 YWHAE YWHAE YWHAE 8705 -0.0082 0.29 NO
37 YWHAB YWHAB YWHAB 8857 -0.012 0.28 NO
38 CSNK1G1 CSNK1G1 CSNK1G1 9086 -0.019 0.27 NO
39 YWHAQ YWHAQ YWHAQ 9420 -0.028 0.26 NO
40 ZFAND5 ZFAND5 ZFAND5 10130 -0.05 0.22 NO
41 CSNK1E CSNK1E CSNK1E 10679 -0.066 0.2 NO
42 BCL2L11 BCL2L11 BCL2L11 11610 -0.097 0.16 NO
43 RALB RALB RALB 11690 -0.1 0.17 NO
44 MST1 MST1 MST1 11701 -0.1 0.18 NO
45 CDKN1B CDKN1B CDKN1B 12309 -0.12 0.16 NO
46 GADD45A GADD45A GADD45A 12487 -0.13 0.16 NO
47 SOD2 SOD2 SOD2 14611 -0.25 0.076 NO
48 FASLG FASLG FASLG 15744 -0.37 0.057 NO
49 SFN SFN SFN 16150 -0.43 0.086 NO

Figure S63.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA CARM ER PATHWAY.

Figure S64.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA CARM ER PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA CREB PATHWAY

Table S33.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 MAPK8 MAPK8 MAPK8 593 0.48 0.031 YES
2 SKP2 SKP2 SKP2 1064 0.38 0.054 YES
3 EP300 EP300 EP300 1226 0.35 0.092 YES
4 PPM1D PPM1D PPM1D 2041 0.26 0.081 YES
5 CSNK1G3 CSNK1G3 CSNK1G3 2067 0.26 0.11 YES
6 ATM ATM ATM 2105 0.26 0.15 YES
7 SETD7 SETD7 SETD7 2207 0.25 0.17 YES
8 KAT2B KAT2B KAT2B 2458 0.23 0.19 YES
9 PPP1R13L PPP1R13L PPP1R13L 2656 0.22 0.21 YES
10 DYRK2 DYRK2 DYRK2 2718 0.21 0.23 YES
11 MDM4 MDM4 MDM4 2823 0.2 0.25 YES
12 HIPK2 HIPK2 HIPK2 2950 0.2 0.27 YES
13 CREBBP CREBBP CREBBP 3335 0.17 0.27 YES
14 SETD8 SETD8 SETD8 3440 0.17 0.29 YES
15 CHEK2 CHEK2 CHEK2 3697 0.16 0.3 YES
16 MAPK9 MAPK9 MAPK9 3819 0.15 0.31 YES
17 CDK2 CDK2 CDK2 3853 0.15 0.33 YES
18 USP7 USP7 USP7 3997 0.14 0.34 YES
19 ATR ATR ATR 4182 0.14 0.34 YES
20 TTC5 TTC5 TTC5 4194 0.13 0.36 YES
21 MAPK14 MAPK14 MAPK14 4199 0.13 0.38 YES
22 TP53 TP53 TP53 4205 0.13 0.4 YES
23 FBXO11 FBXO11 FBXO11 4488 0.12 0.4 YES
24 SMYD2 SMYD2 SMYD2 4667 0.12 0.4 YES
25 CCNG1 CCNG1 CCNG1 5184 0.096 0.39 YES
26 DAXX DAXX DAXX 5229 0.095 0.4 YES
27 CCNA2 CCNA2 CCNA2 5270 0.093 0.41 YES
28 HUWE1 HUWE1 HUWE1 5422 0.087 0.41 YES
29 MDM2 MDM2 MDM2 5458 0.086 0.42 YES
30 CSE1L CSE1L CSE1L 5915 0.072 0.4 NO
31 ABL1 ABL1 ABL1 6142 0.065 0.4 NO
32 YY1 YY1 YY1 6326 0.059 0.4 NO
33 AKT1 AKT1 AKT1 6343 0.059 0.4 NO
34 CSNK1G2 CSNK1G2 CSNK1G2 6616 0.05 0.39 NO
35 UBE2D1 UBE2D1 UBE2D1 6972 0.04 0.38 NO
36 RFWD2 RFWD2 RFWD2 7079 0.037 0.38 NO
37 GSK3B GSK3B GSK3B 7214 0.034 0.38 NO
38 CSNK1D CSNK1D CSNK1D 7500 0.026 0.36 NO
39 CSNK1A1 CSNK1A1 CSNK1A1 8174 0.0062 0.32 NO
40 PRMT5 PRMT5 PRMT5 8348 0.00081 0.32 NO
41 RCHY1 RCHY1 RCHY1 8430 -0.00095 0.31 NO
42 CHEK1 CHEK1 CHEK1 8721 -0.0086 0.3 NO
43 CSNK1G1 CSNK1G1 CSNK1G1 9086 -0.019 0.28 NO
44 PPP2CA PPP2CA PPP2CA 9437 -0.028 0.26 NO
45 E4F1 E4F1 E4F1 9569 -0.032 0.26 NO
46 PRKCD PRKCD PRKCD 9603 -0.033 0.26 NO
47 RPL23 RPL23 RPL23 10319 -0.055 0.23 NO
48 RPL5 RPL5 RPL5 10509 -0.061 0.22 NO
49 CSNK1E CSNK1E CSNK1E 10679 -0.066 0.22 NO
50 KAT5 KAT5 KAT5 10995 -0.076 0.22 NO
51 NEDD8 NEDD8 NEDD8 11238 -0.083 0.21 NO
52 PPP2R4 PPP2R4 PPP2R4 12088 -0.11 0.18 NO
53 TRIM28 TRIM28 TRIM28 12336 -0.12 0.18 NO
54 RASSF1 RASSF1 RASSF1 12440 -0.13 0.19 NO
55 RPL11 RPL11 RPL11 13582 -0.18 0.15 NO
56 PIN1 PIN1 PIN1 13800 -0.19 0.17 NO
57 CDKN2A CDKN2A CDKN2A 15948 -0.4 0.098 NO

Figure S65.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA CREB PATHWAY.

Figure S66.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA CREB PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA VEGF PATHWAY

Table S34.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 BRIP1 BRIP1 BRIP1 92 0.79 0.11 YES
2 SSPO SSPO SSPO 775 0.44 0.13 YES
3 BRCA2 BRCA2 BRCA2 1603 0.31 0.13 YES
4 PALB2 PALB2 PALB2 1961 0.27 0.14 YES
5 BRCA1 BRCA1 BRCA1 1977 0.27 0.18 YES
6 FANCB FANCB FANCB 2074 0.26 0.21 YES
7 ATM ATM ATM 2105 0.26 0.25 YES
8 RMI1 RMI1 RMI1 2250 0.25 0.27 YES
9 FANCM FANCM FANCM 2251 0.25 0.31 YES
10 FANCE FANCE FANCE 2294 0.24 0.34 YES
11 FANCF FANCF FANCF 2732 0.21 0.35 YES
12 RAD17 RAD17 RAD17 2764 0.21 0.37 YES
13 RFC3 RFC3 RFC3 2802 0.2 0.4 YES
14 APITD1 APITD1 APITD1 3240 0.18 0.4 YES
15 FBXW11 FBXW11 FBXW11 3346 0.17 0.42 YES
16 RAD50 RAD50 RAD50 3364 0.17 0.44 YES
17 UBE2T UBE2T UBE2T 3425 0.17 0.46 YES
18 MRE11A MRE11A MRE11A 3634 0.16 0.48 YES
19 C19orf40 C19orf40 C19orf40 3798 0.15 0.49 YES
20 TOPBP1 TOPBP1 TOPBP1 3846 0.15 0.5 YES
21 ATR ATR ATR 4182 0.14 0.5 YES
22 RFC5 RFC5 RFC5 4333 0.13 0.52 YES
23 FANCL FANCL FANCL 4384 0.13 0.53 YES
24 XRCC3 XRCC3 XRCC3 4814 0.11 0.52 NO
25 USP1 USP1 USP1 5577 0.083 0.49 NO
26 FANCI FANCI FANCI 6076 0.067 0.47 NO
27 RAD1 RAD1 RAD1 6262 0.061 0.47 NO
28 FANCG FANCG FANCG 6410 0.056 0.47 NO
29 FANCC FANCC FANCC 6498 0.053 0.47 NO
30 NBN NBN NBN 7047 0.038 0.45 NO
31 HUS1 HUS1 HUS1 7131 0.036 0.45 NO
32 FANCD2 FANCD2 FANCD2 7194 0.034 0.45 NO
33 FANCA FANCA FANCA 7561 0.024 0.43 NO
34 RFC2 RFC2 RFC2 7942 0.013 0.41 NO
35 RPA1 RPA1 RPA1 8119 0.0076 0.4 NO
36 RFC4 RFC4 RFC4 8277 0.003 0.39 NO
37 TOP3A TOP3A TOP3A 8474 -0.0021 0.38 NO
38 CHEK1 CHEK1 CHEK1 8721 -0.0086 0.37 NO
39 WDR48 WDR48 WDR48 9268 -0.024 0.34 NO
40 C17orf70 C17orf70 C17orf70 9365 -0.026 0.34 NO
41 BLM BLM BLM 10652 -0.066 0.28 NO
42 RAD9A RAD9A RAD9A 11080 -0.078 0.26 NO
43 H2AFX H2AFX H2AFX 11087 -0.078 0.27 NO
44 RPA2 RPA2 RPA2 11841 -0.1 0.25 NO
45 ATRIP ATRIP ATRIP 12590 -0.13 0.22 NO
46 HES1 HES1 HES1 16335 -0.46 0.076 NO

Figure S67.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA VEGF PATHWAY.

Figure S68.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA VEGF PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: SIG BCR SIGNALING PATHWAY

Table S35.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 WASF1 WASF1 WASF1 69 0.84 0.069 YES
2 E2F7 E2F7 E2F7 250 0.63 0.11 YES
3 CCNE2 CCNE2 CCNE2 842 0.42 0.12 YES
4 RBL1 RBL1 RBL1 855 0.42 0.15 YES
5 DHFR DHFR DHFR 1028 0.39 0.17 YES
6 EP300 EP300 EP300 1226 0.35 0.19 YES
7 SIRT1 SIRT1 SIRT1 1420 0.33 0.21 YES
8 E2F5 E2F5 E2F5 1421 0.33 0.24 YES
9 APAF1 APAF1 APAF1 1820 0.28 0.24 YES
10 BRCA1 BRCA1 BRCA1 1977 0.27 0.26 YES
11 MYC MYC MYC 2029 0.26 0.27 YES
12 ATM ATM ATM 2105 0.26 0.29 YES
13 TRRAP TRRAP TRRAP 2132 0.26 0.31 YES
14 E2F3 E2F3 E2F3 2230 0.25 0.33 YES
15 POLA1 POLA1 POLA1 2430 0.23 0.34 YES
16 KAT2B KAT2B KAT2B 2458 0.23 0.36 YES
17 RBL2 RBL2 RBL2 2650 0.22 0.36 YES
18 CDK1 CDK1 CDK1 2791 0.21 0.37 YES
19 CDKN2C CDKN2C CDKN2C 3035 0.19 0.38 YES
20 TFDP1 TFDP1 TFDP1 3087 0.19 0.39 YES
21 RB1 RB1 RB1 3108 0.19 0.4 YES
22 KAT2A KAT2A KAT2A 3318 0.18 0.41 YES
23 CREBBP CREBBP CREBBP 3335 0.17 0.42 YES
24 RBBP4 RBBP4 RBBP4 3352 0.17 0.44 YES
25 CDC6 CDC6 CDC6 3530 0.16 0.44 YES
26 HBP1 HBP1 HBP1 3617 0.16 0.45 YES
27 TOPBP1 TOPBP1 TOPBP1 3846 0.15 0.45 YES
28 CDK2 CDK2 CDK2 3853 0.15 0.46 YES
29 SP1 SP1 SP1 4209 0.13 0.45 YES
30 HDAC1 HDAC1 HDAC1 4334 0.13 0.46 YES
31 CBX5 CBX5 CBX5 4514 0.12 0.46 YES
32 CCNE1 CCNE1 CCNE1 4581 0.12 0.46 YES
33 E2F2 E2F2 E2F2 4679 0.12 0.47 YES
34 MCM3 MCM3 MCM3 4917 0.11 0.46 YES
35 E2F1 E2F1 E2F1 5123 0.099 0.46 YES
36 RRM1 RRM1 RRM1 5130 0.098 0.47 YES
37 RBBP8 RBBP8 RBBP8 5198 0.096 0.47 YES
38 CCNA2 CCNA2 CCNA2 5270 0.093 0.48 YES
39 YY1 YY1 YY1 6326 0.059 0.42 NO
40 SERPINE1 SERPINE1 SERPINE1 6724 0.047 0.4 NO
41 TK1 TK1 TK1 6838 0.044 0.4 NO
42 CDC25A CDC25A CDC25A 6989 0.04 0.39 NO
43 CASP7 CASP7 CASP7 7123 0.036 0.39 NO
44 HIC1 HIC1 HIC1 8113 0.0077 0.33 NO
45 CES2 CES2 CES2 8341 0.00088 0.32 NO
46 PRMT5 PRMT5 PRMT5 8348 0.00081 0.32 NO
47 MYBL2 MYBL2 MYBL2 8362 0.00062 0.32 NO
48 PLAU PLAU PLAU 8425 -0.0009 0.32 NO
49 TYMS TYMS TYMS 8463 -0.0017 0.32 NO
50 SMARCA2 SMARCA2 SMARCA2 8726 -0.0087 0.3 NO
51 TFE3 TFE3 TFE3 9248 -0.023 0.27 NO
52 CCND3 CCND3 CCND3 9374 -0.026 0.27 NO
53 XRCC1 XRCC1 XRCC1 9903 -0.042 0.24 NO
54 RANBP1 RANBP1 RANBP1 9947 -0.044 0.24 NO
55 E2F4 E2F4 E2F4 10656 -0.066 0.21 NO
56 RRM2 RRM2 RRM2 10670 -0.066 0.21 NO
57 MCL1 MCL1 MCL1 11172 -0.081 0.19 NO
58 RYBP RYBP RYBP 11485 -0.093 0.18 NO
59 CES3 CES3 CES3 11765 -0.1 0.18 NO
60 TFDP2 TFDP2 TFDP2 11941 -0.11 0.18 NO
61 UXT UXT UXT 12072 -0.11 0.18 NO
62 CDKN1B CDKN1B CDKN1B 12309 -0.12 0.18 NO
63 TRIM28 TRIM28 TRIM28 12336 -0.12 0.18 NO
64 CES1 CES1 CES1 12635 -0.14 0.18 NO
65 CEBPA CEBPA CEBPA 13430 -0.17 0.15 NO
66 E2F6 E2F6 E2F6 13858 -0.2 0.14 NO
67 TP73 TP73 TP73 14150 -0.22 0.14 NO
68 CDKN1A CDKN1A CDKN1A 14776 -0.26 0.13 NO
69 CDKN2A CDKN2A CDKN2A 15948 -0.4 0.098 NO

Figure S69.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: SIG BCR SIGNALING PATHWAY.

Figure S70.  Get High-res Image For the top 5 core enriched genes in the pathway: SIG BCR SIGNALING PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID FANCONI PATHWAY

Table S36.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CCNT1 CCNT1 CCNT1 437 0.54 0.069 YES
2 CDKN2B CDKN2B CDKN2B 706 0.45 0.13 YES
3 RBL1 RBL1 RBL1 855 0.42 0.2 YES
4 E2F5 E2F5 E2F5 1421 0.33 0.22 YES
5 CDK8 CDK8 CDK8 1586 0.31 0.27 YES
6 MYC MYC MYC 2029 0.26 0.29 YES
7 WWTR1 WWTR1 WWTR1 2046 0.26 0.33 YES
8 SMURF2 SMURF2 SMURF2 2331 0.24 0.36 YES
9 USP9X USP9X USP9X 2635 0.22 0.38 YES
10 TFDP1 TFDP1 TFDP1 3087 0.19 0.39 YES
11 SKIL SKIL SKIL 3288 0.18 0.41 YES
12 MEN1 MEN1 MEN1 3333 0.17 0.44 YES
13 PARP1 PARP1 PARP1 3666 0.16 0.44 YES
14 CCNT2 CCNT2 CCNT2 3690 0.16 0.47 YES
15 NCOR2 NCOR2 NCOR2 3779 0.15 0.49 YES
16 TRIM33 TRIM33 TRIM33 4039 0.14 0.5 YES
17 NCOR1 NCOR1 NCOR1 4057 0.14 0.53 YES
18 SMAD3 SMAD3 SMAD3 4146 0.14 0.54 YES
19 SP1 SP1 SP1 4209 0.13 0.56 YES
20 HDAC1 HDAC1 HDAC1 4334 0.13 0.58 YES
21 SMAD4 SMAD4 SMAD4 5657 0.08 0.52 NO
22 PPM1A PPM1A PPM1A 6369 0.058 0.49 NO
23 SERPINE1 SERPINE1 SERPINE1 6724 0.047 0.48 NO
24 UBE2D1 UBE2D1 UBE2D1 6972 0.04 0.47 NO
25 SMAD2 SMAD2 SMAD2 7334 0.03 0.46 NO
26 TGIF2 TGIF2 TGIF2 7405 0.028 0.46 NO
27 SKI SKI SKI 8070 0.0091 0.42 NO
28 SMAD7 SMAD7 SMAD7 8366 0.00058 0.4 NO
29 UBE2D3 UBE2D3 UBE2D3 8737 -0.0089 0.38 NO
30 CCNC CCNC CCNC 9988 -0.045 0.32 NO
31 E2F4 E2F4 E2F4 10656 -0.066 0.29 NO
32 RPS27A RPS27A RPS27A 10878 -0.072 0.29 NO
33 TGIF1 TGIF1 TGIF1 10953 -0.074 0.3 NO
34 CDK9 CDK9 CDK9 12592 -0.13 0.23 NO
35 UBA52 UBA52 UBA52 12778 -0.14 0.25 NO
36 JUNB JUNB JUNB 13228 -0.16 0.25 NO

Figure S71.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID FANCONI PATHWAY.

Figure S72.  Get High-res Image For the top 5 core enriched genes in the pathway: PID FANCONI PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID E2F PATHWAY

Table S37.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CLSPN CLSPN CLSPN 496 0.52 0.048 YES
2 ROCK2 ROCK2 ROCK2 529 0.5 0.12 YES
3 SSPO SSPO SSPO 775 0.44 0.17 YES
4 KIF20A KIF20A KIF20A 1386 0.33 0.18 YES
5 WEE1 WEE1 WEE1 1587 0.31 0.22 YES
6 INCENP INCENP INCENP 2065 0.26 0.23 YES
7 CENPE CENPE CENPE 2231 0.25 0.26 YES
8 NINL NINL NINL 2504 0.23 0.28 YES
9 SGOL1 SGOL1 SGOL1 2742 0.21 0.29 YES
10 CDK1 CDK1 CDK1 2791 0.21 0.32 YES
11 ECT2 ECT2 ECT2 2885 0.2 0.35 YES
12 KIF2A KIF2A KIF2A 3110 0.19 0.36 YES
13 ERCC6L ERCC6L ERCC6L 3323 0.18 0.37 YES
14 SPC24 SPC24 SPC24 3332 0.17 0.4 YES
15 FBXW11 FBXW11 FBXW11 3346 0.17 0.42 YES
16 STAG2 STAG2 STAG2 3808 0.15 0.42 YES
17 CDC25C CDC25C CDC25C 3891 0.15 0.44 YES
18 FBXO5 FBXO5 FBXO5 3980 0.14 0.45 YES
19 CDC14B CDC14B CDC14B 4021 0.14 0.47 YES
20 PLK1S1 PLK1S1 PLK1S1 4159 0.14 0.48 YES
21 PPP1R12A PPP1R12A PPP1R12A 4437 0.12 0.49 YES
22 MLF1IP MLF1IP MLF1IP 4462 0.12 0.5 YES
23 PLK1 PLK1 PLK1 4476 0.12 0.52 YES
24 GOLGA2 GOLGA2 GOLGA2 4505 0.12 0.54 YES
25 PRC1 PRC1 PRC1 5121 0.099 0.52 YES
26 TPX2 TPX2 TPX2 5134 0.098 0.53 YES
27 CCNB1 CCNB1 CCNB1 5315 0.091 0.54 YES
28 BUB1B BUB1B BUB1B 5373 0.089 0.55 YES
29 TUBG1 TUBG1 TUBG1 5584 0.083 0.55 YES
30 ODF2 ODF2 ODF2 5948 0.071 0.54 NO
31 AURKA AURKA AURKA 6324 0.059 0.52 NO
32 BUB1 BUB1 BUB1 7280 0.032 0.47 NO
33 PPP1CB PPP1CB PPP1CB 7492 0.026 0.46 NO
34 NDC80 NDC80 NDC80 7502 0.026 0.47 NO
35 RHOA RHOA RHOA 8307 0.0019 0.42 NO
36 CDC25B CDC25B CDC25B 8343 0.00084 0.42 NO
37 PPP2CA PPP2CA PPP2CA 9437 -0.028 0.36 NO
38 TPT1 TPT1 TPT1 9797 -0.039 0.35 NO
39 RAB1A RAB1A RAB1A 10074 -0.048 0.34 NO
40 GORASP1 GORASP1 GORASP1 10438 -0.059 0.33 NO
41 CDC20 CDC20 CDC20 10913 -0.073 0.31 NO
42 FZR1 FZR1 FZR1 11382 -0.089 0.3 NO
43 NUDC NUDC NUDC 11772 -0.1 0.29 NO
44 PPP2R1A PPP2R1A PPP2R1A 12313 -0.12 0.28 NO
45 PAK1 PAK1 PAK1 13199 -0.16 0.25 NO

Figure S73.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID E2F PATHWAY.

Figure S74.  Get High-res Image For the top 5 core enriched genes in the pathway: PID E2F PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID ATM PATHWAY

Table S38.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PDK4 PDK4 PDK4 898 0.41 0.037 YES
2 PDPR PDPR PDPR 1450 0.32 0.075 YES
3 NNT NNT NNT 1657 0.3 0.13 YES
4 L2HGDH L2HGDH L2HGDH 1725 0.29 0.19 YES
5 PDP1 PDP1 PDP1 1841 0.28 0.24 YES
6 PDK1 PDK1 PDK1 2139 0.26 0.28 YES
7 SLC16A1 SLC16A1 SLC16A1 2244 0.25 0.32 YES
8 PDP2 PDP2 PDP2 2411 0.23 0.36 YES
9 DLAT DLAT DLAT 3899 0.15 0.31 NO
10 CS CS CS 4327 0.13 0.32 NO
11 DLD DLD DLD 4967 0.1 0.3 NO
12 FH FH FH 5178 0.096 0.31 NO
13 SUCLA2 SUCLA2 SUCLA2 5298 0.092 0.32 NO
14 ACO2 ACO2 ACO2 5495 0.085 0.33 NO
15 PDHA1 PDHA1 PDHA1 5541 0.084 0.34 NO
16 PDK2 PDK2 PDK2 5832 0.075 0.34 NO
17 PDK3 PDK3 PDK3 5952 0.071 0.35 NO
18 SUCLG2 SUCLG2 SUCLG2 6361 0.058 0.34 NO
19 OGDH OGDH OGDH 6737 0.047 0.33 NO
20 PDHX PDHX PDHX 7027 0.038 0.32 NO
21 IDH3A IDH3A IDH3A 7070 0.038 0.33 NO
22 SDHC SDHC SDHC 7103 0.037 0.33 NO
23 IDH1 IDH1 IDH1 7241 0.033 0.33 NO
24 SDHD SDHD SDHD 7636 0.022 0.32 NO
25 LDHA LDHA LDHA 7751 0.018 0.31 NO
26 SDHA SDHA SDHA 8234 0.0046 0.29 NO
27 IDH2 IDH2 IDH2 8257 0.004 0.29 NO
28 MDH2 MDH2 MDH2 8572 -0.0044 0.27 NO
29 DLST DLST DLST 8692 -0.008 0.26 NO
30 D2HGDH D2HGDH D2HGDH 9358 -0.026 0.23 NO
31 SUCLG1 SUCLG1 SUCLG1 9448 -0.029 0.23 NO
32 LDHB LDHB LDHB 9614 -0.034 0.23 NO
33 SLC16A3 SLC16A3 SLC16A3 10255 -0.053 0.21 NO
34 PDHB PDHB PDHB 10740 -0.068 0.19 NO
35 SLC16A8 SLC16A8 SLC16A8 10742 -0.068 0.21 NO
36 BSG BSG BSG 11400 -0.09 0.19 NO
37 IDH3B IDH3B IDH3B 11927 -0.11 0.18 NO
38 SDHB SDHB SDHB 12187 -0.12 0.19 NO
39 IDH3G IDH3G IDH3G 12230 -0.12 0.22 NO
40 ADHFE1 ADHFE1 ADHFE1 16148 -0.43 0.086 NO

Figure S75.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID ATM PATHWAY.

Figure S76.  Get High-res Image For the top 5 core enriched genes in the pathway: PID ATM PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID HDAC CLASSI PATHWAY

Table S39.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 GLI2 GLI2 GLI2 386 0.55 0.056 YES
2 PTCH1 PTCH1 PTCH1 429 0.54 0.13 YES
3 SSPO SSPO SSPO 775 0.44 0.17 YES
4 STK36 STK36 STK36 1057 0.38 0.21 YES
5 RAB23 RAB23 RAB23 1413 0.33 0.24 YES
6 SMO SMO SMO 1831 0.28 0.25 YES
7 KIF3A KIF3A KIF3A 1893 0.28 0.29 YES
8 CSNK1G3 CSNK1G3 CSNK1G3 2067 0.26 0.32 YES
9 GLI1 GLI1 GLI1 2129 0.26 0.35 YES
10 RBBP7 RBBP7 RBBP7 2552 0.22 0.36 YES
11 IFT88 IFT88 IFT88 3166 0.18 0.35 YES
12 SAP30 SAP30 SAP30 3234 0.18 0.37 YES
13 IFT172 IFT172 IFT172 3285 0.18 0.39 YES
14 CREBBP CREBBP CREBBP 3335 0.17 0.41 YES
15 FBXW11 FBXW11 FBXW11 3346 0.17 0.44 YES
16 RBBP4 RBBP4 RBBP4 3352 0.17 0.46 YES
17 HDAC1 HDAC1 HDAC1 4334 0.13 0.42 NO
18 MAP2K1 MAP2K1 MAP2K1 4974 0.1 0.4 NO
19 GLI3 GLI3 GLI3 4983 0.1 0.42 NO
20 SIN3B SIN3B SIN3B 5049 0.1 0.43 NO
21 SIN3A SIN3A SIN3A 5469 0.086 0.42 NO
22 XPO1 XPO1 XPO1 5528 0.084 0.42 NO
23 HDAC2 HDAC2 HDAC2 5912 0.073 0.41 NO
24 AKT1 AKT1 AKT1 6343 0.059 0.4 NO
25 CSNK1G2 CSNK1G2 CSNK1G2 6616 0.05 0.39 NO
26 PRKACA PRKACA PRKACA 6880 0.042 0.38 NO
27 GSK3B GSK3B GSK3B 7214 0.034 0.37 NO
28 FOXA2 FOXA2 FOXA2 7277 0.032 0.37 NO
29 CSNK1D CSNK1D CSNK1D 7500 0.026 0.36 NO
30 GNB1 GNB1 GNB1 7715 0.019 0.35 NO
31 SPOP SPOP SPOP 7985 0.011 0.34 NO
32 PIAS1 PIAS1 PIAS1 8016 0.01 0.33 NO
33 CSNK1A1 CSNK1A1 CSNK1A1 8174 0.0062 0.33 NO
34 GNAI1 GNAI1 GNAI1 8943 -0.015 0.28 NO
35 CSNK1G1 CSNK1G1 CSNK1G1 9086 -0.019 0.28 NO
36 GNG2 GNG2 GNG2 9113 -0.02 0.28 NO
37 GNAI3 GNAI3 GNAI3 9187 -0.021 0.28 NO
38 SUFU SUFU SUFU 9567 -0.032 0.26 NO
39 PRKCD PRKCD PRKCD 9603 -0.033 0.26 NO
40 GNAI2 GNAI2 GNAI2 10588 -0.064 0.22 NO
41 CSNK1E CSNK1E CSNK1E 10679 -0.066 0.22 NO
42 GNAZ GNAZ GNAZ 12186 -0.12 0.15 NO
43 SAP18 SAP18 SAP18 12697 -0.14 0.14 NO
44 ARRB2 ARRB2 ARRB2 13041 -0.16 0.15 NO
45 LGALS3 LGALS3 LGALS3 13466 -0.18 0.15 NO
46 MTSS1 MTSS1 MTSS1 14822 -0.27 0.11 NO
47 GNAO1 GNAO1 GNAO1 15747 -0.37 0.11 NO

Figure S77.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID HDAC CLASSI PATHWAY.

Figure S78.  Get High-res Image For the top 5 core enriched genes in the pathway: PID HDAC CLASSI PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID PLK1 PATHWAY

Table S40.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 SMC1A SMC1A SMC1A 1673 0.3 -0.015 YES
2 BRCA1 BRCA1 BRCA1 1977 0.27 0.04 YES
3 ATM ATM ATM 2105 0.26 0.1 YES
4 FAM175A FAM175A FAM175A 2159 0.25 0.17 YES
5 RAD17 RAD17 RAD17 2764 0.21 0.19 YES
6 RAD50 RAD50 RAD50 3364 0.17 0.2 YES
7 MDC1 MDC1 MDC1 3613 0.16 0.23 YES
8 MRE11A MRE11A MRE11A 3634 0.16 0.27 YES
9 CHEK2 CHEK2 CHEK2 3697 0.16 0.31 YES
10 CDC25C CDC25C CDC25C 3891 0.15 0.34 YES
11 SMC3 SMC3 SMC3 4503 0.12 0.34 YES
12 UIMC1 UIMC1 UIMC1 4759 0.11 0.35 YES
13 TERF2 TERF2 TERF2 4821 0.11 0.38 YES
14 RBBP8 RBBP8 RBBP8 5198 0.096 0.38 YES
15 MDM2 MDM2 MDM2 5458 0.086 0.39 YES
16 DCLRE1C DCLRE1C DCLRE1C 5685 0.079 0.4 YES
17 RNF8 RNF8 RNF8 6005 0.07 0.4 YES
18 UBE2N UBE2N UBE2N 6097 0.066 0.41 YES
19 ABL1 ABL1 ABL1 6142 0.065 0.43 YES
20 TP53BP1 TP53BP1 TP53BP1 6212 0.062 0.44 YES
21 XRCC4 XRCC4 XRCC4 6266 0.061 0.45 YES
22 CDC25A CDC25A CDC25A 6989 0.04 0.42 NO
23 NBN NBN NBN 7047 0.038 0.43 NO
24 RFWD2 RFWD2 RFWD2 7079 0.037 0.44 NO
25 FANCD2 FANCD2 FANCD2 7194 0.034 0.44 NO
26 TOP3A TOP3A TOP3A 8474 -0.0021 0.37 NO
27 CTBP1 CTBP1 CTBP1 8527 -0.0036 0.37 NO
28 YWHAB YWHAB YWHAB 8857 -0.012 0.35 NO
29 BLM BLM BLM 10652 -0.066 0.27 NO
30 KAT5 KAT5 KAT5 10995 -0.076 0.27 NO
31 RAD9A RAD9A RAD9A 11080 -0.078 0.28 NO
32 H2AFX H2AFX H2AFX 11087 -0.078 0.3 NO
33 TRIM28 TRIM28 TRIM28 12336 -0.12 0.27 NO
34 BID BID BID 12473 -0.13 0.3 NO

Figure S79.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID PLK1 PATHWAY.

Figure S80.  Get High-res Image For the top 5 core enriched genes in the pathway: PID PLK1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Fold change

For the top enriched genes, if you want to check whether they are

Expression level

For the top enriched genes, if you want to check whether they are

An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap

Significant gene list

For the top enriched genes, if you want to check whether they are

Subtype clus5 enriched pathways

Table 7.  Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus5. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
KEGG OXIDATIVE PHOSPHORYLATION 111 genes.ES.table 0.61 1.8 0.0043 0.99 0.49 0.6 0.2 0.48 0 0.19
KEGG RIBOSOME 85 genes.ES.table 0.73 1.6 0.036 0.35 0.93 0.91 0.24 0.7 0.2 0.071
KEGG PARKINSONS DISEASE 108 genes.ES.table 0.54 1.7 0.023 0.87 0.7 0.65 0.27 0.48 0.31 0.2
KEGG HUNTINGTONS DISEASE 165 genes.ES.table 0.35 1.6 0.048 0.27 0.94 0.52 0.25 0.39 0.16 0.041
REACTOME TRANSLATION 146 genes.ES.table 0.6 1.7 0.027 0.47 0.74 0.66 0.25 0.5 0.18 0.1
REACTOME FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX 49 genes.ES.table 0.63 1.6 0.064 0.39 0.93 0.8 0.23 0.62 0.22 0.088
REACTOME TCA CYCLE AND RESPIRATORY ELECTRON TRANSPORT 115 genes.ES.table 0.49 1.7 0.027 0.59 0.72 0.58 0.24 0.45 0.22 0.12
REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE 109 genes.ES.table 0.65 1.7 0.026 0.45 0.83 0.72 0.24 0.56 0.21 0.11
REACTOME ACTIVATION OF NF KAPPAB IN B CELLS 61 genes.ES.table 0.41 1.6 0.036 0.42 0.88 0.66 0.34 0.43 0.21 0.098
REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S 57 genes.ES.table 0.58 1.6 0.091 0.3 0.94 0.68 0.23 0.53 0.17 0.057
genes ES table in pathway: KEGG OXIDATIVE PHOSPHORYLATION

Table S41.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 COX4I2 COX4I2 COX4I2 324 0.44 0.0092 YES
2 COX7A1 COX7A1 COX7A1 368 0.42 0.033 YES
3 NDUFS8 NDUFS8 NDUFS8 933 0.29 0.019 YES
4 LHPP LHPP LHPP 1002 0.28 0.033 YES
5 NDUFA11 NDUFA11 NDUFA11 1024 0.28 0.049 YES
6 NDUFA3 NDUFA3 NDUFA3 1039 0.28 0.065 YES
7 NDUFB7 NDUFB7 NDUFB7 1044 0.28 0.082 YES
8 NDUFB1 NDUFB1 NDUFB1 1100 0.27 0.096 YES
9 ATP5D ATP5D ATP5D 1124 0.27 0.11 YES
10 ATP5O ATP5O ATP5O 1217 0.26 0.12 YES
11 NDUFS6 NDUFS6 NDUFS6 1237 0.26 0.14 YES
12 COX6B1 COX6B1 COX6B1 1340 0.24 0.15 YES
13 UQCRB UQCRB UQCRB 1443 0.24 0.16 YES
14 NDUFV3 NDUFV3 NDUFV3 1505 0.23 0.17 YES
15 NDUFS7 NDUFS7 NDUFS7 1535 0.23 0.18 YES
16 NDUFAB1 NDUFAB1 NDUFAB1 1549 0.23 0.19 YES
17 ATP5E ATP5E ATP5E 1616 0.22 0.2 YES
18 COX5B COX5B COX5B 1635 0.22 0.22 YES
19 NDUFA1 NDUFA1 NDUFA1 1670 0.22 0.23 YES
20 COX6C COX6C COX6C 1697 0.22 0.24 YES
21 UQCRQ UQCRQ UQCRQ 1707 0.22 0.25 YES
22 NDUFA2 NDUFA2 NDUFA2 1724 0.21 0.26 YES
23 NDUFA8 NDUFA8 NDUFA8 1773 0.21 0.27 YES
24 ATP5J ATP5J ATP5J 1809 0.21 0.28 YES
25 UQCR11 UQCR11 UQCR11 1908 0.2 0.29 YES
26 NDUFB10 NDUFB10 NDUFB10 1927 0.2 0.3 YES
27 ATP5I ATP5I ATP5I 1961 0.2 0.31 YES
28 UQCRHL UQCRHL UQCRHL 1964 0.2 0.33 YES
29 NDUFC2 NDUFC2 NDUFC2 1988 0.2 0.34 YES
30 UQCRH UQCRH UQCRH 2004 0.2 0.35 YES
31 ATP5L ATP5L ATP5L 2044 0.19 0.36 YES
32 COX4I1 COX4I1 COX4I1 2052 0.19 0.37 YES
33 NDUFS4 NDUFS4 NDUFS4 2070 0.19 0.38 YES
34 ATP6V1C2 ATP6V1C2 ATP6V1C2 2129 0.19 0.39 YES
35 NDUFA4L2 NDUFA4L2 NDUFA4L2 2141 0.19 0.4 YES
36 ATP6V1E2 ATP6V1E2 ATP6V1E2 2177 0.18 0.41 YES
37 NDUFB9 NDUFB9 NDUFB9 2180 0.18 0.42 YES
38 NDUFV1 NDUFV1 NDUFV1 2262 0.18 0.43 YES
39 NDUFS3 NDUFS3 NDUFS3 2282 0.18 0.44 YES
40 NDUFC1 NDUFC1 NDUFC1 2391 0.17 0.44 YES
41 COX6A1 COX6A1 COX6A1 2407 0.17 0.45 YES
42 UQCR10 UQCR10 UQCR10 2443 0.17 0.46 YES
43 COX17 COX17 COX17 2472 0.17 0.47 YES
44 COX7C COX7C COX7C 2542 0.16 0.48 YES
45 ATP5G2 ATP5G2 ATP5G2 2544 0.16 0.49 YES
46 NDUFB2 NDUFB2 NDUFB2 2565 0.16 0.5 YES
47 COX7A2 COX7A2 COX7A2 2567 0.16 0.5 YES
48 ATP5H ATP5H ATP5H 2707 0.16 0.51 YES
49 COX7B COX7B COX7B 2719 0.16 0.52 YES
50 COX8A COX8A COX8A 2744 0.16 0.52 YES
51 NDUFS5 NDUFS5 NDUFS5 2870 0.15 0.53 YES
52 NDUFA7 NDUFA7 NDUFA7 2877 0.15 0.54 YES
53 ATP6V1G3 ATP6V1G3 ATP6V1G3 2958 0.15 0.54 YES
54 NDUFA9 NDUFA9 NDUFA9 2983 0.14 0.55 YES
55 ATP5G1 ATP5G1 ATP5G1 3106 0.14 0.55 YES
56 ATP6V0D1 ATP6V0D1 ATP6V0D1 3107 0.14 0.56 YES
57 ATP5J2 ATP5J2 ATP5J2 3121 0.14 0.57 YES
58 NDUFB5 NDUFB5 NDUFB5 3316 0.13 0.56 YES
59 UQCRC1 UQCRC1 UQCRC1 3365 0.13 0.57 YES
60 NDUFA5 NDUFA5 NDUFA5 3406 0.13 0.57 YES
61 ATP6V1B1 ATP6V1B1 ATP6V1B1 3502 0.12 0.58 YES
62 NDUFA4 NDUFA4 NDUFA4 3503 0.12 0.58 YES
63 COX5A COX5A COX5A 3586 0.12 0.59 YES
64 UQCRFS1 UQCRFS1 UQCRFS1 3618 0.12 0.59 YES
65 NDUFA6 NDUFA6 NDUFA6 3621 0.12 0.6 YES
66 NDUFB6 NDUFB6 NDUFB6 3624 0.12 0.61 YES
67 COX7A2L COX7A2L COX7A2L 3845 0.11 0.6 NO
68 NDUFB8 NDUFB8 NDUFB8 4089 0.099 0.59 NO
69 ATP5F1 ATP5F1 ATP5F1 4134 0.097 0.6 NO
70 NDUFV2 NDUFV2 NDUFV2 4209 0.095 0.6 NO
71 ATP6V1E1 ATP6V1E1 ATP6V1E1 4277 0.093 0.6 NO
72 ATP6V0E1 ATP6V0E1 ATP6V0E1 4443 0.087 0.6 NO
73 ATP5G3 ATP5G3 ATP5G3 4470 0.086 0.6 NO
74 ATP6V1D ATP6V1D ATP6V1D 4623 0.08 0.6 NO
75 NDUFB3 NDUFB3 NDUFB3 4742 0.076 0.59 NO
76 ATP6V0E2 ATP6V0E2 ATP6V0E2 5048 0.066 0.58 NO
77 ATP6V0B ATP6V0B ATP6V0B 5053 0.066 0.58 NO
78 ATP6V0A1 ATP6V0A1 ATP6V0A1 5185 0.062 0.58 NO
79 NDUFA10 NDUFA10 NDUFA10 5207 0.062 0.58 NO
80 ATP6V0C ATP6V0C ATP6V0C 5980 0.038 0.54 NO
81 PPA2 PPA2 PPA2 6051 0.036 0.54 NO
82 ATP6V1H ATP6V1H ATP6V1H 6153 0.033 0.54 NO
83 NDUFS2 NDUFS2 NDUFS2 6211 0.031 0.54 NO
84 ATP5C1 ATP5C1 ATP5C1 6314 0.028 0.53 NO
85 TCIRG1 TCIRG1 TCIRG1 6317 0.028 0.53 NO
86 ATP6AP1 ATP6AP1 ATP6AP1 6483 0.023 0.52 NO
87 SDHB SDHB SDHB 6491 0.022 0.53 NO
88 CYC1 CYC1 CYC1 6495 0.022 0.53 NO
89 SDHC SDHC SDHC 6587 0.02 0.52 NO
90 ATP5B ATP5B ATP5B 6860 0.012 0.51 NO
91 ATP6V1G2 ATP6V1G2 ATP6V1G2 6934 0.0093 0.5 NO
92 ATP6V1F ATP6V1F ATP6V1F 7266 -0.00032 0.49 NO
93 NDUFB4 NDUFB4 NDUFB4 7271 -0.00053 0.49 NO
94 COX15 COX15 COX15 7621 -0.011 0.47 NO
95 PPA1 PPA1 PPA1 7672 -0.012 0.46 NO
96 SDHA SDHA SDHA 7733 -0.015 0.46 NO
97 UQCRC2 UQCRC2 UQCRC2 8306 -0.033 0.43 NO
98 ATP5A1 ATP5A1 ATP5A1 8489 -0.037 0.42 NO
99 COX11 COX11 COX11 8513 -0.038 0.42 NO
100 ATP6V1G1 ATP6V1G1 ATP6V1G1 8609 -0.04 0.42 NO
101 ATP4A ATP4A ATP4A 8666 -0.042 0.42 NO
102 ATP6V0A2 ATP6V0A2 ATP6V0A2 9799 -0.079 0.36 NO
103 ATP6V1A ATP6V1A ATP6V1A 9802 -0.079 0.37 NO
104 SDHD SDHD SDHD 9823 -0.08 0.37 NO
105 COX10 COX10 COX10 10236 -0.092 0.35 NO
106 ATP6V0D2 ATP6V0D2 ATP6V0D2 10657 -0.1 0.34 NO
107 ATP6V1C1 ATP6V1C1 ATP6V1C1 10928 -0.11 0.33 NO
108 ATP6V1B2 ATP6V1B2 ATP6V1B2 11227 -0.12 0.32 NO
109 COX6B2 COX6B2 COX6B2 11541 -0.13 0.31 NO
110 NDUFS1 NDUFS1 NDUFS1 13097 -0.19 0.23 NO
111 ATP4B ATP4B ATP4B 16522 -0.47 0.065 NO

Figure S81.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG OXIDATIVE PHOSPHORYLATION.

Figure S82.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG OXIDATIVE PHOSPHORYLATION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG RIBOSOME

Table S42.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 COX4I2 COX4I2 COX4I2 324 0.44 0.0096 YES
2 COX7A1 COX7A1 COX7A1 368 0.42 0.034 YES
3 SLC25A4 SLC25A4 SLC25A4 683 0.33 0.037 YES
4 SNCAIP SNCAIP SNCAIP 764 0.32 0.052 YES
5 NDUFS8 NDUFS8 NDUFS8 933 0.29 0.061 YES
6 NDUFA3 NDUFA3 NDUFA3 1039 0.28 0.073 YES
7 NDUFB7 NDUFB7 NDUFB7 1044 0.28 0.09 YES
8 NDUFB1 NDUFB1 NDUFB1 1100 0.27 0.1 YES
9 ATP5D ATP5D ATP5D 1124 0.27 0.12 YES
10 ATP5O ATP5O ATP5O 1217 0.26 0.13 YES
11 NDUFS6 NDUFS6 NDUFS6 1237 0.26 0.14 YES
12 COX6B1 COX6B1 COX6B1 1340 0.24 0.16 YES
13 UQCRB UQCRB UQCRB 1443 0.24 0.16 YES
14 NDUFV3 NDUFV3 NDUFV3 1505 0.23 0.18 YES
15 NDUFS7 NDUFS7 NDUFS7 1535 0.23 0.19 YES
16 NDUFAB1 NDUFAB1 NDUFAB1 1549 0.23 0.2 YES
17 ATP5E ATP5E ATP5E 1616 0.22 0.21 YES
18 COX5B COX5B COX5B 1635 0.22 0.22 YES
19 NDUFA1 NDUFA1 NDUFA1 1670 0.22 0.24 YES
20 COX6C COX6C COX6C 1697 0.22 0.25 YES
21 UQCRQ UQCRQ UQCRQ 1707 0.22 0.26 YES
22 NDUFA2 NDUFA2 NDUFA2 1724 0.21 0.27 YES
23 NDUFA8 NDUFA8 NDUFA8 1773 0.21 0.28 YES
24 ATP5J ATP5J ATP5J 1809 0.21 0.3 YES
25 UQCR11 UQCR11 UQCR11 1908 0.2 0.3 YES
26 NDUFB10 NDUFB10 NDUFB10 1927 0.2 0.32 YES
27 UQCRHL UQCRHL UQCRHL 1964 0.2 0.32 YES
28 NDUFC2 NDUFC2 NDUFC2 1988 0.2 0.34 YES
29 UQCRH UQCRH UQCRH 2004 0.2 0.35 YES
30 COX4I1 COX4I1 COX4I1 2052 0.19 0.36 YES
31 NDUFS4 NDUFS4 NDUFS4 2070 0.19 0.37 YES
32 NDUFA4L2 NDUFA4L2 NDUFA4L2 2141 0.19 0.38 YES
33 NDUFB9 NDUFB9 NDUFB9 2180 0.18 0.39 YES
34 NDUFV1 NDUFV1 NDUFV1 2262 0.18 0.39 YES
35 NDUFS3 NDUFS3 NDUFS3 2282 0.18 0.4 YES
36 NDUFC1 NDUFC1 NDUFC1 2391 0.17 0.41 YES
37 COX6A1 COX6A1 COX6A1 2407 0.17 0.42 YES
38 UQCR10 UQCR10 UQCR10 2443 0.17 0.43 YES
39 COX7C COX7C COX7C 2542 0.16 0.43 YES
40 ATP5G2 ATP5G2 ATP5G2 2544 0.16 0.44 YES
41 NDUFB2 NDUFB2 NDUFB2 2565 0.16 0.45 YES
42 COX7A2 COX7A2 COX7A2 2567 0.16 0.46 YES
43 ATP5H ATP5H ATP5H 2707 0.16 0.46 YES
44 COX7B COX7B COX7B 2719 0.16 0.47 YES
45 COX8A COX8A COX8A 2744 0.16 0.48 YES
46 NDUFS5 NDUFS5 NDUFS5 2870 0.15 0.48 YES
47 NDUFA7 NDUFA7 NDUFA7 2877 0.15 0.49 YES
48 NDUFA9 NDUFA9 NDUFA9 2983 0.14 0.5 YES
49 ATP5G1 ATP5G1 ATP5G1 3106 0.14 0.5 YES
50 NDUFB5 NDUFB5 NDUFB5 3316 0.13 0.49 YES
51 UQCRC1 UQCRC1 UQCRC1 3365 0.13 0.5 YES
52 NDUFA5 NDUFA5 NDUFA5 3406 0.13 0.5 YES
53 NDUFA4 NDUFA4 NDUFA4 3503 0.12 0.51 YES
54 COX5A COX5A COX5A 3586 0.12 0.51 YES
55 UQCRFS1 UQCRFS1 UQCRFS1 3618 0.12 0.52 YES
56 NDUFA6 NDUFA6 NDUFA6 3621 0.12 0.52 YES
57 NDUFB6 NDUFB6 NDUFB6 3624 0.12 0.53 YES
58 COX7A2L COX7A2L COX7A2L 3845 0.11 0.52 YES
59 UCHL1 UCHL1 UCHL1 3870 0.11 0.53 YES
60 SLC25A5 SLC25A5 SLC25A5 3886 0.11 0.54 YES
61 NDUFB8 NDUFB8 NDUFB8 4089 0.099 0.53 YES
62 ATP5F1 ATP5F1 ATP5F1 4134 0.097 0.53 YES
63 HTRA2 HTRA2 HTRA2 4155 0.097 0.54 YES
64 NDUFV2 NDUFV2 NDUFV2 4209 0.095 0.54 YES
65 UBE2J2 UBE2J2 UBE2J2 4351 0.09 0.54 YES
66 ATP5G3 ATP5G3 ATP5G3 4470 0.086 0.54 YES
67 UBE2L3 UBE2L3 UBE2L3 4593 0.081 0.54 YES
68 UBB UBB UBB 4601 0.081 0.54 YES
69 PARK7 PARK7 PARK7 4674 0.079 0.54 YES
70 NDUFB3 NDUFB3 NDUFB3 4742 0.076 0.54 YES
71 SEPT5 SEPT5 SEPT5 4907 0.07 0.54 NO
72 NDUFA10 NDUFA10 NDUFA10 5207 0.062 0.52 NO
73 UBE2J1 UBE2J1 UBE2J1 5231 0.061 0.53 NO
74 CASP3 CASP3 CASP3 5254 0.06 0.53 NO
75 VDAC2 VDAC2 VDAC2 5267 0.06 0.53 NO
76 SLC25A6 SLC25A6 SLC25A6 5284 0.059 0.54 NO
77 UBE2G2 UBE2G2 UBE2G2 5324 0.058 0.54 NO
78 GPR37 GPR37 GPR37 5360 0.057 0.54 NO
79 UBA1 UBA1 UBA1 6184 0.032 0.49 NO
80 NDUFS2 NDUFS2 NDUFS2 6211 0.031 0.49 NO
81 ATP5C1 ATP5C1 ATP5C1 6314 0.028 0.49 NO
82 CYCS CYCS CYCS 6389 0.025 0.49 NO
83 SDHB SDHB SDHB 6491 0.022 0.48 NO
84 CYC1 CYC1 CYC1 6495 0.022 0.48 NO
85 SDHC SDHC SDHC 6587 0.02 0.48 NO
86 PINK1 PINK1 PINK1 6629 0.019 0.48 NO
87 ATP5B ATP5B ATP5B 6860 0.012 0.47 NO
88 VDAC3 VDAC3 VDAC3 7070 0.0053 0.46 NO
89 NDUFB4 NDUFB4 NDUFB4 7271 -0.00053 0.44 NO
90 SDHA SDHA SDHA 7733 -0.015 0.42 NO
91 PPID PPID PPID 7919 -0.02 0.41 NO
92 UQCRC2 UQCRC2 UQCRC2 8306 -0.033 0.39 NO
93 ATP5A1 ATP5A1 ATP5A1 8489 -0.037 0.38 NO
94 CASP9 CASP9 CASP9 8491 -0.037 0.38 NO
95 VDAC1 VDAC1 VDAC1 9164 -0.059 0.35 NO
96 UBE2L6 UBE2L6 UBE2L6 9234 -0.061 0.35 NO
97 SLC18A1 SLC18A1 SLC18A1 9677 -0.075 0.33 NO
98 SDHD SDHD SDHD 9823 -0.08 0.33 NO
99 UBE2G1 UBE2G1 UBE2G1 10088 -0.087 0.32 NO
100 SLC6A3 SLC6A3 SLC6A3 10598 -0.1 0.29 NO
101 UBA7 UBA7 UBA7 10851 -0.11 0.29 NO
102 SNCA SNCA SNCA 11405 -0.13 0.26 NO
103 APAF1 APAF1 APAF1 11509 -0.13 0.26 NO
104 COX6B2 COX6B2 COX6B2 11541 -0.13 0.27 NO
105 NDUFS1 NDUFS1 NDUFS1 13097 -0.19 0.2 NO
106 PARK2 PARK2 PARK2 15178 -0.31 0.097 NO
107 SLC18A2 SLC18A2 SLC18A2 15265 -0.32 0.11 NO
108 LRRK2 LRRK2 LRRK2 16050 -0.4 0.092 NO

Figure S83.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG RIBOSOME.

Figure S84.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG RIBOSOME, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG PARKINSONS DISEASE

Table S43.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 SLC16A8 SLC16A8 SLC16A8 360 0.43 0.0039 YES
2 ETFB ETFB ETFB 682 0.33 0.0046 YES
3 NDUFA13 NDUFA13 NDUFA13 792 0.31 0.016 YES
4 PDK3 PDK3 PDK3 883 0.3 0.028 YES
5 NDUFS8 NDUFS8 NDUFS8 933 0.29 0.042 YES
6 NDUFA11 NDUFA11 NDUFA11 1024 0.28 0.053 YES
7 NDUFA3 NDUFA3 NDUFA3 1039 0.28 0.068 YES
8 NDUFB7 NDUFB7 NDUFB7 1044 0.28 0.083 YES
9 NDUFB1 NDUFB1 NDUFB1 1100 0.27 0.096 YES
10 ATP5D ATP5D ATP5D 1124 0.27 0.11 YES
11 ATP5O ATP5O ATP5O 1217 0.26 0.12 YES
12 NDUFS6 NDUFS6 NDUFS6 1237 0.26 0.13 YES
13 COX6B1 COX6B1 COX6B1 1340 0.24 0.14 YES
14 UQCRB UQCRB UQCRB 1443 0.24 0.15 YES
15 NDUFV3 NDUFV3 NDUFV3 1505 0.23 0.16 YES
16 NDUFS7 NDUFS7 NDUFS7 1535 0.23 0.17 YES
17 NDUFAB1 NDUFAB1 NDUFAB1 1549 0.23 0.18 YES
18 ATP5E ATP5E ATP5E 1616 0.22 0.19 YES
19 COX5B COX5B COX5B 1635 0.22 0.2 YES
20 NDUFA1 NDUFA1 NDUFA1 1670 0.22 0.21 YES
21 COX6C COX6C COX6C 1697 0.22 0.22 YES
22 UQCRQ UQCRQ UQCRQ 1707 0.22 0.24 YES
23 NDUFA2 NDUFA2 NDUFA2 1724 0.21 0.25 YES
24 NDUFA8 NDUFA8 NDUFA8 1773 0.21 0.26 YES
25 ATP5J ATP5J ATP5J 1809 0.21 0.27 YES
26 UQCR11 UQCR11 UQCR11 1908 0.2 0.27 YES
27 NDUFB10 NDUFB10 NDUFB10 1927 0.2 0.28 YES
28 ATP5I ATP5I ATP5I 1961 0.2 0.29 YES
29 UQCRHL UQCRHL UQCRHL 1964 0.2 0.3 YES
30 NDUFC2 NDUFC2 NDUFC2 1988 0.2 0.31 YES
31 UQCRH UQCRH UQCRH 2004 0.2 0.32 YES
32 ATP5L ATP5L ATP5L 2044 0.19 0.33 YES
33 COX4I1 COX4I1 COX4I1 2052 0.19 0.34 YES
34 NDUFS4 NDUFS4 NDUFS4 2070 0.19 0.35 YES
35 NDUFB9 NDUFB9 NDUFB9 2180 0.18 0.36 YES
36 NDUFV1 NDUFV1 NDUFV1 2262 0.18 0.36 YES
37 NDUFS3 NDUFS3 NDUFS3 2282 0.18 0.37 YES
38 NDUFC1 NDUFC1 NDUFC1 2391 0.17 0.38 YES
39 COX6A1 COX6A1 COX6A1 2407 0.17 0.38 YES
40 COX7C COX7C COX7C 2542 0.16 0.39 YES
41 NDUFB2 NDUFB2 NDUFB2 2565 0.16 0.39 YES
42 ATP5H ATP5H ATP5H 2707 0.16 0.4 YES
43 COX7B COX7B COX7B 2719 0.16 0.4 YES
44 COX8A COX8A COX8A 2744 0.16 0.41 YES
45 NDUFS5 NDUFS5 NDUFS5 2870 0.15 0.41 YES
46 NDUFA7 NDUFA7 NDUFA7 2877 0.15 0.42 YES
47 NDUFA9 NDUFA9 NDUFA9 2983 0.14 0.42 YES
48 IDH3G IDH3G IDH3G 3003 0.14 0.43 YES
49 ATP5G1 ATP5G1 ATP5G1 3106 0.14 0.43 YES
50 ATP5J2 ATP5J2 ATP5J2 3121 0.14 0.44 YES
51 SUCLG1 SUCLG1 SUCLG1 3125 0.14 0.45 YES
52 NDUFB5 NDUFB5 NDUFB5 3316 0.13 0.44 YES
53 UQCRC1 UQCRC1 UQCRC1 3365 0.13 0.45 YES
54 IDH3B IDH3B IDH3B 3392 0.13 0.45 YES
55 NDUFA5 NDUFA5 NDUFA5 3406 0.13 0.46 YES
56 NDUFA4 NDUFA4 NDUFA4 3503 0.12 0.46 YES
57 COX5A COX5A COX5A 3586 0.12 0.46 YES
58 FH FH FH 3605 0.12 0.47 YES
59 UQCRFS1 UQCRFS1 UQCRFS1 3618 0.12 0.48 YES
60 NDUFA6 NDUFA6 NDUFA6 3621 0.12 0.48 YES
61 NDUFB6 NDUFB6 NDUFB6 3624 0.12 0.49 YES
62 MDH2 MDH2 MDH2 3812 0.11 0.48 YES
63 COX7A2L COX7A2L COX7A2L 3845 0.11 0.49 YES
64 NDUFB8 NDUFB8 NDUFB8 4089 0.099 0.48 YES
65 ATP5F1 ATP5F1 ATP5F1 4134 0.097 0.48 YES
66 PDHA1 PDHA1 PDHA1 4177 0.096 0.49 YES
67 NDUFV2 NDUFV2 NDUFV2 4209 0.095 0.49 YES
68 IDH2 IDH2 IDH2 4469 0.086 0.48 NO
69 NDUFB3 NDUFB3 NDUFB3 4742 0.076 0.47 NO
70 D2HGDH D2HGDH D2HGDH 4924 0.07 0.46 NO
71 NDUFA10 NDUFA10 NDUFA10 5207 0.062 0.45 NO
72 NDUFA12 NDUFA12 NDUFA12 5333 0.058 0.45 NO
73 BSG BSG BSG 5596 0.05 0.43 NO
74 PDK2 PDK2 PDK2 5725 0.046 0.43 NO
75 PDHB PDHB PDHB 5957 0.039 0.42 NO
76 NDUFS2 NDUFS2 NDUFS2 6211 0.031 0.41 NO
77 ACO2 ACO2 ACO2 6255 0.03 0.4 NO
78 ATP5C1 ATP5C1 ATP5C1 6314 0.028 0.4 NO
79 CYCS CYCS CYCS 6389 0.025 0.4 NO
80 LDHB LDHB LDHB 6449 0.024 0.4 NO
81 SDHB SDHB SDHB 6491 0.022 0.4 NO
82 CYC1 CYC1 CYC1 6495 0.022 0.4 NO
83 SDHC SDHC SDHC 6587 0.02 0.4 NO
84 LDHA LDHA LDHA 6734 0.016 0.39 NO
85 PDHX PDHX PDHX 6799 0.014 0.38 NO
86 ATP5B ATP5B ATP5B 6860 0.012 0.38 NO
87 DLD DLD DLD 6867 0.011 0.38 NO
88 NDUFB4 NDUFB4 NDUFB4 7271 -0.00053 0.36 NO
89 UCP2 UCP2 UCP2 7409 -0.0045 0.35 NO
90 SLC16A3 SLC16A3 SLC16A3 7726 -0.014 0.33 NO
91 SDHA SDHA SDHA 7733 -0.015 0.34 NO
92 UQCRC2 UQCRC2 UQCRC2 8306 -0.033 0.3 NO
93 ATP5A1 ATP5A1 ATP5A1 8489 -0.037 0.3 NO
94 NNT NNT NNT 8628 -0.041 0.29 NO
95 SLC16A1 SLC16A1 SLC16A1 8877 -0.05 0.28 NO
96 CS CS CS 8963 -0.052 0.28 NO
97 PDK1 PDK1 PDK1 9412 -0.066 0.26 NO
98 SDHD SDHD SDHD 9823 -0.08 0.24 NO
99 ETFDH ETFDH ETFDH 9852 -0.08 0.24 NO
100 DLST DLST DLST 10004 -0.085 0.24 NO
101 ETFA ETFA ETFA 10095 -0.087 0.24 NO
102 DLAT DLAT DLAT 10726 -0.11 0.21 NO
103 SUCLG2 SUCLG2 SUCLG2 11239 -0.12 0.18 NO
104 PDK4 PDK4 PDK4 12369 -0.16 0.13 NO
105 IDH3A IDH3A IDH3A 12578 -0.17 0.13 NO
106 NDUFS1 NDUFS1 NDUFS1 13097 -0.19 0.11 NO
107 L2HGDH L2HGDH L2HGDH 13362 -0.2 0.1 NO
108 OGDH OGDH OGDH 13389 -0.21 0.12 NO
109 ADHFE1 ADHFE1 ADHFE1 13968 -0.24 0.096 NO
110 IDH1 IDH1 IDH1 14016 -0.24 0.11 NO
111 SUCLA2 SUCLA2 SUCLA2 14308 -0.25 0.1 NO
112 PDP1 PDP1 PDP1 14569 -0.27 0.1 NO
113 UCP3 UCP3 UCP3 14912 -0.29 0.1 NO
114 PDPR PDPR PDPR 16230 -0.42 0.051 NO
115 PDP2 PDP2 PDP2 16927 -0.55 0.042 NO

Figure S85.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG PARKINSONS DISEASE.

Figure S86.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PARKINSONS DISEASE, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG HUNTINGTONS DISEASE

Table S44.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 RPL21 RPL21 RPL21 4 0.85 0.041 YES
2 RPL9 RPL9 RPL9 200 0.51 0.054 YES
3 RPL39 RPL39 RPL39 278 0.46 0.072 YES
4 RPSAP9 RPSAP9 RPSAP9 985 0.28 0.046 YES
5 RPL36 RPL36 RPL36 1156 0.26 0.049 YES
6 EIF3K EIF3K EIF3K 1233 0.26 0.057 YES
7 RPLP2 RPLP2 RPLP2 1353 0.24 0.062 YES
8 RPL35 RPL35 RPL35 1413 0.24 0.07 YES
9 RPL38 RPL38 RPL38 1457 0.24 0.079 YES
10 RPL13 RPL13 RPL13 1464 0.23 0.09 YES
11 RPS15 RPS15 RPS15 1518 0.23 0.098 YES
12 RPS19 RPS19 RPS19 1618 0.22 0.1 YES
13 RPS21 RPS21 RPS21 1640 0.22 0.11 YES
14 RPL27A RPL27A RPL27A 1733 0.21 0.12 YES
15 RPS29 RPS29 RPS29 1790 0.21 0.12 YES
16 RPL34 RPL34 RPL34 1797 0.21 0.13 YES
17 RPL18 RPL18 RPL18 1832 0.21 0.14 YES
18 RPS10 RPS10 RPS10 1864 0.2 0.15 YES
19 RPL28 RPL28 RPL28 1867 0.2 0.16 YES
20 RPL37 RPL37 RPL37 1876 0.2 0.17 YES
21 RPL23 RPL23 RPL23 1880 0.2 0.18 YES
22 RPL24 RPL24 RPL24 1895 0.2 0.19 YES
23 RPL37A RPL37A RPL37A 1898 0.2 0.2 YES
24 UBA52 UBA52 UBA52 1899 0.2 0.21 YES
25 RPL18A RPL18A RPL18A 1923 0.2 0.22 YES
26 RPL23A RPL23A RPL23A 1936 0.2 0.22 YES
27 RPS15A RPS15A RPS15A 1942 0.2 0.23 YES
28 EIF3F EIF3F EIF3F 1943 0.2 0.24 YES
29 EEF1D EEF1D EEF1D 1946 0.2 0.25 YES
30 RPS7 RPS7 RPS7 1967 0.2 0.26 YES
31 RPS4X RPS4X RPS4X 1982 0.2 0.27 YES
32 FAU FAU FAU 1984 0.2 0.28 YES
33 RPS27A RPS27A RPS27A 2012 0.2 0.29 YES
34 RPL11 RPL11 RPL11 2136 0.19 0.29 YES
35 RPS5 RPS5 RPS5 2175 0.18 0.3 YES
36 EIF3G EIF3G EIF3G 2184 0.18 0.3 YES
37 RPL30 RPL30 RPL30 2207 0.18 0.31 YES
38 RPS9 RPS9 RPS9 2232 0.18 0.32 YES
39 RPL8 RPL8 RPL8 2296 0.18 0.32 YES
40 RPS3A RPS3A RPS3A 2330 0.18 0.33 YES
41 RPL31 RPL31 RPL31 2333 0.18 0.34 YES
42 RPS11 RPS11 RPS11 2416 0.17 0.34 YES
43 RPS3 RPS3 RPS3 2452 0.17 0.35 YES
44 RPL7 RPL7 RPL7 2470 0.17 0.36 YES
45 RPL12 RPL12 RPL12 2502 0.17 0.36 YES
46 GSPT2 GSPT2 GSPT2 2505 0.17 0.37 YES
47 RPS16 RPS16 RPS16 2569 0.16 0.38 YES
48 RPS12 RPS12 RPS12 2570 0.16 0.38 YES
49 RPL32 RPL32 RPL32 2573 0.16 0.39 YES
50 RPL7A RPL7A RPL7A 2586 0.16 0.4 YES
51 RPL29 RPL29 RPL29 2618 0.16 0.4 YES
52 SEC61G SEC61G SEC61G 2661 0.16 0.41 YES
53 RPS20 RPS20 RPS20 2665 0.16 0.42 YES
54 RPL14 RPL14 RPL14 2753 0.16 0.42 YES
55 RPS6 RPS6 RPS6 2769 0.16 0.43 YES
56 RPL41 RPL41 RPL41 2793 0.15 0.43 YES
57 RPL27 RPL27 RPL27 2798 0.15 0.44 YES
58 RPS24 RPS24 RPS24 2807 0.15 0.45 YES
59 SSR4 SSR4 SSR4 2809 0.15 0.45 YES
60 RPL36A RPL36A RPL36A 2811 0.15 0.46 YES
61 RPS25 RPS25 RPS25 2831 0.15 0.47 YES
62 RPS13 RPS13 RPS13 2852 0.15 0.47 YES
63 RPSA RPSA RPSA 2869 0.15 0.48 YES
64 RPS8 RPS8 RPS8 2881 0.15 0.49 YES
65 RPS14 RPS14 RPS14 2902 0.15 0.49 YES
66 RPL22 RPL22 RPL22 2984 0.14 0.5 YES
67 RPL13A RPL13A RPL13A 3013 0.14 0.5 YES
68 RPS27 RPS27 RPS27 3101 0.14 0.5 YES
69 EIF2B4 EIF2B4 EIF2B4 3110 0.14 0.51 YES
70 EEF1G EEF1G EEF1G 3120 0.14 0.52 YES
71 RPS17 RPS17 RPS17 3174 0.14 0.52 YES
72 EIF2B3 EIF2B3 EIF2B3 3181 0.14 0.52 YES
73 RPL10A RPL10A RPL10A 3194 0.14 0.53 YES
74 EIF2S2 EIF2S2 EIF2S2 3282 0.13 0.53 YES
75 RPL35A RPL35A RPL35A 3294 0.13 0.54 YES
76 EIF3H EIF3H EIF3H 3297 0.13 0.54 YES
77 RPL5 RPL5 RPL5 3318 0.13 0.55 YES
78 RPS2 RPS2 RPS2 3321 0.13 0.56 YES
79 RPL19 RPL19 RPL19 3328 0.13 0.56 YES
80 RPS18 RPS18 RPS18 3372 0.13 0.56 YES
81 RPL10 RPL10 RPL10 3490 0.12 0.56 YES
82 RPL6 RPL6 RPL6 3500 0.12 0.57 YES
83 RPL15 RPL15 RPL15 3597 0.12 0.57 YES
84 EIF3I EIF3I EIF3I 3609 0.12 0.57 YES
85 RPLP1 RPLP1 RPLP1 3700 0.11 0.57 YES
86 EEF1B2 EEF1B2 EEF1B2 3818 0.11 0.57 YES
87 SSR2 SSR2 SSR2 3838 0.11 0.58 YES
88 RPS23 RPS23 RPS23 3881 0.11 0.58 YES
89 EIF3D EIF3D EIF3D 3882 0.11 0.59 YES
90 EIF2B2 EIF2B2 EIF2B2 3948 0.1 0.59 YES
91 EIF3B EIF3B EIF3B 4036 0.1 0.59 YES
92 RPL4 RPL4 RPL4 4085 0.099 0.59 YES
93 RPL26 RPL26 RPL26 4099 0.099 0.59 YES
94 RPLP0 RPLP0 RPLP0 4172 0.096 0.59 YES
95 RPN2 RPN2 RPN2 4333 0.091 0.59 YES
96 EIF2B1 EIF2B1 EIF2B1 4344 0.09 0.59 YES
97 EIF2S3 EIF2S3 EIF2S3 4346 0.09 0.6 YES
98 EIF4EBP1 EIF4EBP1 EIF4EBP1 4599 0.081 0.59 NO
99 SEC61B SEC61B SEC61B 4733 0.077 0.58 NO
100 EIF5B EIF5B EIF5B 4824 0.074 0.58 NO
101 SRP19 SRP19 SRP19 4852 0.072 0.58 NO
102 RPL17 RPL17 RPL17 4891 0.071 0.58 NO
103 EIF3E EIF3E EIF3E 4904 0.07 0.59 NO
104 SEC11C SEC11C SEC11C 5251 0.06 0.57 NO
105 SRP9 SRP9 SRP9 5535 0.052 0.56 NO
106 EIF1AX EIF1AX EIF1AX 5586 0.05 0.56 NO
107 RPL3 RPL3 RPL3 5665 0.048 0.55 NO
108 EIF4B EIF4B EIF4B 5793 0.044 0.55 NO
109 EIF2S1 EIF2S1 EIF2S1 5946 0.039 0.54 NO
110 EEF1A1 EEF1A1 EEF1A1 6036 0.037 0.54 NO
111 RPS28 RPS28 RPS28 6298 0.028 0.52 NO
112 SRP14 SRP14 SRP14 6428 0.024 0.52 NO
113 RPS26 RPS26 RPS26 6567 0.02 0.51 NO
114 EIF4A1 EIF4A1 EIF4A1 6583 0.02 0.51 NO
115 SPCS1 SPCS1 SPCS1 6593 0.02 0.51 NO
116 RPN1 RPN1 RPN1 6837 0.012 0.5 NO
117 SPCS2 SPCS2 SPCS2 7284 -0.00092 0.47 NO
118 SEC61A1 SEC61A1 SEC61A1 7351 -0.0027 0.47 NO
119 SRPR SRPR SRPR 7397 -0.0042 0.47 NO
120 SEC11A SEC11A SEC11A 7445 -0.0059 0.46 NO
121 EEF2 EEF2 EEF2 7524 -0.008 0.46 NO
122 SSR3 SSR3 SSR3 7556 -0.0088 0.46 NO
123 LOC653566 LOC653566 LOC653566 7623 -0.011 0.46 NO
124 EIF2B5 EIF2B5 EIF2B5 7658 -0.012 0.46 NO
125 PABPC1 PABPC1 PABPC1 7683 -0.013 0.46 NO
126 SRPRB SRPRB SRPRB 7724 -0.014 0.45 NO
127 SRP68 SRP68 SRP68 7920 -0.02 0.44 NO
128 EIF5 EIF5 EIF5 8007 -0.023 0.44 NO
129 DDOST DDOST DDOST 8326 -0.033 0.42 NO
130 EIF4H EIF4H EIF4H 8332 -0.033 0.42 NO
131 EIF4E EIF4E EIF4E 8492 -0.037 0.42 NO
132 EIF3J EIF3J EIF3J 8672 -0.043 0.41 NO
133 ETF1 ETF1 ETF1 8791 -0.046 0.4 NO
134 SSR1 SSR1 SSR1 9421 -0.067 0.37 NO
135 SRP72 SRP72 SRP72 9454 -0.068 0.37 NO
136 SRP54 SRP54 SRP54 9899 -0.082 0.35 NO
137 TRAM1 TRAM1 TRAM1 10033 -0.086 0.35 NO
138 EIF4A2 EIF4A2 EIF4A2 10058 -0.086 0.35 NO
139 SPCS3 SPCS3 SPCS3 10211 -0.091 0.35 NO
140 RPS4Y1 RPS4Y1 RPS4Y1 11175 -0.12 0.3 NO
141 EIF3A EIF3A EIF3A 11880 -0.14 0.26 NO
142 EIF4G1 EIF4G1 EIF4G1 11885 -0.14 0.27 NO
143 RPL26L1 RPL26L1 RPL26L1 12727 -0.18 0.23 NO
144 FAM153A FAM153A FAM153A 13059 -0.19 0.22 NO
145 SEC61A2 SEC61A2 SEC61A2 15762 -0.36 0.085 NO
146 EIF3C EIF3C EIF3C 16658 -0.49 0.058 NO

Figure S87.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG HUNTINGTONS DISEASE.

Figure S88.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG HUNTINGTONS DISEASE, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: REACTOME TRANSLATION

Table S45.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 RPL21 RPL21 RPL21 4 0.85 0.031 YES
2 RPL9 RPL9 RPL9 200 0.51 0.038 YES
3 RPL39 RPL39 RPL39 278 0.46 0.051 YES
4 RPSAP9 RPSAP9 RPSAP9 985 0.28 0.02 YES
5 RPL36 RPL36 RPL36 1156 0.26 0.02 YES
6 EXOSC4 EXOSC4 EXOSC4 1243 0.26 0.025 YES
7 HSPB1 HSPB1 HSPB1 1327 0.25 0.029 YES
8 PSMB3 PSMB3 PSMB3 1333 0.24 0.037 YES
9 RPLP2 RPLP2 RPLP2 1353 0.24 0.045 YES
10 RPL35 RPL35 RPL35 1413 0.24 0.05 YES
11 RPL38 RPL38 RPL38 1457 0.24 0.056 YES
12 RPL13 RPL13 RPL13 1464 0.23 0.065 YES
13 RPS15 RPS15 RPS15 1518 0.23 0.07 YES
14 RPS19 RPS19 RPS19 1618 0.22 0.072 YES
15 RPS21 RPS21 RPS21 1640 0.22 0.079 YES
16 PSMC1 PSMC1 PSMC1 1732 0.21 0.082 YES
17 RPL27A RPL27A RPL27A 1733 0.21 0.09 YES
18 RPS29 RPS29 RPS29 1790 0.21 0.094 YES
19 RPL34 RPL34 RPL34 1797 0.21 0.1 YES
20 RPL18 RPL18 RPL18 1832 0.21 0.11 YES
21 RPS10 RPS10 RPS10 1864 0.2 0.11 YES
22 RPL28 RPL28 RPL28 1867 0.2 0.12 YES
23 RPL37 RPL37 RPL37 1876 0.2 0.13 YES
24 RPL23 RPL23 RPL23 1880 0.2 0.13 YES
25 RPL24 RPL24 RPL24 1895 0.2 0.14 YES
26 RPL37A RPL37A RPL37A 1898 0.2 0.15 YES
27 UBA52 UBA52 UBA52 1899 0.2 0.16 YES
28 RPL18A RPL18A RPL18A 1923 0.2 0.16 YES
29 RPL23A RPL23A RPL23A 1936 0.2 0.17 YES
30 RPS15A RPS15A RPS15A 1942 0.2 0.18 YES
31 RPS7 RPS7 RPS7 1967 0.2 0.18 YES
32 RPS4X RPS4X RPS4X 1982 0.2 0.19 YES
33 FAU FAU FAU 1984 0.2 0.19 YES
34 RPS27A RPS27A RPS27A 2012 0.2 0.2 YES
35 RPL11 RPL11 RPL11 2136 0.19 0.2 YES
36 DCPS DCPS DCPS 2172 0.18 0.2 YES
37 RPS5 RPS5 RPS5 2175 0.18 0.21 YES
38 PSMD4 PSMD4 PSMD4 2195 0.18 0.22 YES
39 RPL30 RPL30 RPL30 2207 0.18 0.22 YES
40 RPS9 RPS9 RPS9 2232 0.18 0.23 YES
41 RPL8 RPL8 RPL8 2296 0.18 0.23 YES
42 RPS3A RPS3A RPS3A 2330 0.18 0.24 YES
43 RPL31 RPL31 RPL31 2333 0.18 0.24 YES
44 LSM4 LSM4 LSM4 2358 0.18 0.25 YES
45 RPS11 RPS11 RPS11 2416 0.17 0.25 YES
46 PSMC5 PSMC5 PSMC5 2418 0.17 0.26 YES
47 PSMB10 PSMB10 PSMB10 2441 0.17 0.26 YES
48 RPS3 RPS3 RPS3 2452 0.17 0.27 YES
49 RPL7 RPL7 RPL7 2470 0.17 0.27 YES
50 PARN PARN PARN 2479 0.17 0.28 YES
51 RPL12 RPL12 RPL12 2502 0.17 0.28 YES
52 GSPT2 GSPT2 GSPT2 2505 0.17 0.29 YES
53 PSMB6 PSMB6 PSMB6 2513 0.17 0.29 YES
54 PSMD9 PSMD9 PSMD9 2535 0.16 0.3 YES
55 PSMD13 PSMD13 PSMD13 2538 0.16 0.3 YES
56 PSMB7 PSMB7 PSMB7 2564 0.16 0.31 YES
57 RPS16 RPS16 RPS16 2569 0.16 0.31 YES
58 RPS12 RPS12 RPS12 2570 0.16 0.32 YES
59 RPL32 RPL32 RPL32 2573 0.16 0.33 YES
60 RPL7A RPL7A RPL7A 2586 0.16 0.33 YES
61 PSMC3 PSMC3 PSMC3 2595 0.16 0.34 YES
62 RPL29 RPL29 RPL29 2618 0.16 0.34 YES
63 RPS20 RPS20 RPS20 2665 0.16 0.34 YES
64 EXOSC5 EXOSC5 EXOSC5 2678 0.16 0.35 YES
65 RPL14 RPL14 RPL14 2753 0.16 0.35 YES
66 RPS6 RPS6 RPS6 2769 0.16 0.36 YES
67 RPL41 RPL41 RPL41 2793 0.15 0.36 YES
68 RPL27 RPL27 RPL27 2798 0.15 0.36 YES
69 RPS24 RPS24 RPS24 2807 0.15 0.37 YES
70 RPL36A RPL36A RPL36A 2811 0.15 0.38 YES
71 RPS25 RPS25 RPS25 2831 0.15 0.38 YES
72 RPS13 RPS13 RPS13 2852 0.15 0.38 YES
73 LSM2 LSM2 LSM2 2856 0.15 0.39 YES
74 RPSA RPSA RPSA 2869 0.15 0.39 YES
75 RPS8 RPS8 RPS8 2881 0.15 0.4 YES
76 RPS14 RPS14 RPS14 2902 0.15 0.4 YES
77 LSM5 LSM5 LSM5 2925 0.15 0.41 YES
78 PSMB1 PSMB1 PSMB1 2926 0.15 0.41 YES
79 RPL22 RPL22 RPL22 2984 0.14 0.42 YES
80 LSM3 LSM3 LSM3 3002 0.14 0.42 YES
81 RPL13A RPL13A RPL13A 3013 0.14 0.42 YES
82 PSMA7 PSMA7 PSMA7 3019 0.14 0.43 YES
83 PPP2R1A PPP2R1A PPP2R1A 3098 0.14 0.43 YES
84 RPS27 RPS27 RPS27 3101 0.14 0.43 YES
85 PSMB4 PSMB4 PSMB4 3165 0.14 0.44 YES
86 RPS17 RPS17 RPS17 3174 0.14 0.44 YES
87 RPL10A RPL10A RPL10A 3194 0.14 0.44 YES
88 EXOSC7 EXOSC7 EXOSC7 3263 0.13 0.44 YES
89 RPL35A RPL35A RPL35A 3294 0.13 0.45 YES
90 RPL5 RPL5 RPL5 3318 0.13 0.45 YES
91 RPS2 RPS2 RPS2 3321 0.13 0.46 YES
92 RPL19 RPL19 RPL19 3328 0.13 0.46 YES
93 RPS18 RPS18 RPS18 3372 0.13 0.46 YES
94 PSMC4 PSMC4 PSMC4 3410 0.13 0.46 YES
95 RBM8A RBM8A RBM8A 3423 0.13 0.47 YES
96 RPL10 RPL10 RPL10 3490 0.12 0.47 YES
97 RPL6 RPL6 RPL6 3500 0.12 0.47 YES
98 RPL15 RPL15 RPL15 3597 0.12 0.47 YES
99 RPLP1 RPLP1 RPLP1 3700 0.11 0.47 YES
100 MAPK11 MAPK11 MAPK11 3737 0.11 0.47 YES
101 PSMA2 PSMA2 PSMA2 3742 0.11 0.48 YES
102 MAGOH MAGOH MAGOH 3747 0.11 0.48 YES
103 RPS23 RPS23 RPS23 3881 0.11 0.48 YES
104 YWHAB YWHAB YWHAB 3982 0.1 0.48 YES
105 PSMD10 PSMD10 PSMD10 4023 0.1 0.48 YES
106 RPL4 RPL4 RPL4 4085 0.099 0.48 YES
107 RPL26 RPL26 RPL26 4099 0.099 0.48 YES
108 DCP1B DCP1B DCP1B 4163 0.096 0.48 YES
109 RPLP0 RPLP0 RPLP0 4172 0.096 0.48 YES
110 PSMD8 PSMD8 PSMD8 4223 0.094 0.48 YES
111 UPF3B UPF3B UPF3B 4228 0.094 0.49 YES
112 PSMA4 PSMA4 PSMA4 4241 0.094 0.49 YES
113 PSME2 PSME2 PSME2 4314 0.091 0.49 NO
114 LSM1 LSM1 LSM1 4468 0.086 0.48 NO
115 NCBP2 NCBP2 NCBP2 4567 0.082 0.48 NO
116 PSMA6 PSMA6 PSMA6 4591 0.081 0.48 NO
117 EXOSC6 EXOSC6 EXOSC6 4680 0.079 0.48 NO
118 EXOSC1 EXOSC1 EXOSC1 4799 0.074 0.48 NO
119 RPL17 RPL17 RPL17 4891 0.071 0.47 NO
120 PSMA5 PSMA5 PSMA5 4925 0.07 0.47 NO
121 CNOT10 CNOT10 CNOT10 4943 0.069 0.47 NO
122 EXOSC2 EXOSC2 EXOSC2 5006 0.067 0.47 NO
123 PSMB5 PSMB5 PSMB5 5071 0.065 0.47 NO
124 ANP32A ANP32A ANP32A 5106 0.064 0.47 NO
125 PSMD6 PSMD6 PSMD6 5107 0.064 0.48 NO
126 C2orf29 C2orf29 C2orf29 5329 0.058 0.46 NO
127 PSMA3 PSMA3 PSMA3 5408 0.056 0.46 NO
128 PSMD7 PSMD7 PSMD7 5438 0.055 0.46 NO
129 PPP2R2A PPP2R2A PPP2R2A 5463 0.054 0.46 NO
130 PSMC2 PSMC2 PSMC2 5503 0.053 0.46 NO
131 XPO1 XPO1 XPO1 5529 0.052 0.46 NO
132 PPP2CA PPP2CA PPP2CA 5628 0.049 0.46 NO
133 RPL3 RPL3 RPL3 5665 0.048 0.46 NO
134 PSME1 PSME1 PSME1 5670 0.048 0.46 NO
135 PSMB9 PSMB9 PSMB9 5747 0.045 0.46 NO
136 ELAVL1 ELAVL1 ELAVL1 5763 0.045 0.46 NO
137 EXOSC3 EXOSC3 EXOSC3 5764 0.044 0.46 NO
138 EIF4B EIF4B EIF4B 5793 0.044 0.46 NO
139 RNPS1 RNPS1 RNPS1 5886 0.041 0.46 NO
140 PSMF1 PSMF1 PSMF1 5919 0.04 0.46 NO
141 PSMB2 PSMB2 PSMB2 5987 0.038 0.45 NO
142 PSMD1 PSMD1 PSMD1 5991 0.038 0.45 NO
143 PSMC6 PSMC6 PSMC6 6053 0.036 0.45 NO
144 EXOSC9 EXOSC9 EXOSC9 6134 0.034 0.45 NO
145 EDC4 EDC4 EDC4 6142 0.033 0.45 NO
146 ZFP36L1 ZFP36L1 ZFP36L1 6213 0.031 0.45 NO
147 PSMA1 PSMA1 PSMA1 6293 0.028 0.44 NO
148 RPS28 RPS28 RPS28 6298 0.028 0.44 NO
149 LSM6 LSM6 LSM6 6417 0.024 0.44 NO
150 EXOSC8 EXOSC8 EXOSC8 6566 0.02 0.43 NO
151 RPS26 RPS26 RPS26 6567 0.02 0.43 NO
152 EIF4A1 EIF4A1 EIF4A1 6583 0.02 0.43 NO
153 CNOT7 CNOT7 CNOT7 6702 0.016 0.42 NO
154 HNRNPD HNRNPD HNRNPD 6725 0.016 0.42 NO
155 SMG5 SMG5 SMG5 6772 0.014 0.42 NO
156 PSMD14 PSMD14 PSMD14 6775 0.014 0.42 NO
157 EDC3 EDC3 EDC3 6807 0.013 0.42 NO
158 DCP2 DCP2 DCP2 6885 0.011 0.42 NO
159 PSMD11 PSMD11 PSMD11 6897 0.01 0.42 NO
160 PSMB8 PSMB8 PSMB8 6918 0.0098 0.42 NO
161 CNOT2 CNOT2 CNOT2 7007 0.0072 0.41 NO
162 PRKCD PRKCD PRKCD 7083 0.0049 0.41 NO
163 CNOT3 CNOT3 CNOT3 7297 -0.0013 0.4 NO
164 YWHAZ YWHAZ YWHAZ 7331 -0.0022 0.39 NO
165 PABPC1 PABPC1 PABPC1 7683 -0.013 0.37 NO
166 HSPA8 HSPA8 HSPA8 7713 -0.014 0.37 NO
167 PSMD2 PSMD2 PSMD2 7817 -0.017 0.37 NO
168 SMG6 SMG6 SMG6 7969 -0.022 0.36 NO
169 MAPKAPK2 MAPKAPK2 MAPKAPK2 8043 -0.024 0.36 NO
170 DDX6 DDX6 DDX6 8145 -0.028 0.35 NO
171 PSMD3 PSMD3 PSMD3 8202 -0.029 0.35 NO
172 CASC3 CASC3 CASC3 8455 -0.036 0.34 NO
173 EIF4E EIF4E EIF4E 8492 -0.037 0.34 NO
174 KHSRP KHSRP KHSRP 8535 -0.038 0.33 NO
175 PSME4 PSME4 PSME4 8570 -0.039 0.33 NO
176 EIF4A3 EIF4A3 EIF4A3 8614 -0.041 0.33 NO
177 ETF1 ETF1 ETF1 8791 -0.046 0.32 NO
178 SMG7 SMG7 SMG7 8949 -0.052 0.32 NO
179 PAIP1 PAIP1 PAIP1 9005 -0.053 0.32 NO
180 PSMA8 PSMA8 PSMA8 9025 -0.054 0.32 NO
181 MAPK14 MAPK14 MAPK14 9146 -0.058 0.31 NO
182 NCBP1 NCBP1 NCBP1 9240 -0.061 0.31 NO
183 NUP214 NUP214 NUP214 9409 -0.066 0.3 NO
184 PSMD12 PSMD12 PSMD12 9660 -0.074 0.29 NO
185 CNOT8 CNOT8 CNOT8 9975 -0.084 0.28 NO
186 EIF4A2 EIF4A2 EIF4A2 10058 -0.086 0.27 NO
187 TNKS1BP1 TNKS1BP1 TNKS1BP1 10215 -0.091 0.27 NO
188 UPF3A UPF3A UPF3A 10306 -0.094 0.27 NO
189 TNPO1 TNPO1 TNPO1 10479 -0.1 0.26 NO
190 DIS3 DIS3 DIS3 10675 -0.1 0.25 NO
191 CNOT4 CNOT4 CNOT4 10893 -0.11 0.24 NO
192 RPS4Y1 RPS4Y1 RPS4Y1 11175 -0.12 0.23 NO
193 CNOT6 CNOT6 CNOT6 11669 -0.14 0.21 NO
194 DCP1A DCP1A DCP1A 11865 -0.14 0.2 NO
195 EIF4G1 EIF4G1 EIF4G1 11885 -0.14 0.21 NO
196 AKT1 AKT1 AKT1 12074 -0.15 0.2 NO
197 RPL26L1 RPL26L1 RPL26L1 12727 -0.18 0.17 NO
198 FAM153A FAM153A FAM153A 13059 -0.19 0.16 NO
199 PSMD5 PSMD5 PSMD5 13209 -0.2 0.16 NO
200 SMG1 SMG1 SMG1 13566 -0.21 0.15 NO
201 PRKCA PRKCA PRKCA 14286 -0.25 0.11 NO
202 TNFSF13 TNFSF13 TNFSF13 14495 -0.26 0.11 NO
203 PATL1 PATL1 PATL1 14532 -0.26 0.12 NO
204 UPF2 UPF2 UPF2 14728 -0.28 0.12 NO
205 HSPA1B HSPA1B HSPA1B 14796 -0.28 0.12 NO
206 ZFP36 ZFP36 ZFP36 15314 -0.32 0.11 NO
207 XRN1 XRN1 XRN1 15645 -0.35 0.1 NO
208 RQCD1 RQCD1 RQCD1 16298 -0.43 0.078 NO

Figure S89.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME TRANSLATION.

Figure S90.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME TRANSLATION, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: REACTOME FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX

Table S46.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 RPL21 RPL21 RPL21 4 0.85 0.051 YES
2 RPL9 RPL9 RPL9 200 0.51 0.07 YES
3 RPL39 RPL39 RPL39 278 0.46 0.093 YES
4 RPSAP9 RPSAP9 RPSAP9 985 0.28 0.07 YES
5 RPL36 RPL36 RPL36 1156 0.26 0.076 YES
6 RPLP2 RPLP2 RPLP2 1353 0.24 0.079 YES
7 RPL35 RPL35 RPL35 1413 0.24 0.09 YES
8 RPL38 RPL38 RPL38 1457 0.24 0.1 YES
9 RPL13 RPL13 RPL13 1464 0.23 0.12 YES
10 RPS15 RPS15 RPS15 1518 0.23 0.12 YES
11 RPS19 RPS19 RPS19 1618 0.22 0.13 YES
12 RPS21 RPS21 RPS21 1640 0.22 0.14 YES
13 RPL27A RPL27A RPL27A 1733 0.21 0.15 YES
14 RPS29 RPS29 RPS29 1790 0.21 0.16 YES
15 RPL34 RPL34 RPL34 1797 0.21 0.17 YES
16 RPL18 RPL18 RPL18 1832 0.21 0.18 YES
17 RPS10 RPS10 RPS10 1864 0.2 0.2 YES
18 RPL28 RPL28 RPL28 1867 0.2 0.21 YES
19 RPL37 RPL37 RPL37 1876 0.2 0.22 YES
20 RPL23 RPL23 RPL23 1880 0.2 0.23 YES
21 RPL24 RPL24 RPL24 1895 0.2 0.24 YES
22 RPL37A RPL37A RPL37A 1898 0.2 0.25 YES
23 UBA52 UBA52 UBA52 1899 0.2 0.26 YES
24 RPL18A RPL18A RPL18A 1923 0.2 0.28 YES
25 RPL23A RPL23A RPL23A 1936 0.2 0.29 YES
26 RPS15A RPS15A RPS15A 1942 0.2 0.3 YES
27 RPS7 RPS7 RPS7 1967 0.2 0.31 YES
28 RPS4X RPS4X RPS4X 1982 0.2 0.32 YES
29 FAU FAU FAU 1984 0.2 0.33 YES
30 RPS27A RPS27A RPS27A 2012 0.2 0.34 YES
31 RPL11 RPL11 RPL11 2136 0.19 0.35 YES
32 RPS5 RPS5 RPS5 2175 0.18 0.36 YES
33 RPL30 RPL30 RPL30 2207 0.18 0.36 YES
34 RPS9 RPS9 RPS9 2232 0.18 0.37 YES
35 RPL8 RPL8 RPL8 2296 0.18 0.38 YES
36 RPS3A RPS3A RPS3A 2330 0.18 0.39 YES
37 RPL31 RPL31 RPL31 2333 0.18 0.4 YES
38 RPS11 RPS11 RPS11 2416 0.17 0.4 YES
39 RPS3 RPS3 RPS3 2452 0.17 0.41 YES
40 RPL7 RPL7 RPL7 2470 0.17 0.42 YES
41 RPL12 RPL12 RPL12 2502 0.17 0.43 YES
42 RPS16 RPS16 RPS16 2569 0.16 0.44 YES
43 RPS12 RPS12 RPS12 2570 0.16 0.45 YES
44 RPL32 RPL32 RPL32 2573 0.16 0.46 YES
45 RPL7A RPL7A RPL7A 2586 0.16 0.46 YES
46 RPL29 RPL29 RPL29 2618 0.16 0.47 YES
47 SEC61G SEC61G SEC61G 2661 0.16 0.48 YES
48 RPS20 RPS20 RPS20 2665 0.16 0.49 YES
49 RPL14 RPL14 RPL14 2753 0.16 0.49 YES
50 RPS6 RPS6 RPS6 2769 0.16 0.5 YES
51 RPL41 RPL41 RPL41 2793 0.15 0.51 YES
52 RPL27 RPL27 RPL27 2798 0.15 0.52 YES
53 RPS24 RPS24 RPS24 2807 0.15 0.53 YES
54 SSR4 SSR4 SSR4 2809 0.15 0.54 YES
55 RPL36A RPL36A RPL36A 2811 0.15 0.55 YES
56 RPS25 RPS25 RPS25 2831 0.15 0.55 YES
57 RPS13 RPS13 RPS13 2852 0.15 0.56 YES
58 RPSA RPSA RPSA 2869 0.15 0.57 YES
59 RPS8 RPS8 RPS8 2881 0.15 0.58 YES
60 RPS14 RPS14 RPS14 2902 0.15 0.58 YES
61 RPL22 RPL22 RPL22 2984 0.14 0.59 YES
62 RPL13A RPL13A RPL13A 3013 0.14 0.6 YES
63 RPS27 RPS27 RPS27 3101 0.14 0.6 YES
64 RPS17 RPS17 RPS17 3174 0.14 0.6 YES
65 RPL10A RPL10A RPL10A 3194 0.14 0.61 YES
66 RPL35A RPL35A RPL35A 3294 0.13 0.61 YES
67 RPL5 RPL5 RPL5 3318 0.13 0.62 YES
68 RPS2 RPS2 RPS2 3321 0.13 0.63 YES
69 RPL19 RPL19 RPL19 3328 0.13 0.63 YES
70 RPS18 RPS18 RPS18 3372 0.13 0.64 YES
71 RPL10 RPL10 RPL10 3490 0.12 0.64 YES
72 RPL6 RPL6 RPL6 3500 0.12 0.65 YES
73 RPL15 RPL15 RPL15 3597 0.12 0.65 YES
74 RPLP1 RPLP1 RPLP1 3700 0.11 0.65 YES
75 SSR2 SSR2 SSR2 3838 0.11 0.65 YES
76 RPS23 RPS23 RPS23 3881 0.11 0.65 YES
77 RPL4 RPL4 RPL4 4085 0.099 0.65 YES
78 RPL26 RPL26 RPL26 4099 0.099 0.65 YES
79 RPLP0 RPLP0 RPLP0 4172 0.096 0.65 YES
80 RPN2 RPN2 RPN2 4333 0.091 0.65 NO
81 SEC61B SEC61B SEC61B 4733 0.077 0.63 NO
82 SRP19 SRP19 SRP19 4852 0.072 0.63 NO
83 RPL17 RPL17 RPL17 4891 0.071 0.63 NO
84 SEC11C SEC11C SEC11C 5251 0.06 0.61 NO
85 SRP9 SRP9 SRP9 5535 0.052 0.6 NO
86 RPL3 RPL3 RPL3 5665 0.048 0.6 NO
87 RPS28 RPS28 RPS28 6298 0.028 0.56 NO
88 SRP14 SRP14 SRP14 6428 0.024 0.56 NO
89 RPS26 RPS26 RPS26 6567 0.02 0.55 NO
90 SPCS1 SPCS1 SPCS1 6593 0.02 0.55 NO
91 RPN1 RPN1 RPN1 6837 0.012 0.54 NO
92 SPCS2 SPCS2 SPCS2 7284 -0.00092 0.51 NO
93 SEC61A1 SEC61A1 SEC61A1 7351 -0.0027 0.51 NO
94 SRPR SRPR SRPR 7397 -0.0042 0.5 NO
95 SEC11A SEC11A SEC11A 7445 -0.0059 0.5 NO
96 SSR3 SSR3 SSR3 7556 -0.0088 0.5 NO
97 LOC653566 LOC653566 LOC653566 7623 -0.011 0.49 NO
98 SRPRB SRPRB SRPRB 7724 -0.014 0.49 NO
99 SRP68 SRP68 SRP68 7920 -0.02 0.48 NO
100 DDOST DDOST DDOST 8326 -0.033 0.46 NO
101 SSR1 SSR1 SSR1 9421 -0.067 0.4 NO
102 SRP72 SRP72 SRP72 9454 -0.068 0.4 NO
103 SRP54 SRP54 SRP54 9899 -0.082 0.38 NO
104 TRAM1 TRAM1 TRAM1 10033 -0.086 0.38 NO
105 SPCS3 SPCS3 SPCS3 10211 -0.091 0.37 NO
106 RPS4Y1 RPS4Y1 RPS4Y1 11175 -0.12 0.33 NO
107 RPL26L1 RPL26L1 RPL26L1 12727 -0.18 0.25 NO
108 FAM153A FAM153A FAM153A 13059 -0.19 0.24 NO
109 SEC61A2 SEC61A2 SEC61A2 15762 -0.36 0.11 NO

Figure S91.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX.

Figure S92.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: REACTOME TCA CYCLE AND RESPIRATORY ELECTRON TRANSPORT

Table S47.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 RPL21 RPL21 RPL21 4 0.85 0.05 YES
2 RPL9 RPL9 RPL9 200 0.51 0.069 YES
3 RPL39 RPL39 RPL39 278 0.46 0.092 YES
4 RPSAP9 RPSAP9 RPSAP9 985 0.28 0.068 YES
5 RPL36 RPL36 RPL36 1156 0.26 0.074 YES
6 RPLP2 RPLP2 RPLP2 1353 0.24 0.077 YES
7 RPL35 RPL35 RPL35 1413 0.24 0.088 YES
8 RPL38 RPL38 RPL38 1457 0.24 0.099 YES
9 RPL13 RPL13 RPL13 1464 0.23 0.11 YES
10 RPS15 RPS15 RPS15 1518 0.23 0.12 YES
11 RPS19 RPS19 RPS19 1618 0.22 0.13 YES
12 RPS21 RPS21 RPS21 1640 0.22 0.14 YES
13 RPL27A RPL27A RPL27A 1733 0.21 0.15 YES
14 RPS29 RPS29 RPS29 1790 0.21 0.16 YES
15 RPL34 RPL34 RPL34 1797 0.21 0.17 YES
16 RPL18 RPL18 RPL18 1832 0.21 0.18 YES
17 RPS10 RPS10 RPS10 1864 0.2 0.19 YES
18 RPL28 RPL28 RPL28 1867 0.2 0.2 YES
19 RPL37 RPL37 RPL37 1876 0.2 0.22 YES
20 RPL23 RPL23 RPL23 1880 0.2 0.23 YES
21 RPL24 RPL24 RPL24 1895 0.2 0.24 YES
22 RPL37A RPL37A RPL37A 1898 0.2 0.25 YES
23 UBA52 UBA52 UBA52 1899 0.2 0.26 YES
24 RPL18A RPL18A RPL18A 1923 0.2 0.27 YES
25 RPL23A RPL23A RPL23A 1936 0.2 0.28 YES
26 RPS15A RPS15A RPS15A 1942 0.2 0.29 YES
27 RPS7 RPS7 RPS7 1967 0.2 0.3 YES
28 RPS4X RPS4X RPS4X 1982 0.2 0.32 YES
29 FAU FAU FAU 1984 0.2 0.33 YES
30 RPS27A RPS27A RPS27A 2012 0.2 0.34 YES
31 RPL11 RPL11 RPL11 2136 0.19 0.34 YES
32 RPS5 RPS5 RPS5 2175 0.18 0.35 YES
33 RPL30 RPL30 RPL30 2207 0.18 0.36 YES
34 RPS9 RPS9 RPS9 2232 0.18 0.37 YES
35 RPL8 RPL8 RPL8 2296 0.18 0.37 YES
36 RPS3A RPS3A RPS3A 2330 0.18 0.38 YES
37 RPL31 RPL31 RPL31 2333 0.18 0.39 YES
38 RPS11 RPS11 RPS11 2416 0.17 0.4 YES
39 RPS3 RPS3 RPS3 2452 0.17 0.41 YES
40 RPL7 RPL7 RPL7 2470 0.17 0.42 YES
41 RPL12 RPL12 RPL12 2502 0.17 0.42 YES
42 GSPT2 GSPT2 GSPT2 2505 0.17 0.43 YES
43 RPS16 RPS16 RPS16 2569 0.16 0.44 YES
44 RPS12 RPS12 RPS12 2570 0.16 0.45 YES
45 RPL32 RPL32 RPL32 2573 0.16 0.46 YES
46 RPL7A RPL7A RPL7A 2586 0.16 0.47 YES
47 RPL29 RPL29 RPL29 2618 0.16 0.48 YES
48 RPS20 RPS20 RPS20 2665 0.16 0.48 YES
49 RPL14 RPL14 RPL14 2753 0.16 0.49 YES
50 RPS6 RPS6 RPS6 2769 0.16 0.49 YES
51 RPL41 RPL41 RPL41 2793 0.15 0.5 YES
52 RPL27 RPL27 RPL27 2798 0.15 0.51 YES
53 RPS24 RPS24 RPS24 2807 0.15 0.52 YES
54 RPL36A RPL36A RPL36A 2811 0.15 0.53 YES
55 RPS25 RPS25 RPS25 2831 0.15 0.54 YES
56 RPS13 RPS13 RPS13 2852 0.15 0.54 YES
57 RPSA RPSA RPSA 2869 0.15 0.55 YES
58 RPS8 RPS8 RPS8 2881 0.15 0.56 YES
59 RPS14 RPS14 RPS14 2902 0.15 0.57 YES
60 RPL22 RPL22 RPL22 2984 0.14 0.57 YES
61 RPL13A RPL13A RPL13A 3013 0.14 0.58 YES
62 PPP2R1A PPP2R1A PPP2R1A 3098 0.14 0.58 YES
63 RPS27 RPS27 RPS27 3101 0.14 0.59 YES
64 RPS17 RPS17 RPS17 3174 0.14 0.59 YES
65 RPL10A RPL10A RPL10A 3194 0.14 0.6 YES
66 RPL35A RPL35A RPL35A 3294 0.13 0.6 YES
67 RPL5 RPL5 RPL5 3318 0.13 0.61 YES
68 RPS2 RPS2 RPS2 3321 0.13 0.62 YES
69 RPL19 RPL19 RPL19 3328 0.13 0.62 YES
70 RPS18 RPS18 RPS18 3372 0.13 0.63 YES
71 RBM8A RBM8A RBM8A 3423 0.13 0.63 YES
72 RPL10 RPL10 RPL10 3490 0.12 0.64 YES
73 RPL6 RPL6 RPL6 3500 0.12 0.64 YES
74 RPL15 RPL15 RPL15 3597 0.12 0.64 YES
75 RPLP1 RPLP1 RPLP1 3700 0.11 0.65 YES
76 MAGOH MAGOH MAGOH 3747 0.11 0.65 YES
77 RPS23 RPS23 RPS23 3881 0.11 0.65 YES
78 RPL4 RPL4 RPL4 4085 0.099 0.64 YES
79 RPL26 RPL26 RPL26 4099 0.099 0.65 YES
80 RPLP0 RPLP0 RPLP0 4172 0.096 0.65 YES
81 UPF3B UPF3B UPF3B 4228 0.094 0.65 YES
82 NCBP2 NCBP2 NCBP2 4567 0.082 0.64 NO
83 RPL17 RPL17 RPL17 4891 0.071 0.62 NO
84 PPP2R2A PPP2R2A PPP2R2A 5463 0.054 0.59 NO
85 PPP2CA PPP2CA PPP2CA 5628 0.049 0.59 NO
86 RPL3 RPL3 RPL3 5665 0.048 0.59 NO
87 RNPS1 RNPS1 RNPS1 5886 0.041 0.58 NO
88 RPS28 RPS28 RPS28 6298 0.028 0.56 NO
89 RPS26 RPS26 RPS26 6567 0.02 0.54 NO
90 SMG5 SMG5 SMG5 6772 0.014 0.53 NO
91 PABPC1 PABPC1 PABPC1 7683 -0.013 0.48 NO
92 SMG6 SMG6 SMG6 7969 -0.022 0.47 NO
93 CASC3 CASC3 CASC3 8455 -0.036 0.44 NO
94 EIF4A3 EIF4A3 EIF4A3 8614 -0.041 0.43 NO
95 ETF1 ETF1 ETF1 8791 -0.046 0.43 NO
96 SMG7 SMG7 SMG7 8949 -0.052 0.42 NO
97 NCBP1 NCBP1 NCBP1 9240 -0.061 0.41 NO
98 UPF3A UPF3A UPF3A 10306 -0.094 0.35 NO
99 RPS4Y1 RPS4Y1 RPS4Y1 11175 -0.12 0.31 NO
100 EIF4G1 EIF4G1 EIF4G1 11885 -0.14 0.28 NO
101 RPL26L1 RPL26L1 RPL26L1 12727 -0.18 0.24 NO
102 FAM153A FAM153A FAM153A 13059 -0.19 0.23 NO
103 SMG1 SMG1 SMG1 13566 -0.21 0.22 NO
104 UPF2 UPF2 UPF2 14728 -0.28 0.17 NO

Figure S93.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME TCA CYCLE AND RESPIRATORY ELECTRON TRANSPORT.

Figure S94.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME TCA CYCLE AND RESPIRATORY ELECTRON TRANSPORT, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE

Table S48.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PSMB3 PSMB3 PSMB3 1333 0.24 -0.034 YES
2 PSMC1 PSMC1 PSMC1 1732 0.21 -0.021 YES
3 UBA52 UBA52 UBA52 1899 0.2 0.0039 YES
4 RPS27A RPS27A RPS27A 2012 0.2 0.03 YES
5 PSMD4 PSMD4 PSMD4 2195 0.18 0.051 YES
6 PSMC5 PSMC5 PSMC5 2418 0.17 0.067 YES
7 PSMB10 PSMB10 PSMB10 2441 0.17 0.095 YES
8 PSMB6 PSMB6 PSMB6 2513 0.17 0.12 YES
9 PSMD9 PSMD9 PSMD9 2535 0.16 0.15 YES
10 PSMD13 PSMD13 PSMD13 2538 0.16 0.17 YES
11 PSMB7 PSMB7 PSMB7 2564 0.16 0.2 YES
12 PSMC3 PSMC3 PSMC3 2595 0.16 0.23 YES
13 PSMB1 PSMB1 PSMB1 2926 0.15 0.23 YES
14 PSMA7 PSMA7 PSMA7 3019 0.14 0.25 YES
15 PSMB4 PSMB4 PSMB4 3165 0.14 0.26 YES
16 NFKBIB NFKBIB NFKBIB 3308 0.13 0.28 YES
17 NFKBIE NFKBIE NFKBIE 3334 0.13 0.3 YES
18 PSMC4 PSMC4 PSMC4 3410 0.13 0.32 YES
19 PSMA2 PSMA2 PSMA2 3742 0.11 0.32 YES
20 SKP1 SKP1 SKP1 3973 0.1 0.32 YES
21 PSMD10 PSMD10 PSMD10 4023 0.1 0.34 YES
22 PSMD8 PSMD8 PSMD8 4223 0.094 0.34 YES
23 PSMA4 PSMA4 PSMA4 4241 0.094 0.36 YES
24 PSME2 PSME2 PSME2 4314 0.091 0.37 YES
25 PSMA6 PSMA6 PSMA6 4591 0.081 0.36 YES
26 PSMA5 PSMA5 PSMA5 4925 0.07 0.36 YES
27 PSMB5 PSMB5 PSMB5 5071 0.065 0.36 YES
28 PSMD6 PSMD6 PSMD6 5107 0.064 0.37 YES
29 PSMA3 PSMA3 PSMA3 5408 0.056 0.36 YES
30 PSMD7 PSMD7 PSMD7 5438 0.055 0.37 YES
31 PSMC2 PSMC2 PSMC2 5503 0.053 0.37 YES
32 BCL10 BCL10 BCL10 5640 0.049 0.38 YES
33 PSME1 PSME1 PSME1 5670 0.048 0.38 YES
34 MALT1 MALT1 MALT1 5693 0.047 0.39 YES
35 PSMB9 PSMB9 PSMB9 5747 0.045 0.39 YES
36 PSMF1 PSMF1 PSMF1 5919 0.04 0.39 YES
37 IKBKG IKBKG IKBKG 5954 0.039 0.39 YES
38 PSMB2 PSMB2 PSMB2 5987 0.038 0.4 YES
39 PSMD1 PSMD1 PSMD1 5991 0.038 0.4 YES
40 PSMC6 PSMC6 PSMC6 6053 0.036 0.41 YES
41 PSMA1 PSMA1 PSMA1 6293 0.028 0.4 NO
42 NFKBIA NFKBIA NFKBIA 6464 0.023 0.39 NO
43 REL REL REL 6507 0.022 0.4 NO
44 PSMD14 PSMD14 PSMD14 6775 0.014 0.38 NO
45 PSMD11 PSMD11 PSMD11 6897 0.01 0.38 NO
46 PSMB8 PSMB8 PSMB8 6918 0.0098 0.38 NO
47 RELA RELA RELA 7751 -0.015 0.33 NO
48 PSMD2 PSMD2 PSMD2 7817 -0.017 0.33 NO
49 MAP3K7 MAP3K7 MAP3K7 8040 -0.024 0.32 NO
50 PSMD3 PSMD3 PSMD3 8202 -0.029 0.32 NO
51 PSME4 PSME4 PSME4 8570 -0.039 0.3 NO
52 PSMA8 PSMA8 PSMA8 9025 -0.054 0.29 NO
53 PSMD12 PSMD12 PSMD12 9660 -0.074 0.26 NO
54 PRKCB PRKCB PRKCB 10104 -0.088 0.25 NO
55 FBXW11 FBXW11 FBXW11 10181 -0.09 0.26 NO
56 IKBKB IKBKB IKBKB 11233 -0.12 0.23 NO
57 CARD11 CARD11 CARD11 11581 -0.14 0.23 NO
58 CUL1 CUL1 CUL1 11853 -0.14 0.24 NO
59 BTRC BTRC BTRC 12493 -0.17 0.23 NO
60 CHUK CHUK CHUK 12761 -0.18 0.24 NO
61 PSMD5 PSMD5 PSMD5 13209 -0.2 0.25 NO

Figure S95.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE.

Figure S96.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: REACTOME ACTIVATION OF NF KAPPAB IN B CELLS

Table S49.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 RPL21 RPL21 RPL21 4 0.85 0.048 YES
2 RPL9 RPL9 RPL9 200 0.51 0.066 YES
3 RPL39 RPL39 RPL39 278 0.46 0.088 YES
4 RPSAP9 RPSAP9 RPSAP9 985 0.28 0.064 YES
5 RPL36 RPL36 RPL36 1156 0.26 0.069 YES
6 EIF3K EIF3K EIF3K 1233 0.26 0.079 YES
7 RPLP2 RPLP2 RPLP2 1353 0.24 0.086 YES
8 RPL35 RPL35 RPL35 1413 0.24 0.096 YES
9 RPL38 RPL38 RPL38 1457 0.24 0.11 YES
10 RPL13 RPL13 RPL13 1464 0.23 0.12 YES
11 RPS15 RPS15 RPS15 1518 0.23 0.13 YES
12 RPS19 RPS19 RPS19 1618 0.22 0.14 YES
13 RPS21 RPS21 RPS21 1640 0.22 0.15 YES
14 RPL27A RPL27A RPL27A 1733 0.21 0.16 YES
15 RPS29 RPS29 RPS29 1790 0.21 0.16 YES
16 RPL34 RPL34 RPL34 1797 0.21 0.18 YES
17 RPL18 RPL18 RPL18 1832 0.21 0.18 YES
18 RPS10 RPS10 RPS10 1864 0.2 0.2 YES
19 RPL28 RPL28 RPL28 1867 0.2 0.21 YES
20 RPL37 RPL37 RPL37 1876 0.2 0.22 YES
21 RPL23 RPL23 RPL23 1880 0.2 0.23 YES
22 RPL24 RPL24 RPL24 1895 0.2 0.24 YES
23 RPL37A RPL37A RPL37A 1898 0.2 0.25 YES
24 UBA52 UBA52 UBA52 1899 0.2 0.26 YES
25 RPL18A RPL18A RPL18A 1923 0.2 0.27 YES
26 RPL23A RPL23A RPL23A 1936 0.2 0.28 YES
27 RPS15A RPS15A RPS15A 1942 0.2 0.29 YES
28 EIF3F EIF3F EIF3F 1943 0.2 0.3 YES
29 RPS7 RPS7 RPS7 1967 0.2 0.32 YES
30 RPS4X RPS4X RPS4X 1982 0.2 0.32 YES
31 FAU FAU FAU 1984 0.2 0.34 YES
32 RPS27A RPS27A RPS27A 2012 0.2 0.35 YES
33 RPL11 RPL11 RPL11 2136 0.19 0.35 YES
34 RPS5 RPS5 RPS5 2175 0.18 0.36 YES
35 EIF3G EIF3G EIF3G 2184 0.18 0.37 YES
36 RPL30 RPL30 RPL30 2207 0.18 0.38 YES
37 RPS9 RPS9 RPS9 2232 0.18 0.39 YES
38 RPL8 RPL8 RPL8 2296 0.18 0.39 YES
39 RPS3A RPS3A RPS3A 2330 0.18 0.4 YES
40 RPL31 RPL31 RPL31 2333 0.18 0.41 YES
41 RPS11 RPS11 RPS11 2416 0.17 0.42 YES
42 RPS3 RPS3 RPS3 2452 0.17 0.42 YES
43 RPL7 RPL7 RPL7 2470 0.17 0.43 YES
44 RPL12 RPL12 RPL12 2502 0.17 0.44 YES
45 RPS16 RPS16 RPS16 2569 0.16 0.44 YES
46 RPS12 RPS12 RPS12 2570 0.16 0.45 YES
47 RPL32 RPL32 RPL32 2573 0.16 0.46 YES
48 RPL7A RPL7A RPL7A 2586 0.16 0.47 YES
49 RPL29 RPL29 RPL29 2618 0.16 0.48 YES
50 RPS20 RPS20 RPS20 2665 0.16 0.48 YES
51 RPL14 RPL14 RPL14 2753 0.16 0.49 YES
52 RPS6 RPS6 RPS6 2769 0.16 0.5 YES
53 RPL41 RPL41 RPL41 2793 0.15 0.5 YES
54 RPL27 RPL27 RPL27 2798 0.15 0.51 YES
55 RPS24 RPS24 RPS24 2807 0.15 0.52 YES
56 RPL36A RPL36A RPL36A 2811 0.15 0.53 YES
57 RPS25 RPS25 RPS25 2831 0.15 0.54 YES
58 RPS13 RPS13 RPS13 2852 0.15 0.55 YES
59 RPSA RPSA RPSA 2869 0.15 0.55 YES
60 RPS8 RPS8 RPS8 2881 0.15 0.56 YES
61 RPS14 RPS14 RPS14 2902 0.15 0.57 YES
62 RPL22 RPL22 RPL22 2984 0.14 0.57 YES
63 RPL13A RPL13A RPL13A 3013 0.14 0.58 YES
64 RPS27 RPS27 RPS27 3101 0.14 0.58 YES
65 RPS17 RPS17 RPS17 3174 0.14 0.58 YES
66 RPL10A RPL10A RPL10A 3194 0.14 0.59 YES
67 EIF2S2 EIF2S2 EIF2S2 3282 0.13 0.59 YES
68 RPL35A RPL35A RPL35A 3294 0.13 0.6 YES
69 EIF3H EIF3H EIF3H 3297 0.13 0.61 YES
70 RPL5 RPL5 RPL5 3318 0.13 0.61 YES
71 RPS2 RPS2 RPS2 3321 0.13 0.62 YES
72 RPL19 RPL19 RPL19 3328 0.13 0.63 YES
73 RPS18 RPS18 RPS18 3372 0.13 0.63 YES
74 RPL10 RPL10 RPL10 3490 0.12 0.63 YES
75 RPL6 RPL6 RPL6 3500 0.12 0.64 YES
76 RPL15 RPL15 RPL15 3597 0.12 0.64 YES
77 EIF3I EIF3I EIF3I 3609 0.12 0.65 YES
78 RPLP1 RPLP1 RPLP1 3700 0.11 0.65 YES
79 RPS23 RPS23 RPS23 3881 0.11 0.64 YES
80 EIF3D EIF3D EIF3D 3882 0.11 0.65 YES
81 EIF3B EIF3B EIF3B 4036 0.1 0.65 YES
82 RPL4 RPL4 RPL4 4085 0.099 0.65 YES
83 RPL26 RPL26 RPL26 4099 0.099 0.66 YES
84 RPLP0 RPLP0 RPLP0 4172 0.096 0.66 YES
85 EIF2S3 EIF2S3 EIF2S3 4346 0.09 0.65 NO
86 RPL17 RPL17 RPL17 4891 0.071 0.62 NO
87 EIF3E EIF3E EIF3E 4904 0.07 0.63 NO
88 EIF1AX EIF1AX EIF1AX 5586 0.05 0.59 NO
89 RPL3 RPL3 RPL3 5665 0.048 0.59 NO
90 EIF4B EIF4B EIF4B 5793 0.044 0.58 NO
91 EIF2S1 EIF2S1 EIF2S1 5946 0.039 0.58 NO
92 RPS28 RPS28 RPS28 6298 0.028 0.56 NO
93 RPS26 RPS26 RPS26 6567 0.02 0.55 NO
94 EIF4A1 EIF4A1 EIF4A1 6583 0.02 0.55 NO
95 PABPC1 PABPC1 PABPC1 7683 -0.013 0.48 NO
96 EIF4H EIF4H EIF4H 8332 -0.033 0.45 NO
97 EIF4E EIF4E EIF4E 8492 -0.037 0.44 NO
98 EIF3J EIF3J EIF3J 8672 -0.043 0.44 NO
99 EIF4A2 EIF4A2 EIF4A2 10058 -0.086 0.36 NO
100 RPS4Y1 RPS4Y1 RPS4Y1 11175 -0.12 0.3 NO
101 EIF3A EIF3A EIF3A 11880 -0.14 0.27 NO
102 EIF4G1 EIF4G1 EIF4G1 11885 -0.14 0.28 NO
103 RPL26L1 RPL26L1 RPL26L1 12727 -0.18 0.24 NO
104 FAM153A FAM153A FAM153A 13059 -0.19 0.24 NO
105 EIF3C EIF3C EIF3C 16658 -0.49 0.057 NO

Figure S97.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME ACTIVATION OF NF KAPPAB IN B CELLS.

Figure S98.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME ACTIVATION OF NF KAPPAB IN B CELLS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S

Table S50.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 ETFB ETFB ETFB 682 0.33 -0.012 YES
2 NDUFA13 NDUFA13 NDUFA13 792 0.31 0.0071 YES
3 NDUFS8 NDUFS8 NDUFS8 933 0.29 0.022 YES
4 NDUFA11 NDUFA11 NDUFA11 1024 0.28 0.04 YES
5 NDUFA3 NDUFA3 NDUFA3 1039 0.28 0.061 YES
6 NDUFB7 NDUFB7 NDUFB7 1044 0.28 0.083 YES
7 NDUFB1 NDUFB1 NDUFB1 1100 0.27 0.1 YES
8 ATP5D ATP5D ATP5D 1124 0.27 0.12 YES
9 ATP5O ATP5O ATP5O 1217 0.26 0.14 YES
10 NDUFS6 NDUFS6 NDUFS6 1237 0.26 0.16 YES
11 COX6B1 COX6B1 COX6B1 1340 0.24 0.17 YES
12 UQCRB UQCRB UQCRB 1443 0.24 0.18 YES
13 NDUFV3 NDUFV3 NDUFV3 1505 0.23 0.2 YES
14 NDUFS7 NDUFS7 NDUFS7 1535 0.23 0.22 YES
15 NDUFAB1 NDUFAB1 NDUFAB1 1549 0.23 0.23 YES
16 ATP5E ATP5E ATP5E 1616 0.22 0.25 YES
17 COX5B COX5B COX5B 1635 0.22 0.26 YES
18 NDUFA1 NDUFA1 NDUFA1 1670 0.22 0.28 YES
19 COX6C COX6C COX6C 1697 0.22 0.3 YES
20 UQCRQ UQCRQ UQCRQ 1707 0.22 0.31 YES
21 NDUFA2 NDUFA2 NDUFA2 1724 0.21 0.33 YES
22 NDUFA8 NDUFA8 NDUFA8 1773 0.21 0.34 YES
23 ATP5J ATP5J ATP5J 1809 0.21 0.36 YES
24 UQCR11 UQCR11 UQCR11 1908 0.2 0.37 YES
25 NDUFB10 NDUFB10 NDUFB10 1927 0.2 0.38 YES
26 ATP5I ATP5I ATP5I 1961 0.2 0.4 YES
27 UQCRHL UQCRHL UQCRHL 1964 0.2 0.41 YES
28 NDUFC2 NDUFC2 NDUFC2 1988 0.2 0.43 YES
29 UQCRH UQCRH UQCRH 2004 0.2 0.44 YES
30 ATP5L ATP5L ATP5L 2044 0.19 0.46 YES
31 COX4I1 COX4I1 COX4I1 2052 0.19 0.47 YES
32 NDUFS4 NDUFS4 NDUFS4 2070 0.19 0.48 YES
33 NDUFB9 NDUFB9 NDUFB9 2180 0.18 0.49 YES
34 NDUFV1 NDUFV1 NDUFV1 2262 0.18 0.5 YES
35 NDUFS3 NDUFS3 NDUFS3 2282 0.18 0.52 YES
36 NDUFC1 NDUFC1 NDUFC1 2391 0.17 0.52 YES
37 COX6A1 COX6A1 COX6A1 2407 0.17 0.54 YES
38 COX7C COX7C COX7C 2542 0.16 0.54 YES
39 NDUFB2 NDUFB2 NDUFB2 2565 0.16 0.56 YES
40 ATP5H ATP5H ATP5H 2707 0.16 0.56 YES
41 COX7B COX7B COX7B 2719 0.16 0.57 YES
42 COX8A COX8A COX8A 2744 0.16 0.58 YES
43 NDUFS5 NDUFS5 NDUFS5 2870 0.15 0.59 YES
44 NDUFA7 NDUFA7 NDUFA7 2877 0.15 0.6 YES
45 NDUFA9 NDUFA9 NDUFA9 2983 0.14 0.6 YES
46 ATP5G1 ATP5G1 ATP5G1 3106 0.14 0.61 YES
47 ATP5J2 ATP5J2 ATP5J2 3121 0.14 0.62 YES
48 NDUFB5 NDUFB5 NDUFB5 3316 0.13 0.62 YES
49 UQCRC1 UQCRC1 UQCRC1 3365 0.13 0.63 YES
50 NDUFA5 NDUFA5 NDUFA5 3406 0.13 0.64 YES
51 NDUFA4 NDUFA4 NDUFA4 3503 0.12 0.64 YES
52 COX5A COX5A COX5A 3586 0.12 0.64 YES
53 UQCRFS1 UQCRFS1 UQCRFS1 3618 0.12 0.65 YES
54 NDUFA6 NDUFA6 NDUFA6 3621 0.12 0.66 YES
55 NDUFB6 NDUFB6 NDUFB6 3624 0.12 0.67 YES
56 COX7A2L COX7A2L COX7A2L 3845 0.11 0.67 NO
57 NDUFB8 NDUFB8 NDUFB8 4089 0.099 0.66 NO
58 ATP5F1 ATP5F1 ATP5F1 4134 0.097 0.67 NO
59 NDUFV2 NDUFV2 NDUFV2 4209 0.095 0.67 NO
60 NDUFB3 NDUFB3 NDUFB3 4742 0.076 0.64 NO
61 NDUFA10 NDUFA10 NDUFA10 5207 0.062 0.62 NO
62 NDUFA12 NDUFA12 NDUFA12 5333 0.058 0.62 NO
63 NDUFS2 NDUFS2 NDUFS2 6211 0.031 0.57 NO
64 ATP5C1 ATP5C1 ATP5C1 6314 0.028 0.57 NO
65 CYCS CYCS CYCS 6389 0.025 0.57 NO
66 SDHB SDHB SDHB 6491 0.022 0.56 NO
67 CYC1 CYC1 CYC1 6495 0.022 0.57 NO
68 SDHC SDHC SDHC 6587 0.02 0.56 NO
69 ATP5B ATP5B ATP5B 6860 0.012 0.55 NO
70 NDUFB4 NDUFB4 NDUFB4 7271 -0.00053 0.52 NO
71 UCP2 UCP2 UCP2 7409 -0.0045 0.52 NO
72 SDHA SDHA SDHA 7733 -0.015 0.5 NO
73 UQCRC2 UQCRC2 UQCRC2 8306 -0.033 0.47 NO
74 ATP5A1 ATP5A1 ATP5A1 8489 -0.037 0.46 NO
75 SDHD SDHD SDHD 9823 -0.08 0.39 NO
76 ETFDH ETFDH ETFDH 9852 -0.08 0.4 NO
77 ETFA ETFA ETFA 10095 -0.087 0.39 NO
78 NDUFS1 NDUFS1 NDUFS1 13097 -0.19 0.24 NO
79 UCP3 UCP3 UCP3 14912 -0.29 0.16 NO

Figure S99.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S.

Figure S100.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Fold change

For the top enriched genes, if you want to check whether they are

Expression level

For the top enriched genes, if you want to check whether they are

An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap

Significant gene list

For the top enriched genes, if you want to check whether they are

Subtype clus6 enriched pathways

Table 8.  Get Full Table This table shows top 10 pathways which are significantly enriched in cluster clus6. It displays only significant gene sets satisfying nom.p.val.threshold (-1), fwer.p.val.threshold (-1) , fdr.q.val.threshold (0.25) and the default table is sorted by Normalized Enrichment Score (NES). Further details on NES statistics, please visit The Broad GSEA website.

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
KEGG LYSOSOME 119 genes.ES.table 0.47 1.7 0.075 0.45 0.67 0.58 0.33 0.39 0.15 0.1
KEGG TOLL LIKE RECEPTOR SIGNALING PATHWAY 90 genes.ES.table 0.55 1.7 0.0063 0.54 0.63 0.58 0.31 0.4 0.18 0.12
KEGG NOD LIKE RECEPTOR SIGNALING PATHWAY 61 genes.ES.table 0.58 1.7 0.0082 0.51 0.64 0.36 0.17 0.3 0.17 0.11
KEGG THYROID CANCER 29 genes.ES.table 0.61 1.8 0.015 0.57 0.59 0.31 0.16 0.26 0.16 0.12
ST TUMOR NECROSIS FACTOR PATHWAY 28 genes.ES.table 0.55 1.9 0.0077 0.5 0.36 0.46 0.28 0.33 0 0.091
ST G ALPHA I PATHWAY 34 genes.ES.table 0.58 1.7 0.0022 0.51 0.67 0.38 0.21 0.3 0.17 0.12
ST GAQ PATHWAY 27 genes.ES.table 0.54 1.8 0.0061 0.53 0.44 0.44 0.24 0.34 0 0.098
PID ERBB2ERBB3PATHWAY 44 genes.ES.table 0.46 1.7 0.014 0.43 0.73 0.27 0.23 0.21 0.16 0.11
REACTOME ANTIVIRAL MECHANISM BY IFN STIMULATED GENES 65 genes.ES.table 0.46 1.8 0.032 0.56 0.5 0.14 0.087 0.13 0.13 0.12
REACTOME TRIGLYCERIDE BIOSYNTHESIS 38 genes.ES.table 0.52 1.7 0.017 0.49 0.67 0.24 0.13 0.21 0.16 0.11
genes ES table in pathway: KEGG LYSOSOME

Table S51.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 GBP6 GBP6 GBP6 87 0.79 0.024 YES
2 IFNG IFNG IFNG 99 0.78 0.053 YES
3 HERC5 HERC5 HERC5 139 0.72 0.077 YES
4 FCGR1B FCGR1B FCGR1B 229 0.66 0.096 YES
5 FCGR1A FCGR1A FCGR1A 234 0.65 0.12 YES
6 IFIT3 IFIT3 IFIT3 245 0.65 0.14 YES
7 OASL OASL OASL 266 0.63 0.17 YES
8 OAS3 OAS3 OAS3 295 0.61 0.19 YES
9 USP18 USP18 USP18 298 0.61 0.21 YES
10 IFIT2 IFIT2 IFIT2 326 0.6 0.23 YES
11 IFIT1 IFIT1 IFIT1 330 0.59 0.25 YES
12 GBP5 GBP5 GBP5 389 0.57 0.27 YES
13 CAMK2A CAMK2A CAMK2A 485 0.53 0.28 YES
14 GBP4 GBP4 GBP4 490 0.53 0.3 YES
15 GBP1 GBP1 GBP1 498 0.53 0.32 YES
16 PTAFR PTAFR PTAFR 601 0.5 0.34 YES
17 IFI6 IFI6 IFI6 685 0.47 0.35 YES
18 EIF2AK2 EIF2AK2 EIF2AK2 711 0.47 0.36 YES
19 XAF1 XAF1 XAF1 756 0.46 0.38 YES
20 GBP7 GBP7 GBP7 788 0.45 0.39 YES
21 MX1 MX1 MX1 794 0.45 0.41 YES
22 MT2A MT2A MT2A 913 0.43 0.42 YES
23 DDX58 DDX58 DDX58 1293 0.36 0.41 YES
24 IFI27 IFI27 IFI27 1303 0.36 0.42 YES
25 ISG15 ISG15 ISG15 1318 0.36 0.44 YES
26 SOCS1 SOCS1 SOCS1 1346 0.36 0.45 YES
27 EIF4E3 EIF4E3 EIF4E3 1361 0.36 0.46 YES
28 JAK2 JAK2 JAK2 1430 0.35 0.47 YES
29 STAT1 STAT1 STAT1 1534 0.34 0.48 YES
30 GBP2 GBP2 GBP2 1751 0.31 0.48 YES
31 SOCS3 SOCS3 SOCS3 1807 0.31 0.48 YES
32 IRF1 IRF1 IRF1 1909 0.3 0.49 YES
33 OAS1 OAS1 OAS1 1918 0.3 0.5 YES
34 ICAM1 ICAM1 ICAM1 2012 0.29 0.5 YES
35 OAS2 OAS2 OAS2 2080 0.29 0.51 YES
36 IFI35 IFI35 IFI35 2529 0.25 0.5 YES
37 IFITM1 IFITM1 IFITM1 2681 0.24 0.5 YES
38 IFNB1 IFNB1 IFNB1 2716 0.23 0.5 YES
39 STAT2 STAT2 STAT2 2830 0.23 0.5 YES
40 PML PML PML 2844 0.23 0.51 YES
41 MX2 MX2 MX2 2875 0.22 0.52 YES
42 IRF7 IRF7 IRF7 2935 0.22 0.52 YES
43 HLA-G HLA-G HLA-G 3355 0.2 0.51 YES
44 VCAM1 VCAM1 VCAM1 3523 0.18 0.5 YES
45 FLNB FLNB FLNB 3535 0.18 0.51 YES
46 IRF6 IRF6 IRF6 3569 0.18 0.52 YES
47 IFITM3 IFITM3 IFITM3 3597 0.18 0.52 YES
48 CD44 CD44 CD44 3666 0.18 0.52 YES
49 PIAS1 PIAS1 PIAS1 3724 0.17 0.53 YES
50 UBE2L6 UBE2L6 UBE2L6 3799 0.17 0.53 YES
51 HLA-F HLA-F HLA-F 3900 0.16 0.53 YES
52 HLA-DQA2 HLA-DQA2 HLA-DQA2 3934 0.16 0.53 YES
53 PTPN1 PTPN1 PTPN1 4061 0.16 0.53 YES
54 ADAR ADAR ADAR 4087 0.16 0.54 YES
55 IFNAR1 IFNAR1 IFNAR1 4113 0.16 0.54 YES
56 UBA7 UBA7 UBA7 4534 0.14 0.52 NO
57 IFNAR2 IFNAR2 IFNAR2 4664 0.13 0.52 NO
58 HLA-C HLA-C HLA-C 4728 0.13 0.52 NO
59 IRF9 IRF9 IRF9 4770 0.13 0.52 NO
60 HLA-A HLA-A HLA-A 4938 0.12 0.52 NO
61 NUP62 NUP62 NUP62 4944 0.12 0.52 NO
62 TYK2 TYK2 TYK2 5037 0.12 0.52 NO
63 TRIM25 TRIM25 TRIM25 5101 0.11 0.52 NO
64 IRF2 IRF2 IRF2 5285 0.11 0.52 NO
65 B2M B2M B2M 5322 0.1 0.52 NO
66 IFNGR2 IFNGR2 IFNGR2 5451 0.1 0.51 NO
67 ISG20 ISG20 ISG20 5617 0.096 0.51 NO
68 IRF5 IRF5 IRF5 5671 0.094 0.51 NO
69 NUPL1 NUPL1 NUPL1 5676 0.094 0.51 NO
70 IRF4 IRF4 IRF4 5925 0.086 0.5 NO
71 NUP214 NUP214 NUP214 6142 0.08 0.49 NO
72 IFNGR1 IFNGR1 IFNGR1 6170 0.079 0.49 NO
73 RNASEL RNASEL RNASEL 6273 0.076 0.49 NO
74 RANBP2 RANBP2 RANBP2 6526 0.068 0.48 NO
75 HLA-B HLA-B HLA-B 6544 0.068 0.48 NO
76 ARIH1 ARIH1 ARIH1 6718 0.064 0.47 NO
77 PRKCD PRKCD PRKCD 6865 0.059 0.46 NO
78 PSMB8 PSMB8 PSMB8 7050 0.054 0.46 NO
79 PTPN2 PTPN2 PTPN2 7127 0.052 0.45 NO
80 NUP155 NUP155 NUP155 7153 0.052 0.46 NO
81 KPNA3 KPNA3 KPNA3 7155 0.052 0.46 NO
82 IFITM2 IFITM2 IFITM2 7405 0.046 0.44 NO
83 EIF4G2 EIF4G2 EIF4G2 7428 0.045 0.44 NO
84 NUP153 NUP153 NUP153 7564 0.042 0.44 NO
85 PPM1B PPM1B PPM1B 7639 0.04 0.44 NO
86 PTPN6 PTPN6 PTPN6 7669 0.039 0.44 NO
87 EIF4G1 EIF4G1 EIF4G1 7683 0.039 0.44 NO
88 TPR TPR TPR 7865 0.035 0.43 NO
89 SP100 SP100 SP100 7940 0.033 0.42 NO
90 HLA-DPA1 HLA-DPA1 HLA-DPA1 8174 0.027 0.41 NO
91 EIF4E2 EIF4E2 EIF4E2 8278 0.025 0.41 NO
92 NUP50 NUP50 NUP50 8367 0.024 0.4 NO
93 HLA-DRB5 HLA-DRB5 HLA-DRB5 8406 0.023 0.4 NO
94 KPNB1 KPNB1 KPNB1 8471 0.021 0.4 NO
95 NUP188 NUP188 NUP188 8804 0.015 0.38 NO
96 PLCG1 PLCG1 PLCG1 8908 0.013 0.38 NO
97 NUP93 NUP93 NUP93 9595 -0.0012 0.34 NO
98 JAK1 JAK1 JAK1 9870 -0.007 0.32 NO
99 IRF8 IRF8 IRF8 9884 -0.0073 0.32 NO
100 NEDD4 NEDD4 NEDD4 9983 -0.009 0.32 NO
101 KPNA4 KPNA4 KPNA4 9991 -0.0092 0.32 NO
102 MAPK3 MAPK3 MAPK3 9998 -0.0093 0.32 NO
103 EIF4G3 EIF4G3 EIF4G3 10166 -0.012 0.3 NO
104 UBE2E1 UBE2E1 UBE2E1 10273 -0.014 0.3 NO
105 KPNA1 KPNA1 KPNA1 10282 -0.015 0.3 NO
106 HLA-DPB1 HLA-DPB1 HLA-DPB1 10547 -0.02 0.29 NO
107 EIF4A1 EIF4A1 EIF4A1 10608 -0.021 0.28 NO
108 EIF4E EIF4E EIF4E 10733 -0.024 0.28 NO
109 KPNA5 KPNA5 KPNA5 10758 -0.024 0.28 NO
110 PIN1 PIN1 PIN1 11011 -0.029 0.26 NO
111 EIF4A3 EIF4A3 EIF4A3 11207 -0.034 0.25 NO
112 SUMO1 SUMO1 SUMO1 11253 -0.034 0.25 NO
113 EGR1 EGR1 EGR1 11283 -0.035 0.25 NO
114 UBE2N UBE2N UBE2N 11423 -0.038 0.24 NO
115 KPNA2 KPNA2 KPNA2 11518 -0.04 0.24 NO
116 RAE1 RAE1 RAE1 11690 -0.044 0.23 NO
117 EIF4A2 EIF4A2 EIF4A2 11727 -0.045 0.23 NO
118 IRF3 IRF3 IRF3 11824 -0.047 0.23 NO
119 IFNA21 IFNA21 IFNA21 12051 -0.052 0.22 NO
120 NUP133 NUP133 NUP133 12101 -0.053 0.22 NO
121 NUP43 NUP43 NUP43 12106 -0.053 0.22 NO
122 NUP54 NUP54 NUP54 12302 -0.057 0.21 NO
123 NUP205 NUP205 NUP205 12454 -0.06 0.2 NO
124 POM121 POM121 POM121 12719 -0.066 0.19 NO
125 AAAS AAAS AAAS 12728 -0.066 0.19 NO
126 NUP85 NUP85 NUP85 12771 -0.067 0.19 NO
127 UBA52 UBA52 UBA52 13253 -0.079 0.17 NO
128 NUP107 NUP107 NUP107 13364 -0.082 0.16 NO
129 HLA-DQA1 HLA-DQA1 HLA-DQA1 13474 -0.085 0.16 NO
130 NUP210 NUP210 NUP210 13511 -0.086 0.16 NO
131 IP6K2 IP6K2 IP6K2 13570 -0.088 0.16 NO
132 NUP37 NUP37 NUP37 14245 -0.11 0.13 NO
133 RPS27A RPS27A RPS27A 14352 -0.11 0.13 NO
134 NUP88 NUP88 NUP88 14418 -0.12 0.13 NO
135 HLA-DRB1 HLA-DRB1 HLA-DRB1 14559 -0.12 0.12 NO
136 NUP35 NUP35 NUP35 14702 -0.13 0.12 NO
137 SEH1L SEH1L SEH1L 14952 -0.14 0.11 NO
138 NCAM1 NCAM1 NCAM1 15482 -0.17 0.088 NO
139 CAMK2D CAMK2D CAMK2D 15601 -0.17 0.087 NO
140 NUPL2 NUPL2 NUPL2 15757 -0.18 0.085 NO
141 CIITA CIITA CIITA 16304 -0.23 0.062 NO
142 CAMK2B CAMK2B CAMK2B 17306 -0.41 0.02 NO

Figure S101.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG LYSOSOME.

Figure S102.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG LYSOSOME, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG TOLL LIKE RECEPTOR SIGNALING PATHWAY

Table S52.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 HERC5 HERC5 HERC5 139 0.72 0.15 YES
2 IFIH1 IFIH1 IFIH1 818 0.44 0.21 YES
3 TNFAIP3 TNFAIP3 TNFAIP3 1189 0.38 0.27 YES
4 DDX58 DDX58 DDX58 1293 0.36 0.34 YES
5 ISG15 ISG15 ISG15 1318 0.36 0.42 YES
6 RNF125 RNF125 RNF125 1655 0.32 0.47 YES
7 CYLD CYLD CYLD 2725 0.23 0.46 YES
8 UBE2D1 UBE2D1 UBE2D1 3261 0.2 0.47 YES
9 IKBKE IKBKE IKBKE 3395 0.2 0.51 YES
10 UBE2L6 UBE2L6 UBE2L6 3799 0.17 0.52 YES
11 NLRC5 NLRC5 NLRC5 3929 0.16 0.55 YES
12 UBA7 UBA7 UBA7 4534 0.14 0.54 YES
13 TRAF3 TRAF3 TRAF3 4765 0.13 0.56 YES
14 TRIM25 TRIM25 TRIM25 5101 0.11 0.56 YES
15 TBK1 TBK1 TBK1 5853 0.088 0.54 NO
16 UBE2K UBE2K UBE2K 6910 0.058 0.49 NO
17 MAVS MAVS MAVS 8230 0.026 0.42 NO
18 UBE2D3 UBE2D3 UBE2D3 8647 0.018 0.4 NO
19 ATG5 ATG5 ATG5 8689 0.017 0.41 NO
20 NLRX1 NLRX1 NLRX1 8827 0.014 0.4 NO
21 TAX1BP1 TAX1BP1 TAX1BP1 9043 0.01 0.39 NO
22 OTUD5 OTUD5 OTUD5 10031 -0.0098 0.34 NO
23 RNF135 RNF135 RNF135 10165 -0.012 0.33 NO
24 PIN1 PIN1 PIN1 11011 -0.029 0.29 NO
25 PCBP2 PCBP2 PCBP2 11282 -0.035 0.28 NO
26 UBE2D2 UBE2D2 UBE2D2 11788 -0.046 0.26 NO
27 IRF3 IRF3 IRF3 11824 -0.047 0.27 NO
28 ATG12 ATG12 ATG12 13020 -0.074 0.22 NO
29 UBA52 UBA52 UBA52 13253 -0.079 0.23 NO
30 RPS27A RPS27A RPS27A 14352 -0.11 0.19 NO

Figure S103.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG TOLL LIKE RECEPTOR SIGNALING PATHWAY.

Figure S104.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG TOLL LIKE RECEPTOR SIGNALING PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG NOD LIKE RECEPTOR SIGNALING PATHWAY

Table S53.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 HERC5 HERC5 HERC5 139 0.72 0.07 YES
2 S100A12 S100A12 S100A12 373 0.57 0.12 YES
3 IFIH1 IFIH1 IFIH1 818 0.44 0.14 YES
4 DHX58 DHX58 DHX58 1065 0.4 0.17 YES
5 TNFAIP3 TNFAIP3 TNFAIP3 1189 0.38 0.2 YES
6 CASP10 CASP10 CASP10 1241 0.37 0.24 YES
7 DDX58 DDX58 DDX58 1293 0.36 0.28 YES
8 ISG15 ISG15 ISG15 1318 0.36 0.32 YES
9 RNF125 RNF125 RNF125 1655 0.32 0.33 YES
10 IRF1 IRF1 IRF1 1909 0.3 0.35 YES
11 IFNB1 IFNB1 IFNB1 2716 0.23 0.33 YES
12 CYLD CYLD CYLD 2725 0.23 0.36 YES
13 TRAF6 TRAF6 TRAF6 2931 0.22 0.37 YES
14 IRF7 IRF7 IRF7 2935 0.22 0.39 YES
15 UBE2D1 UBE2D1 UBE2D1 3261 0.2 0.39 YES
16 IKBKE IKBKE IKBKE 3395 0.2 0.41 YES
17 TANK TANK TANK 3409 0.19 0.43 YES
18 NFKBIA NFKBIA NFKBIA 3582 0.18 0.44 YES
19 APP APP APP 3657 0.18 0.45 YES
20 NFKB2 NFKB2 NFKB2 3704 0.18 0.47 YES
21 UBE2L6 UBE2L6 UBE2L6 3799 0.17 0.48 YES
22 NLRC5 NLRC5 NLRC5 3929 0.16 0.49 YES
23 S100B S100B S100B 4092 0.16 0.5 YES
24 RIPK1 RIPK1 RIPK1 4386 0.14 0.5 YES
25 UBA7 UBA7 UBA7 4534 0.14 0.51 YES
26 TRAF3 TRAF3 TRAF3 4765 0.13 0.51 YES
27 CHUK CHUK CHUK 5020 0.12 0.5 YES
28 TRIM25 TRIM25 TRIM25 5101 0.11 0.51 YES
29 IRF2 IRF2 IRF2 5285 0.11 0.51 YES
30 SAA1 SAA1 SAA1 5456 0.1 0.52 YES
31 TBK1 TBK1 TBK1 5853 0.088 0.5 NO
32 EP300 EP300 EP300 6458 0.07 0.48 NO
33 UBE2K UBE2K UBE2K 6910 0.058 0.46 NO
34 TRAF2 TRAF2 TRAF2 7163 0.052 0.45 NO
35 IKBKB IKBKB IKBKB 7202 0.05 0.45 NO
36 CASP8 CASP8 CASP8 7676 0.039 0.43 NO
37 AGER AGER AGER 7721 0.038 0.43 NO
38 FADD FADD FADD 8136 0.028 0.41 NO
39 MAVS MAVS MAVS 8230 0.026 0.41 NO
40 RELA RELA RELA 8411 0.023 0.4 NO
41 CREBBP CREBBP CREBBP 8533 0.02 0.39 NO
42 UBE2D3 UBE2D3 UBE2D3 8647 0.018 0.39 NO
43 ATG5 ATG5 ATG5 8689 0.017 0.39 NO
44 IKBKG IKBKG IKBKG 8750 0.016 0.39 NO
45 NLRX1 NLRX1 NLRX1 8827 0.014 0.38 NO
46 TAX1BP1 TAX1BP1 TAX1BP1 9043 0.01 0.37 NO
47 OTUD5 OTUD5 OTUD5 10031 -0.0098 0.32 NO
48 RNF135 RNF135 RNF135 10165 -0.012 0.31 NO
49 PIN1 PIN1 PIN1 11011 -0.029 0.27 NO
50 PCBP2 PCBP2 PCBP2 11282 -0.035 0.26 NO
51 NFKBIB NFKBIB NFKBIB 11534 -0.04 0.25 NO
52 UBE2D2 UBE2D2 UBE2D2 11788 -0.046 0.24 NO
53 IRF3 IRF3 IRF3 11824 -0.047 0.24 NO
54 IFNA21 IFNA21 IFNA21 12051 -0.052 0.23 NO
55 SIKE1 SIKE1 SIKE1 12194 -0.055 0.23 NO
56 ATG12 ATG12 ATG12 13020 -0.074 0.19 NO
57 UBA52 UBA52 UBA52 13253 -0.079 0.19 NO
58 DAK DAK DAK 14289 -0.11 0.14 NO
59 RPS27A RPS27A RPS27A 14352 -0.11 0.15 NO
60 HMGB1 HMGB1 HMGB1 15341 -0.16 0.11 NO
61 MAP3K1 MAP3K1 MAP3K1 16026 -0.2 0.093 NO

Figure S105.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG NOD LIKE RECEPTOR SIGNALING PATHWAY.

Figure S106.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG NOD LIKE RECEPTOR SIGNALING PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: KEGG THYROID CANCER

Table S54.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 GBP6 GBP6 GBP6 87 0.79 0.013 YES
2 IL1RN IL1RN IL1RN 96 0.78 0.03 YES
3 IFNG IFNG IFNG 99 0.78 0.048 YES
4 HGF HGF HGF 124 0.74 0.063 YES
5 HERC5 HERC5 HERC5 139 0.72 0.079 YES
6 FCGR1B FCGR1B FCGR1B 229 0.66 0.089 YES
7 FCGR1A FCGR1A FCGR1A 234 0.65 0.1 YES
8 IL1R2 IL1R2 IL1R2 241 0.65 0.12 YES
9 IFIT3 IFIT3 IFIT3 245 0.65 0.13 YES
10 OASL OASL OASL 266 0.63 0.15 YES
11 OAS3 OAS3 OAS3 295 0.61 0.16 YES
12 USP18 USP18 USP18 298 0.61 0.17 YES
13 PRLR PRLR PRLR 299 0.61 0.19 YES
14 IL1B IL1B IL1B 314 0.6 0.2 YES
15 IFIT2 IFIT2 IFIT2 326 0.6 0.21 YES
16 IFIT1 IFIT1 IFIT1 330 0.59 0.22 YES
17 NOD2 NOD2 NOD2 356 0.58 0.24 YES
18 GBP5 GBP5 GBP5 389 0.57 0.25 YES
19 CAMK2A CAMK2A CAMK2A 485 0.53 0.25 YES
20 GBP4 GBP4 GBP4 490 0.53 0.27 YES
21 GBP1 GBP1 GBP1 498 0.53 0.28 YES
22 IRAK3 IRAK3 IRAK3 596 0.5 0.28 YES
23 PTAFR PTAFR PTAFR 601 0.5 0.29 YES
24 IL6R IL6R IL6R 678 0.48 0.3 YES
25 IFI6 IFI6 IFI6 685 0.47 0.31 YES
26 EIF2AK2 EIF2AK2 EIF2AK2 711 0.47 0.32 YES
27 XAF1 XAF1 XAF1 756 0.46 0.33 YES
28 GBP7 GBP7 GBP7 788 0.45 0.34 YES
29 MX1 MX1 MX1 794 0.45 0.35 YES
30 MT2A MT2A MT2A 913 0.43 0.35 YES
31 CISH CISH CISH 1016 0.41 0.35 YES
32 IL5RA IL5RA IL5RA 1047 0.4 0.36 YES
33 IL6 IL6 IL6 1086 0.4 0.37 YES
34 IL7R IL7R IL7R 1179 0.38 0.37 YES
35 CSF2 CSF2 CSF2 1279 0.36 0.37 YES
36 DDX58 DDX58 DDX58 1293 0.36 0.38 YES
37 IFI27 IFI27 IFI27 1303 0.36 0.39 YES
38 ISG15 ISG15 ISG15 1318 0.36 0.4 YES
39 SOCS1 SOCS1 SOCS1 1346 0.36 0.4 YES
40 EIF4E3 EIF4E3 EIF4E3 1361 0.36 0.41 YES
41 JAK2 JAK2 JAK2 1430 0.35 0.41 YES
42 YES1 YES1 YES1 1496 0.34 0.42 YES
43 IRAK2 IRAK2 IRAK2 1517 0.34 0.42 YES
44 STAT1 STAT1 STAT1 1534 0.34 0.43 YES
45 IL1R1 IL1R1 IL1R1 1545 0.34 0.44 YES
46 IL3RA IL3RA IL3RA 1685 0.32 0.44 YES
47 IL6ST IL6ST IL6ST 1718 0.32 0.44 YES
48 GBP2 GBP2 GBP2 1751 0.31 0.45 YES
49 SOCS3 SOCS3 SOCS3 1807 0.31 0.45 YES
50 CSF2RB CSF2RB CSF2RB 1848 0.3 0.46 YES
51 IRF1 IRF1 IRF1 1909 0.3 0.46 YES
52 OAS1 OAS1 OAS1 1918 0.3 0.47 YES
53 ICAM1 ICAM1 ICAM1 2012 0.29 0.47 YES
54 OAS2 OAS2 OAS2 2080 0.29 0.47 YES
55 IL2RB IL2RB IL2RB 2217 0.27 0.47 YES
56 IFI35 IFI35 IFI35 2529 0.25 0.46 YES
57 PELI2 PELI2 PELI2 2656 0.24 0.46 YES
58 IFITM1 IFITM1 IFITM1 2681 0.24 0.46 YES
59 IFNB1 IFNB1 IFNB1 2716 0.23 0.46 YES
60 STAT2 STAT2 STAT2 2830 0.23 0.46 YES
61 PML PML PML 2844 0.23 0.46 YES
62 MX2 MX2 MX2 2875 0.22 0.47 YES
63 TRAF6 TRAF6 TRAF6 2931 0.22 0.47 YES
64 IRF7 IRF7 IRF7 2935 0.22 0.48 YES
65 IL1RAP IL1RAP IL1RAP 3027 0.22 0.48 YES
66 RIPK2 RIPK2 RIPK2 3079 0.21 0.48 YES
67 PIK3R3 PIK3R3 PIK3R3 3335 0.2 0.47 YES
68 TNIP2 TNIP2 TNIP2 3338 0.2 0.47 YES
69 HLA-G HLA-G HLA-G 3355 0.2 0.48 YES
70 CSF2RA CSF2RA CSF2RA 3481 0.19 0.47 YES
71 VCAM1 VCAM1 VCAM1 3523 0.18 0.47 YES
72 FLNB FLNB FLNB 3535 0.18 0.48 YES
73 IRF6 IRF6 IRF6 3569 0.18 0.48 YES
74 IFITM3 IFITM3 IFITM3 3597 0.18 0.48 YES
75 PIK3CB PIK3CB PIK3CB 3622 0.18 0.48 YES
76 HCK HCK HCK 3629 0.18 0.49 YES
77 FYN FYN FYN 3630 0.18 0.49 YES
78 CD44 CD44 CD44 3666 0.18 0.5 YES
79 NFKB2 NFKB2 NFKB2 3704 0.18 0.5 YES
80 PIAS1 PIAS1 PIAS1 3724 0.17 0.5 YES
81 UBE2L6 UBE2L6 UBE2L6 3799 0.17 0.5 YES
82 HLA-F HLA-F HLA-F 3900 0.16 0.5 YES
83 IRS2 IRS2 IRS2 3933 0.16 0.5 YES
84 HLA-DQA2 HLA-DQA2 HLA-DQA2 3934 0.16 0.5 YES
85 PTPN1 PTPN1 PTPN1 4061 0.16 0.5 YES
86 ADAR ADAR ADAR 4087 0.16 0.5 YES
87 PIK3R1 PIK3R1 PIK3R1 4109 0.16 0.5 YES
88 IFNAR1 IFNAR1 IFNAR1 4113 0.16 0.51 YES
89 IL2RG IL2RG IL2RG 4257 0.15 0.5 NO
90 CASP1 CASP1 CASP1 4348 0.14 0.5 NO
91 SQSTM1 SQSTM1 SQSTM1 4520 0.14 0.49 NO
92 UBA7 UBA7 UBA7 4534 0.14 0.5 NO
93 JAK3 JAK3 JAK3 4548 0.14 0.5 NO
94 GAB2 GAB2 GAB2 4660 0.13 0.5 NO
95 IFNAR2 IFNAR2 IFNAR2 4664 0.13 0.5 NO
96 HLA-C HLA-C HLA-C 4728 0.13 0.5 NO
97 IRF9 IRF9 IRF9 4770 0.13 0.5 NO
98 HLA-A HLA-A HLA-A 4938 0.12 0.49 NO
99 NUP62 NUP62 NUP62 4944 0.12 0.49 NO
100 MAP3K3 MAP3K3 MAP3K3 4983 0.12 0.49 NO
101 CHUK CHUK CHUK 5020 0.12 0.49 NO
102 TYK2 TYK2 TYK2 5037 0.12 0.5 NO
103 STAT5A STAT5A STAT5A 5060 0.12 0.5 NO
104 TRIM25 TRIM25 TRIM25 5101 0.11 0.5 NO
105 MYD88 MYD88 MYD88 5136 0.11 0.5 NO
106 ADAM17 ADAM17 ADAM17 5186 0.11 0.5 NO
107 IRF2 IRF2 IRF2 5285 0.11 0.5 NO
108 MAP2K6 MAP2K6 MAP2K6 5308 0.11 0.5 NO
109 B2M B2M B2M 5322 0.1 0.5 NO
110 CRK CRK CRK 5323 0.1 0.5 NO
111 MAP2K1 MAP2K1 MAP2K1 5338 0.1 0.5 NO
112 PIK3CD PIK3CD PIK3CD 5358 0.1 0.5 NO
113 IFNGR2 IFNGR2 IFNGR2 5451 0.1 0.5 NO
114 ISG20 ISG20 ISG20 5617 0.096 0.49 NO
115 STAT3 STAT3 STAT3 5667 0.095 0.49 NO
116 IRF5 IRF5 IRF5 5671 0.094 0.49 NO
117 NUPL1 NUPL1 NUPL1 5676 0.094 0.5 NO
118 PTK2B PTK2B PTK2B 5732 0.093 0.5 NO
119 PRL PRL PRL 5802 0.09 0.49 NO
120 IRF4 IRF4 IRF4 5925 0.086 0.49 NO
121 MAP3K8 MAP3K8 MAP3K8 5978 0.085 0.49 NO
122 STAT5B STAT5B STAT5B 5980 0.085 0.49 NO
123 TAB2 TAB2 TAB2 6006 0.084 0.49 NO
124 NUP214 NUP214 NUP214 6142 0.08 0.48 NO
125 IFNGR1 IFNGR1 IFNGR1 6170 0.079 0.48 NO
126 IL2 IL2 IL2 6271 0.076 0.48 NO
127 RNASEL RNASEL RNASEL 6273 0.076 0.48 NO
128 IL1A IL1A IL1A 6326 0.074 0.48 NO
129 RANBP2 RANBP2 RANBP2 6526 0.068 0.47 NO
130 HLA-B HLA-B HLA-B 6544 0.068 0.47 NO
131 TAB3 TAB3 TAB3 6650 0.065 0.47 NO
132 ARIH1 ARIH1 ARIH1 6718 0.064 0.46 NO
133 CBL CBL CBL 6723 0.064 0.46 NO
134 IL18 IL18 IL18 6786 0.061 0.46 NO
135 MAP2K2 MAP2K2 MAP2K2 6802 0.061 0.46 NO
136 PRKCD PRKCD PRKCD 6865 0.059 0.46 NO
137 PSMB8 PSMB8 PSMB8 7050 0.054 0.45 NO
138 VAV1 VAV1 VAV1 7059 0.054 0.45 NO
139 PTPN2 PTPN2 PTPN2 7127 0.052 0.45 NO
140 NRAS NRAS NRAS 7137 0.052 0.45 NO
141 NUP155 NUP155 NUP155 7153 0.052 0.45 NO
142 KPNA3 KPNA3 KPNA3 7155 0.052 0.45 NO
143 IKBKB IKBKB IKBKB 7202 0.05 0.45 NO
144 IRAK1 IRAK1 IRAK1 7397 0.046 0.44 NO
145 IFITM2 IFITM2 IFITM2 7405 0.046 0.44 NO
146 EIF4G2 EIF4G2 EIF4G2 7428 0.045 0.44 NO
147 NUP153 NUP153 NUP153 7564 0.042 0.43 NO
148 KRAS KRAS KRAS 7618 0.04 0.43 NO
149 PPM1B PPM1B PPM1B 7639 0.04 0.43 NO
150 PTPN6 PTPN6 PTPN6 7669 0.039 0.43 NO
151 EIF4G1 EIF4G1 EIF4G1 7683 0.039 0.43 NO
152 PELI3 PELI3 PELI3 7728 0.038 0.43 NO
153 IL2RA IL2RA IL2RA 7848 0.035 0.42 NO
154 RAF1 RAF1 RAF1 7858 0.035 0.42 NO
155 TPR TPR TPR 7865 0.035 0.42 NO
156 SP100 SP100 SP100 7940 0.033 0.42 NO
157 TOLLIP TOLLIP TOLLIP 8029 0.031 0.42 NO
158 MAP2K4 MAP2K4 MAP2K4 8103 0.029 0.41 NO
159 HLA-DPA1 HLA-DPA1 HLA-DPA1 8174 0.027 0.41 NO
160 YWHAZ YWHAZ YWHAZ 8194 0.027 0.41 NO
161 EIF4E2 EIF4E2 EIF4E2 8278 0.025 0.4 NO
162 NUP50 NUP50 NUP50 8367 0.024 0.4 NO
163 HLA-DRB5 HLA-DRB5 HLA-DRB5 8406 0.023 0.4 NO
164 RELA RELA RELA 8411 0.023 0.4 NO
165 SHC1 SHC1 SHC1 8438 0.022 0.4 NO
166 KPNB1 KPNB1 KPNB1 8471 0.021 0.4 NO
167 RAPGEF1 RAPGEF1 RAPGEF1 8524 0.02 0.39 NO
168 IKBKG IKBKG IKBKG 8750 0.016 0.38 NO
169 NUP188 NUP188 NUP188 8804 0.015 0.38 NO
170 CUL1 CUL1 CUL1 8885 0.013 0.37 NO
171 LYN LYN LYN 8896 0.013 0.37 NO
172 PLCG1 PLCG1 PLCG1 8908 0.013 0.37 NO
173 YWHAB YWHAB YWHAB 9263 0.0052 0.35 NO
174 LCK LCK LCK 9267 0.0051 0.35 NO
175 BTRC BTRC BTRC 9289 0.0046 0.35 NO
176 SKP1 SKP1 SKP1 9397 0.0024 0.35 NO
177 IRAK4 IRAK4 IRAK4 9415 0.0022 0.34 NO
178 GHR GHR GHR 9563 -0.00059 0.34 NO
179 NUP93 NUP93 NUP93 9595 -0.0012 0.34 NO
180 GRB2 GRB2 GRB2 9626 -0.002 0.33 NO
181 SOS1 SOS1 SOS1 9673 -0.0027 0.33 NO
182 NOD1 NOD1 NOD1 9756 -0.0046 0.33 NO
183 JAK1 JAK1 JAK1 9870 -0.007 0.32 NO
184 IRF8 IRF8 IRF8 9884 -0.0073 0.32 NO
185 PIK3CA PIK3CA PIK3CA 9924 -0.008 0.32 NO
186 INPPL1 INPPL1 INPPL1 9978 -0.0089 0.31 NO
187 NEDD4 NEDD4 NEDD4 9983 -0.009 0.31 NO
188 KPNA4 KPNA4 KPNA4 9991 -0.0092 0.31 NO
189 MAPK3 MAPK3 MAPK3 9998 -0.0093 0.31 NO
190 CRKL CRKL CRKL 10062 -0.01 0.31 NO
191 EIF4G3 EIF4G3 EIF4G3 10166 -0.012 0.3 NO
192 UBE2E1 UBE2E1 UBE2E1 10273 -0.014 0.3 NO
193 KPNA1 KPNA1 KPNA1 10282 -0.015 0.3 NO
194 HLA-DPB1 HLA-DPB1 HLA-DPB1 10547 -0.02 0.28 NO
195 EIF4A1 EIF4A1 EIF4A1 10608 -0.021 0.28 NO
196 EIF4E EIF4E EIF4E 10733 -0.024 0.28 NO
197 KPNA5 KPNA5 KPNA5 10758 -0.024 0.27 NO
198 RBX1 RBX1 RBX1 10765 -0.024 0.27 NO
199 TAB1 TAB1 TAB1 10826 -0.026 0.27 NO
200 MAPK1 MAPK1 MAPK1 10844 -0.026 0.27 NO
201 PIN1 PIN1 PIN1 11011 -0.029 0.26 NO
202 EIF4A3 EIF4A3 EIF4A3 11207 -0.034 0.25 NO
203 SUMO1 SUMO1 SUMO1 11253 -0.034 0.25 NO
204 EGR1 EGR1 EGR1 11283 -0.035 0.25 NO
205 TEC TEC TEC 11323 -0.036 0.25 NO
206 UBE2N UBE2N UBE2N 11423 -0.038 0.24 NO
207 KPNA2 KPNA2 KPNA2 11518 -0.04 0.24 NO
208 PIK3R2 PIK3R2 PIK3R2 11662 -0.043 0.23 NO
209 RAE1 RAE1 RAE1 11690 -0.044 0.23 NO
210 EIF4A2 EIF4A2 EIF4A2 11727 -0.045 0.23 NO
211 MAP3K7 MAP3K7 MAP3K7 11756 -0.045 0.23 NO
212 IRF3 IRF3 IRF3 11824 -0.047 0.23 NO
213 IFNA21 IFNA21 IFNA21 12051 -0.052 0.21 NO
214 NUP133 NUP133 NUP133 12101 -0.053 0.21 NO
215 NUP43 NUP43 NUP43 12106 -0.053 0.21 NO
216 NUP54 NUP54 NUP54 12302 -0.057 0.2 NO
217 NUP205 NUP205 NUP205 12454 -0.06 0.2 NO
218 POM121 POM121 POM121 12719 -0.066 0.18 NO
219 AAAS AAAS AAAS 12728 -0.066 0.18 NO
220 NUP85 NUP85 NUP85 12771 -0.067 0.18 NO
221 HRAS HRAS HRAS 12995 -0.073 0.17 NO
222 SOCS2 SOCS2 SOCS2 13053 -0.075 0.17 NO
223 UBA52 UBA52 UBA52 13253 -0.079 0.16 NO
224 NUP107 NUP107 NUP107 13364 -0.082 0.16 NO
225 PELI1 PELI1 PELI1 13393 -0.083 0.16 NO
226 SH2B1 SH2B1 SH2B1 13464 -0.085 0.15 NO
227 HLA-DQA1 HLA-DQA1 HLA-DQA1 13474 -0.085 0.16 NO
228 NUP210 NUP210 NUP210 13511 -0.086 0.16 NO
229 IP6K2 IP6K2 IP6K2 13570 -0.088 0.15 NO
230 NUP37 NUP37 NUP37 14245 -0.11 0.12 NO
231 RPS27A RPS27A RPS27A 14352 -0.11 0.12 NO
232 NUP88 NUP88 NUP88 14418 -0.12 0.11 NO
233 PRKACB PRKACB PRKACB 14467 -0.12 0.11 NO
234 HLA-DRB1 HLA-DRB1 HLA-DRB1 14559 -0.12 0.11 NO
235 NUP35 NUP35 NUP35 14702 -0.13 0.11 NO
236 SEH1L SEH1L SEH1L 14952 -0.14 0.095 NO
237 CDK1 CDK1 CDK1 15276 -0.16 0.08 NO
238 SYK SYK SYK 15458 -0.16 0.073 NO
239 NCAM1 NCAM1 NCAM1 15482 -0.17 0.075 NO
240 CAMK2D CAMK2D CAMK2D 15601 -0.17 0.072 NO
241 NUPL2 NUPL2 NUPL2 15757 -0.18 0.068 NO
242 IL7 IL7 IL7 16279 -0.23 0.043 NO
243 CIITA CIITA CIITA 16304 -0.23 0.047 NO
244 BLNK BLNK BLNK 16385 -0.24 0.048 NO
245 IRS1 IRS1 IRS1 16754 -0.28 0.033 NO
246 CAMK2B CAMK2B CAMK2B 17306 -0.41 0.011 NO
247 GH1 GH1 GH1 17369 -0.44 0.017 NO

Figure S107.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG THYROID CANCER.

Figure S108.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG THYROID CANCER, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: ST TUMOR NECROSIS FACTOR PATHWAY

Table S55.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 TNFAIP3 TNFAIP3 TNFAIP3 1189 0.38 0.059 YES
2 JUN JUN JUN 2449 0.25 0.072 YES
3 BAG4 BAG4 BAG4 2862 0.22 0.12 YES
4 TNFRSF1B TNFRSF1B TNFRSF1B 3310 0.2 0.16 YES
5 CFLAR CFLAR CFLAR 3342 0.2 0.23 YES
6 NFKBIA NFKBIA NFKBIA 3582 0.18 0.28 YES
7 TNFRSF1A TNFRSF1A TNFRSF1A 3672 0.18 0.33 YES
8 NFKB2 NFKB2 NFKB2 3704 0.18 0.39 YES
9 TNF TNF TNF 3779 0.17 0.44 YES
10 RIPK1 RIPK1 RIPK1 4386 0.14 0.46 YES
11 BIRC3 BIRC3 BIRC3 4577 0.13 0.49 YES
12 TRADD TRADD TRADD 4863 0.12 0.51 YES
13 MAP3K3 MAP3K3 MAP3K3 4983 0.12 0.55 YES
14 NFKB1 NFKB1 NFKB1 6140 0.08 0.51 NO
15 NR2C2 NR2C2 NR2C2 6334 0.074 0.52 NO
16 TRAF2 TRAF2 TRAF2 7163 0.052 0.49 NO
17 AGFG1 AGFG1 AGFG1 7223 0.05 0.5 NO
18 CASP8 CASP8 CASP8 7676 0.039 0.49 NO
19 MAP2K4 MAP2K4 MAP2K4 8103 0.029 0.48 NO
20 FADD FADD FADD 8136 0.028 0.49 NO
21 CASP3 CASP3 CASP3 8167 0.028 0.49 NO
22 IKBKG IKBKG IKBKG 8750 0.016 0.46 NO
23 BIRC2 BIRC2 BIRC2 9086 0.0092 0.45 NO
24 NFKBIE NFKBIE NFKBIE 9566 -0.00082 0.42 NO
25 NFKBIL1 NFKBIL1 NFKBIL1 10052 -0.01 0.4 NO
26 RALBP1 RALBP1 RALBP1 10197 -0.013 0.4 NO
27 NFKBIB NFKBIB NFKBIB 11534 -0.04 0.33 NO
28 MAP3K7 MAP3K7 MAP3K7 11756 -0.045 0.34 NO

Figure S109.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: ST TUMOR NECROSIS FACTOR PATHWAY.

Figure S110.  Get High-res Image For the top 5 core enriched genes in the pathway: ST TUMOR NECROSIS FACTOR PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: ST G ALPHA I PATHWAY

Table S56.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CFB CFB CFB 1058 0.4 0.044 YES
2 PITX2 PITX2 PITX2 1425 0.35 0.11 YES
3 ITPKA ITPKA ITPKA 1689 0.32 0.18 YES
4 PLD1 PLD1 PLD1 1818 0.31 0.25 YES
5 AKT3 AKT3 AKT3 2416 0.26 0.29 YES
6 GNAQ GNAQ GNAQ 2510 0.25 0.34 YES
7 ITPR1 ITPR1 ITPR1 2998 0.22 0.37 YES
8 PLD3 PLD3 PLD3 3241 0.2 0.41 YES
9 NFKBIA NFKBIA NFKBIA 3582 0.18 0.44 YES
10 PIK3CB PIK3CB PIK3CB 3622 0.18 0.48 YES
11 NFKB2 NFKB2 NFKB2 3704 0.18 0.53 YES
12 PLD2 PLD2 PLD2 4166 0.15 0.54 YES
13 ITPKB ITPKB ITPKB 5738 0.093 0.48 NO
14 NFKB1 NFKB1 NFKB1 6140 0.08 0.47 NO
15 DAG1 DAG1 DAG1 7374 0.046 0.42 NO
16 IKBKG IKBKG IKBKG 8750 0.016 0.34 NO
17 ITPR2 ITPR2 ITPR2 8934 0.012 0.33 NO
18 NFKBIE NFKBIE NFKBIE 9566 -0.00082 0.3 NO
19 NFKBIL1 NFKBIL1 NFKBIL1 10052 -0.01 0.27 NO
20 AKT1 AKT1 AKT1 10149 -0.012 0.27 NO
21 ADRBK1 ADRBK1 ADRBK1 10349 -0.016 0.26 NO
22 AKT2 AKT2 AKT2 10834 -0.026 0.24 NO
23 NFKBIB NFKBIB NFKBIB 11534 -0.04 0.21 NO
24 PHKA2 PHKA2 PHKA2 11722 -0.045 0.22 NO
25 ITPR3 ITPR3 ITPR3 11810 -0.047 0.22 NO
26 PDK1 PDK1 PDK1 14652 -0.12 0.093 NO
27 VN1R1 VN1R1 VN1R1 16846 -0.3 0.046 NO

Figure S111.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: ST G ALPHA I PATHWAY.

Figure S112.  Get High-res Image For the top 5 core enriched genes in the pathway: ST G ALPHA I PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: ST GAQ PATHWAY

Table S57.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 HERC5 HERC5 HERC5 139 0.72 0.084 YES
2 USP18 USP18 USP18 298 0.61 0.15 YES
3 IFIT1 IFIT1 IFIT1 330 0.59 0.23 YES
4 EIF2AK2 EIF2AK2 EIF2AK2 711 0.47 0.27 YES
5 MX1 MX1 MX1 794 0.45 0.32 YES
6 DDX58 DDX58 DDX58 1293 0.36 0.34 YES
7 ISG15 ISG15 ISG15 1318 0.36 0.38 YES
8 EIF4E3 EIF4E3 EIF4E3 1361 0.36 0.43 YES
9 STAT1 STAT1 STAT1 1534 0.34 0.46 YES
10 MX2 MX2 MX2 2875 0.22 0.41 NO
11 FLNB FLNB FLNB 3535 0.18 0.4 NO
12 UBE2L6 UBE2L6 UBE2L6 3799 0.17 0.41 NO
13 UBA7 UBA7 UBA7 4534 0.14 0.38 NO
14 NUP62 NUP62 NUP62 4944 0.12 0.37 NO
15 TRIM25 TRIM25 TRIM25 5101 0.11 0.38 NO
16 NUPL1 NUPL1 NUPL1 5676 0.094 0.36 NO
17 NUP214 NUP214 NUP214 6142 0.08 0.34 NO
18 RANBP2 RANBP2 RANBP2 6526 0.068 0.33 NO
19 ARIH1 ARIH1 ARIH1 6718 0.064 0.33 NO
20 NUP155 NUP155 NUP155 7153 0.052 0.31 NO
21 KPNA3 KPNA3 KPNA3 7155 0.052 0.32 NO
22 EIF4G2 EIF4G2 EIF4G2 7428 0.045 0.31 NO
23 NUP153 NUP153 NUP153 7564 0.042 0.3 NO
24 PPM1B PPM1B PPM1B 7639 0.04 0.3 NO
25 EIF4G1 EIF4G1 EIF4G1 7683 0.039 0.31 NO
26 TPR TPR TPR 7865 0.035 0.3 NO
27 EIF4E2 EIF4E2 EIF4E2 8278 0.025 0.28 NO
28 NUP50 NUP50 NUP50 8367 0.024 0.28 NO
29 KPNB1 KPNB1 KPNB1 8471 0.021 0.28 NO
30 NUP188 NUP188 NUP188 8804 0.015 0.26 NO
31 PLCG1 PLCG1 PLCG1 8908 0.013 0.26 NO
32 NUP93 NUP93 NUP93 9595 -0.0012 0.22 NO
33 JAK1 JAK1 JAK1 9870 -0.007 0.2 NO
34 NEDD4 NEDD4 NEDD4 9983 -0.009 0.2 NO
35 KPNA4 KPNA4 KPNA4 9991 -0.0092 0.2 NO
36 MAPK3 MAPK3 MAPK3 9998 -0.0093 0.2 NO
37 EIF4G3 EIF4G3 EIF4G3 10166 -0.012 0.19 NO
38 UBE2E1 UBE2E1 UBE2E1 10273 -0.014 0.18 NO
39 KPNA1 KPNA1 KPNA1 10282 -0.015 0.19 NO
40 EIF4A1 EIF4A1 EIF4A1 10608 -0.021 0.17 NO
41 EIF4E EIF4E EIF4E 10733 -0.024 0.17 NO
42 KPNA5 KPNA5 KPNA5 10758 -0.024 0.17 NO
43 PIN1 PIN1 PIN1 11011 -0.029 0.16 NO
44 EIF4A3 EIF4A3 EIF4A3 11207 -0.034 0.15 NO
45 UBE2N UBE2N UBE2N 11423 -0.038 0.14 NO
46 KPNA2 KPNA2 KPNA2 11518 -0.04 0.14 NO
47 RAE1 RAE1 RAE1 11690 -0.044 0.14 NO
48 EIF4A2 EIF4A2 EIF4A2 11727 -0.045 0.14 NO
49 IRF3 IRF3 IRF3 11824 -0.047 0.14 NO
50 NUP133 NUP133 NUP133 12101 -0.053 0.14 NO
51 NUP43 NUP43 NUP43 12106 -0.053 0.14 NO
52 NUP54 NUP54 NUP54 12302 -0.057 0.14 NO
53 NUP205 NUP205 NUP205 12454 -0.06 0.14 NO
54 POM121 POM121 POM121 12719 -0.066 0.13 NO
55 AAAS AAAS AAAS 12728 -0.066 0.14 NO
56 NUP85 NUP85 NUP85 12771 -0.067 0.14 NO
57 UBA52 UBA52 UBA52 13253 -0.079 0.13 NO
58 NUP107 NUP107 NUP107 13364 -0.082 0.13 NO
59 NUP210 NUP210 NUP210 13511 -0.086 0.14 NO
60 NUP37 NUP37 NUP37 14245 -0.11 0.11 NO
61 RPS27A RPS27A RPS27A 14352 -0.11 0.12 NO
62 NUP88 NUP88 NUP88 14418 -0.12 0.13 NO
63 NUP35 NUP35 NUP35 14702 -0.13 0.13 NO
64 SEH1L SEH1L SEH1L 14952 -0.14 0.13 NO
65 NUPL2 NUPL2 NUPL2 15757 -0.18 0.11 NO

Figure S113.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: ST GAQ PATHWAY.

Figure S114.  Get High-res Image For the top 5 core enriched genes in the pathway: ST GAQ PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID ERBB2ERBB3PATHWAY

Table S58.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 IL1RN IL1RN IL1RN 96 0.78 0.044 YES
2 HGF HGF HGF 124 0.74 0.088 YES
3 IL1R2 IL1R2 IL1R2 241 0.65 0.12 YES
4 IL1B IL1B IL1B 314 0.6 0.16 YES
5 NOD2 NOD2 NOD2 356 0.58 0.19 YES
6 IRAK3 IRAK3 IRAK3 596 0.5 0.21 YES
7 IL6R IL6R IL6R 678 0.48 0.23 YES
8 IL5RA IL5RA IL5RA 1047 0.4 0.24 YES
9 IL6 IL6 IL6 1086 0.4 0.26 YES
10 IL7R IL7R IL7R 1179 0.38 0.28 YES
11 CSF2 CSF2 CSF2 1279 0.36 0.3 YES
12 JAK2 JAK2 JAK2 1430 0.35 0.31 YES
13 YES1 YES1 YES1 1496 0.34 0.33 YES
14 IRAK2 IRAK2 IRAK2 1517 0.34 0.35 YES
15 STAT1 STAT1 STAT1 1534 0.34 0.37 YES
16 IL1R1 IL1R1 IL1R1 1545 0.34 0.39 YES
17 IL3RA IL3RA IL3RA 1685 0.32 0.4 YES
18 IL6ST IL6ST IL6ST 1718 0.32 0.42 YES
19 SOCS3 SOCS3 SOCS3 1807 0.31 0.43 YES
20 CSF2RB CSF2RB CSF2RB 1848 0.3 0.45 YES
21 IL2RB IL2RB IL2RB 2217 0.27 0.45 YES
22 PELI2 PELI2 PELI2 2656 0.24 0.44 YES
23 TRAF6 TRAF6 TRAF6 2931 0.22 0.43 YES
24 IL1RAP IL1RAP IL1RAP 3027 0.22 0.44 YES
25 RIPK2 RIPK2 RIPK2 3079 0.21 0.45 YES
26 PIK3R3 PIK3R3 PIK3R3 3335 0.2 0.45 YES
27 TNIP2 TNIP2 TNIP2 3338 0.2 0.46 YES
28 CSF2RA CSF2RA CSF2RA 3481 0.19 0.47 YES
29 PIK3CB PIK3CB PIK3CB 3622 0.18 0.47 YES
30 HCK HCK HCK 3629 0.18 0.48 YES
31 FYN FYN FYN 3630 0.18 0.49 YES
32 NFKB2 NFKB2 NFKB2 3704 0.18 0.5 YES
33 PIK3R1 PIK3R1 PIK3R1 4109 0.16 0.49 YES
34 IL2RG IL2RG IL2RG 4257 0.15 0.49 YES
35 CASP1 CASP1 CASP1 4348 0.14 0.49 YES
36 SQSTM1 SQSTM1 SQSTM1 4520 0.14 0.49 YES
37 JAK3 JAK3 JAK3 4548 0.14 0.5 YES
38 GAB2 GAB2 GAB2 4660 0.13 0.5 YES
39 MAP3K3 MAP3K3 MAP3K3 4983 0.12 0.49 YES
40 CHUK CHUK CHUK 5020 0.12 0.49 YES
41 TYK2 TYK2 TYK2 5037 0.12 0.5 YES
42 STAT5A STAT5A STAT5A 5060 0.12 0.5 YES
43 MYD88 MYD88 MYD88 5136 0.11 0.51 YES
44 MAP2K6 MAP2K6 MAP2K6 5308 0.11 0.5 YES
45 CRK CRK CRK 5323 0.1 0.51 YES
46 MAP2K1 MAP2K1 MAP2K1 5338 0.1 0.52 YES
47 PIK3CD PIK3CD PIK3CD 5358 0.1 0.52 YES
48 STAT3 STAT3 STAT3 5667 0.095 0.51 NO
49 PTK2B PTK2B PTK2B 5732 0.093 0.51 NO
50 MAP3K8 MAP3K8 MAP3K8 5978 0.085 0.5 NO
51 STAT5B STAT5B STAT5B 5980 0.085 0.51 NO
52 TAB2 TAB2 TAB2 6006 0.084 0.51 NO
53 IL2 IL2 IL2 6271 0.076 0.5 NO
54 IL1A IL1A IL1A 6326 0.074 0.5 NO
55 TAB3 TAB3 TAB3 6650 0.065 0.49 NO
56 CBL CBL CBL 6723 0.064 0.49 NO
57 IL18 IL18 IL18 6786 0.061 0.49 NO
58 MAP2K2 MAP2K2 MAP2K2 6802 0.061 0.49 NO
59 VAV1 VAV1 VAV1 7059 0.054 0.48 NO
60 NRAS NRAS NRAS 7137 0.052 0.48 NO
61 IKBKB IKBKB IKBKB 7202 0.05 0.48 NO
62 IRAK1 IRAK1 IRAK1 7397 0.046 0.47 NO
63 KRAS KRAS KRAS 7618 0.04 0.46 NO
64 PTPN6 PTPN6 PTPN6 7669 0.039 0.46 NO
65 PELI3 PELI3 PELI3 7728 0.038 0.46 NO
66 IL2RA IL2RA IL2RA 7848 0.035 0.46 NO
67 RAF1 RAF1 RAF1 7858 0.035 0.46 NO
68 TOLLIP TOLLIP TOLLIP 8029 0.031 0.45 NO
69 MAP2K4 MAP2K4 MAP2K4 8103 0.029 0.45 NO
70 YWHAZ YWHAZ YWHAZ 8194 0.027 0.44 NO
71 RELA RELA RELA 8411 0.023 0.43 NO
72 SHC1 SHC1 SHC1 8438 0.022 0.43 NO
73 RAPGEF1 RAPGEF1 RAPGEF1 8524 0.02 0.43 NO
74 IKBKG IKBKG IKBKG 8750 0.016 0.42 NO
75 CUL1 CUL1 CUL1 8885 0.013 0.41 NO
76 LYN LYN LYN 8896 0.013 0.41 NO
77 YWHAB YWHAB YWHAB 9263 0.0052 0.39 NO
78 LCK LCK LCK 9267 0.0051 0.39 NO
79 BTRC BTRC BTRC 9289 0.0046 0.39 NO
80 SKP1 SKP1 SKP1 9397 0.0024 0.38 NO
81 IRAK4 IRAK4 IRAK4 9415 0.0022 0.38 NO
82 GRB2 GRB2 GRB2 9626 -0.002 0.37 NO
83 SOS1 SOS1 SOS1 9673 -0.0027 0.37 NO
84 NOD1 NOD1 NOD1 9756 -0.0046 0.36 NO
85 JAK1 JAK1 JAK1 9870 -0.007 0.36 NO
86 PIK3CA PIK3CA PIK3CA 9924 -0.008 0.36 NO
87 INPPL1 INPPL1 INPPL1 9978 -0.0089 0.35 NO
88 MAPK3 MAPK3 MAPK3 9998 -0.0093 0.35 NO
89 CRKL CRKL CRKL 10062 -0.01 0.35 NO
90 RBX1 RBX1 RBX1 10765 -0.024 0.31 NO
91 TAB1 TAB1 TAB1 10826 -0.026 0.31 NO
92 MAPK1 MAPK1 MAPK1 10844 -0.026 0.31 NO
93 TEC TEC TEC 11323 -0.036 0.29 NO
94 UBE2N UBE2N UBE2N 11423 -0.038 0.28 NO
95 PIK3R2 PIK3R2 PIK3R2 11662 -0.043 0.27 NO
96 MAP3K7 MAP3K7 MAP3K7 11756 -0.045 0.27 NO
97 HRAS HRAS HRAS 12995 -0.073 0.2 NO
98 PELI1 PELI1 PELI1 13393 -0.083 0.19 NO
99 PRKACB PRKACB PRKACB 14467 -0.12 0.13 NO
100 CDK1 CDK1 CDK1 15276 -0.16 0.096 NO
101 SYK SYK SYK 15458 -0.16 0.096 NO
102 IL7 IL7 IL7 16279 -0.23 0.064 NO
103 BLNK BLNK BLNK 16385 -0.24 0.073 NO

Figure S115.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID ERBB2ERBB3PATHWAY.

Figure S116.  Get High-res Image For the top 5 core enriched genes in the pathway: PID ERBB2ERBB3PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: REACTOME ANTIVIRAL MECHANISM BY IFN STIMULATED GENES

Table S59.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 CDH1 CDH1 CDH1 487 0.53 0.11 YES
2 RXRG RXRG RXRG 935 0.42 0.19 YES
3 TCF7L2 TCF7L2 TCF7L2 1146 0.38 0.28 YES
4 TCF7 TCF7 TCF7 1289 0.36 0.36 YES
5 CCND1 CCND1 CCND1 1486 0.34 0.44 YES
6 NTRK1 NTRK1 NTRK1 2147 0.28 0.47 YES
7 TCF7L1 TCF7L1 TCF7L1 2434 0.25 0.52 YES
8 RET RET RET 2570 0.24 0.57 YES
9 RXRA RXRA RXRA 2837 0.23 0.61 YES
10 NCOA4 NCOA4 NCOA4 4761 0.13 0.54 NO
11 MAP2K1 MAP2K1 MAP2K1 5338 0.1 0.53 NO
12 PAX8 PAX8 PAX8 6165 0.079 0.5 NO
13 MAP2K2 MAP2K2 MAP2K2 6802 0.061 0.48 NO
14 NRAS NRAS NRAS 7137 0.052 0.48 NO
15 TFG TFG TFG 7489 0.044 0.47 NO
16 KRAS KRAS KRAS 7618 0.04 0.47 NO
17 TPR TPR TPR 7865 0.035 0.47 NO
18 LEF1 LEF1 LEF1 8909 0.013 0.41 NO
19 CTNNB1 CTNNB1 CTNNB1 9112 0.0085 0.4 NO
20 TPM3 TPM3 TPM3 9259 0.0053 0.4 NO
21 MAPK3 MAPK3 MAPK3 9998 -0.0093 0.36 NO
22 CCDC6 CCDC6 CCDC6 10266 -0.014 0.34 NO
23 TP53 TP53 TP53 10818 -0.025 0.32 NO
24 MAPK1 MAPK1 MAPK1 10844 -0.026 0.32 NO
25 BRAF BRAF BRAF 11105 -0.031 0.32 NO
26 PPARG PPARG PPARG 11350 -0.036 0.31 NO
27 RXRB RXRB RXRB 11856 -0.048 0.3 NO
28 MYC MYC MYC 12264 -0.056 0.29 NO
29 HRAS HRAS HRAS 12995 -0.073 0.26 NO

Figure S117.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME ANTIVIRAL MECHANISM BY IFN STIMULATED GENES.

Figure S118.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME ANTIVIRAL MECHANISM BY IFN STIMULATED GENES, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: REACTOME TRIGLYCERIDE BIOSYNTHESIS

Table S60.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 IL1RN IL1RN IL1RN 96 0.78 0.12 YES
2 IL1R2 IL1R2 IL1R2 241 0.65 0.21 YES
3 IL1B IL1B IL1B 314 0.6 0.3 YES
4 NOD2 NOD2 NOD2 356 0.58 0.39 YES
5 IRAK3 IRAK3 IRAK3 596 0.5 0.46 YES
6 IRAK2 IRAK2 IRAK2 1517 0.34 0.46 YES
7 IL1R1 IL1R1 IL1R1 1545 0.34 0.51 YES
8 PELI2 PELI2 PELI2 2656 0.24 0.49 YES
9 TRAF6 TRAF6 TRAF6 2931 0.22 0.5 YES
10 IL1RAP IL1RAP IL1RAP 3027 0.22 0.53 YES
11 RIPK2 RIPK2 RIPK2 3079 0.21 0.56 YES
12 TNIP2 TNIP2 TNIP2 3338 0.2 0.58 YES
13 SQSTM1 SQSTM1 SQSTM1 4520 0.14 0.54 NO
14 MAP3K3 MAP3K3 MAP3K3 4983 0.12 0.53 NO
15 CHUK CHUK CHUK 5020 0.12 0.55 NO
16 MYD88 MYD88 MYD88 5136 0.11 0.56 NO
17 MAP2K6 MAP2K6 MAP2K6 5308 0.11 0.56 NO
18 MAP2K1 MAP2K1 MAP2K1 5338 0.1 0.58 NO
19 MAP3K8 MAP3K8 MAP3K8 5978 0.085 0.56 NO
20 TAB2 TAB2 TAB2 6006 0.084 0.57 NO
21 IL1A IL1A IL1A 6326 0.074 0.56 NO
22 TAB3 TAB3 TAB3 6650 0.065 0.55 NO
23 IKBKB IKBKB IKBKB 7202 0.05 0.53 NO
24 IRAK1 IRAK1 IRAK1 7397 0.046 0.52 NO
25 PELI3 PELI3 PELI3 7728 0.038 0.51 NO
26 TOLLIP TOLLIP TOLLIP 8029 0.031 0.5 NO
27 MAP2K4 MAP2K4 MAP2K4 8103 0.029 0.5 NO
28 IKBKG IKBKG IKBKG 8750 0.016 0.47 NO
29 CUL1 CUL1 CUL1 8885 0.013 0.46 NO
30 BTRC BTRC BTRC 9289 0.0046 0.44 NO
31 SKP1 SKP1 SKP1 9397 0.0024 0.43 NO
32 IRAK4 IRAK4 IRAK4 9415 0.0022 0.43 NO
33 NOD1 NOD1 NOD1 9756 -0.0046 0.41 NO
34 RBX1 RBX1 RBX1 10765 -0.024 0.36 NO
35 TAB1 TAB1 TAB1 10826 -0.026 0.36 NO
36 UBE2N UBE2N UBE2N 11423 -0.038 0.33 NO
37 MAP3K7 MAP3K7 MAP3K7 11756 -0.045 0.32 NO
38 PELI1 PELI1 PELI1 13393 -0.083 0.24 NO

Figure S119.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME TRIGLYCERIDE BIOSYNTHESIS.

Figure S120.  Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME TRIGLYCERIDE BIOSYNTHESIS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Fold change

For the top enriched genes, if you want to check whether they are

Expression level

For the top enriched genes, if you want to check whether they are

An expression pattern of top(30%)/middle(30%)/low(30%) in this subtype against other subtypes is available in a heatmap

Significant gene list

For the top enriched genes, if you want to check whether they are

Methods & Data
Input

  • Gene set database = c2.cp.v4.0.symbols.gmt

  • Expression data file = DLBC-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt

  • Phenotype data file = DLBC-TP.mergedcluster.txt

GSEA analysis

For the Gene Set Enrichment Analysis (GSEA), Broad GSEA-P-R.1.0 version is used with class2: canonical pathways geneses from MSigDB. Further details about statistics are available inThe Broad GSEA website.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Subramanian, A. et al, Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles., Proc. Natl. Acad. Sci. USA 102(43) (2005)
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