GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in UVM-TP
Uveal Melanoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C14749CW
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 UVM-TP. Broad Institute of MIT and Harvard. doi:10.7908/C14749CW
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 "UVM-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: 694
Number of samples: 80
Original number of Gene Sets: 1320
Maximum gene set size: 933

Table 2.  Get Full Table pheno data info

phenotype info
pheno.type: 1 - 4 :[ clus1 ] 18
pheno.type: 2 - 4 :[ clus2 ] 15
pheno.type: 3 - 4 :[ clus3 ] 32
pheno.type: 4 - 4 :[ clus4 ] 15

For the expression subtypes of 17361 genes in 81 samples, GSEA found enriched gene sets in each cluster using 80 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

  • clus1

    • Top enriched gene sets are KEGG DNA REPLICATION, KEGG HOMOLOGOUS RECOMBINATION, KEGG CELL CYCLE, ST ERK1 ERK2 MAPK PATHWAY, PID NECTIN PATHWAY, PID PLK1 PATHWAY, PID FOXM1PATHWAY, PID AURORA A PATHWAY, REACTOME METABOLISM OF NON CODING RNA, REACTOME CELL CYCLE MITOTIC

    • And common core enriched genes are RPA4, CCNA2, CCNB1, CDK1, BRCA2, AURKB, BIRC5, CCNB2, CDC25B, CENPA

  • clus2

    • Top enriched gene sets are KEGG GLYCOLYSIS GLUCONEOGENESIS, KEGG STEROID HORMONE BIOSYNTHESIS, KEGG PURINE METABOLISM, KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM, KEGG GLYCINE SERINE AND THREONINE METABOLISM, KEGG ARGININE AND PROLINE METABOLISM, KEGG HISTIDINE METABOLISM, KEGG TYROSINE METABOLISM, KEGG TRYPTOPHAN METABOLISM, KEGG GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE

    • And common core enriched genes are GNGT1, CCND2, CXXC4, DKK1, FOSL1, FZD2, FZD5, FZD7, FZD8, LEF1

  • clus3

    • Top enriched gene sets are KEGG RIBOSOME, KEGG RNA POLYMERASE, KEGG SPLICEOSOME, PID MYC PATHWAY, PID RXR VDR PATHWAY, PID P53REGULATIONPATHWAY, REACTOME TRANSLATION, REACTOME FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX, REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE, 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 EIF4G1, FAU, RPS10, RPS11, RPS12, RPS13, RPS14, RPS15, RPS15A, RPS16

  • clus4

    • Top enriched gene sets are KEGG PYRIMIDINE METABOLISM, KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM, KEGG INOSITOL PHOSPHATE METABOLISM, KEGG DRUG METABOLISM OTHER ENZYMES, KEGG PROTEASOME, KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION, KEGG CHEMOKINE SIGNALING PATHWAY, KEGG PHOSPHATIDYLINOSITOL SIGNALING SYSTEM, KEGG LYSOSOME, KEGG ENDOCYTOSIS

    • And common core enriched genes are LCK, PSMB10, PSMB8, PSMB9, PSME2, APOBEC3G, B2M, CD247, CD28, CD4

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 DNA REPLICATION 36 genes.ES.table 0.48 1.6 0.072 0.85 0.87 0.61 0.35 0.4 0.41 0.28
KEGG HOMOLOGOUS RECOMBINATION 26 genes.ES.table 0.71 1.7 0.008 1 0.66 0.46 0.13 0.4 1 0.6
KEGG CELL CYCLE 118 genes.ES.table 0.51 1.6 0.04 1 0.8 0.43 0.25 0.33 0.75 0.43
ST ERK1 ERK2 MAPK PATHWAY 31 genes.ES.table 0.44 1.7 0.014 1 0.68 0.45 0.29 0.32 1 0.52
PID NECTIN PATHWAY 30 genes.ES.table 0.5 1.6 0.024 1 0.8 0.47 0.29 0.33 0.66 0.4
PID PLK1 PATHWAY 45 genes.ES.table 0.7 1.6 0.053 1 0.81 0.47 0.11 0.42 0.59 0.37
PID FOXM1PATHWAY 39 genes.ES.table 0.69 1.7 0.038 1 0.72 0.44 0.11 0.39 0.86 0.47
PID AURORA A PATHWAY 31 genes.ES.table 0.53 1.6 0.086 0.92 0.86 0.23 0.09 0.21 0.44 0.3
REACTOME METABOLISM OF NON CODING RNA 47 genes.ES.table 0.47 1.6 0.06 1 0.83 0.53 0.35 0.35 0.52 0.34
REACTOME CELL CYCLE MITOTIC 297 genes.ES.table 0.52 1.6 0.038 1 0.76 0.38 0.21 0.31 0.82 0.46
genes ES table in pathway: KEGG DNA REPLICATION

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 RAD54B RAD54B RAD54B 305 0.39 0.097 YES
2 BRCA2 BRCA2 BRCA2 567 0.32 0.17 YES
3 XRCC2 XRCC2 XRCC2 710 0.29 0.25 YES
4 EME1 EME1 EME1 778 0.28 0.33 YES
5 RAD51 RAD51 RAD51 1059 0.24 0.38 YES
6 RPA4 RPA4 RPA4 1085 0.24 0.45 YES
7 RAD50 RAD50 RAD50 1118 0.24 0.52 YES
8 NBN NBN NBN 1496 0.2 0.55 YES
9 RAD54L RAD54L RAD54L 1510 0.2 0.61 YES
10 MRE11A MRE11A MRE11A 1938 0.17 0.64 YES
11 BLM BLM BLM 2123 0.16 0.67 YES
12 RAD52 RAD52 RAD52 2259 0.15 0.71 YES
13 XRCC3 XRCC3 XRCC3 3964 0.094 0.64 NO
14 POLD3 POLD3 POLD3 5553 0.058 0.56 NO
15 MUS81 MUS81 MUS81 5619 0.057 0.58 NO
16 SSBP1 SSBP1 SSBP1 5702 0.055 0.59 NO
17 RAD51C RAD51C RAD51C 7447 0.02 0.49 NO
18 SHFM1 SHFM1 SHFM1 7767 0.014 0.48 NO
19 TOP3A TOP3A TOP3A 8312 0.0044 0.45 NO
20 POLD2 POLD2 POLD2 8863 -0.0059 0.42 NO
21 RPA3 RPA3 RPA3 9426 -0.017 0.39 NO
22 POLD4 POLD4 POLD4 9901 -0.024 0.37 NO
23 RPA1 RPA1 RPA1 9955 -0.026 0.38 NO
24 TOP3B TOP3B TOP3B 10697 -0.04 0.34 NO
25 POLD1 POLD1 POLD1 11686 -0.062 0.31 NO
26 RPA2 RPA2 RPA2 12077 -0.072 0.3 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 DNA REPLICATION.

Figure S2.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG DNA REPLICATION, 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 HOMOLOGOUS RECOMBINATION

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 MAP3K8 MAP3K8 MAP3K8 1089 0.24 0.034 YES
2 CREB5 CREB5 CREB5 1188 0.23 0.12 YES
3 RPS6KA2 RPS6KA2 RPS6KA2 1589 0.2 0.18 YES
4 DUSP9 DUSP9 DUSP9 1736 0.18 0.24 YES
5 SOS1 SOS1 SOS1 2581 0.14 0.25 YES
6 TRAF3 TRAF3 TRAF3 2800 0.13 0.29 YES
7 EIF4E EIF4E EIF4E 3873 0.096 0.27 YES
8 ATF1 ATF1 ATF1 3875 0.096 0.31 YES
9 NFKB1 NFKB1 NFKB1 4080 0.091 0.34 YES
10 SHC1 SHC1 SHC1 4381 0.084 0.35 YES
11 BRAF BRAF BRAF 4564 0.08 0.37 YES
12 CREB1 CREB1 CREB1 4632 0.078 0.4 YES
13 MAPK1 MAPK1 MAPK1 4700 0.077 0.43 YES
14 MAP2K1 MAP2K1 MAP2K1 4959 0.071 0.44 YES
15 MKNK2 MKNK2 MKNK2 7108 0.026 0.33 NO
16 EEF2K EEF2K EEF2K 7235 0.024 0.33 NO
17 KLF6 KLF6 KLF6 7262 0.024 0.34 NO
18 SOS2 SOS2 SOS2 8093 0.0084 0.3 NO
19 MAP2K2 MAP2K2 MAP2K2 8145 0.0076 0.3 NO
20 RPS6KA3 RPS6KA3 RPS6KA3 8243 0.0057 0.29 NO
21 BAD BAD BAD 8566 -0.00039 0.27 NO
22 ARAF ARAF ARAF 9008 -0.0085 0.25 NO
23 GRB2 GRB2 GRB2 9590 -0.019 0.23 NO
24 KAT5 KAT5 KAT5 10594 -0.038 0.18 NO
25 CREB3 CREB3 CREB3 10923 -0.045 0.18 NO
26 MKNK1 MKNK1 MKNK1 11257 -0.052 0.18 NO
27 RPS6KA1 RPS6KA1 RPS6KA1 11310 -0.053 0.2 NO
28 MAPK3 MAPK3 MAPK3 11770 -0.064 0.2 NO
29 DUSP6 DUSP6 DUSP6 11804 -0.064 0.23 NO
30 RAP1A RAP1A RAP1A 12671 -0.09 0.21 NO
31 DUSP4 DUSP4 DUSP4 13881 -0.14 0.2 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 HOMOLOGOUS RECOMBINATION.

Figure S4.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG HOMOLOGOUS RECOMBINATION, 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 CELL CYCLE

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 NEK2 NEK2 NEK2 280 0.4 0.048 YES
2 CENPA CENPA CENPA 306 0.39 0.11 YES
3 CCNB2 CCNB2 CCNB2 327 0.39 0.17 YES
4 CDK1 CDK1 CDK1 361 0.37 0.23 YES
5 ONECUT1 ONECUT1 ONECUT1 372 0.37 0.29 YES
6 CENPF CENPF CENPF 444 0.35 0.34 YES
7 CCNA2 CCNA2 CCNA2 555 0.32 0.38 YES
8 BRCA2 BRCA2 BRCA2 567 0.32 0.43 YES
9 FOXM1 FOXM1 FOXM1 721 0.29 0.47 YES
10 BIRC5 BIRC5 BIRC5 898 0.26 0.5 YES
11 PLK1 PLK1 PLK1 1074 0.24 0.53 YES
12 CDC25B CDC25B CDC25B 1086 0.24 0.57 YES
13 FOS FOS FOS 1165 0.23 0.6 YES
14 AURKB AURKB AURKB 1172 0.23 0.64 YES
15 CHEK2 CHEK2 CHEK2 1419 0.21 0.66 YES
16 ESR1 ESR1 ESR1 1570 0.2 0.68 YES
17 CCNB1 CCNB1 CCNB1 1948 0.17 0.69 YES
18 MMP2 MMP2 MMP2 2955 0.13 0.65 NO
19 SKP2 SKP2 SKP2 3008 0.12 0.66 NO
20 CKS1B CKS1B CKS1B 3045 0.12 0.68 NO
21 TGFA TGFA TGFA 4952 0.071 0.58 NO
22 MAP2K1 MAP2K1 MAP2K1 4959 0.071 0.6 NO
23 CCNE1 CCNE1 CCNE1 5281 0.063 0.59 NO
24 EP300 EP300 EP300 5916 0.05 0.56 NO
25 MYC MYC MYC 6556 0.036 0.53 NO
26 CREBBP CREBBP CREBBP 7010 0.028 0.51 NO
27 CCND1 CCND1 CCND1 7202 0.025 0.5 NO
28 RB1 RB1 RB1 7743 0.015 0.47 NO
29 CENPB CENPB CENPB 8677 -0.0026 0.42 NO
30 CDKN2A CDKN2A CDKN2A 8910 -0.0065 0.4 NO
31 SP1 SP1 SP1 9487 -0.018 0.37 NO
32 XRCC1 XRCC1 XRCC1 9546 -0.019 0.37 NO
33 GSK3A GSK3A GSK3A 9617 -0.02 0.37 NO
34 CDK4 CDK4 CDK4 9990 -0.026 0.36 NO
35 NFATC3 NFATC3 NFATC3 10386 -0.034 0.34 NO
36 ETV5 ETV5 ETV5 10826 -0.043 0.32 NO
37 LAMA4 LAMA4 LAMA4 11949 -0.068 0.26 NO
38 CDK2 CDK2 CDK2 14017 -0.14 0.17 NO
39 GAS1 GAS1 GAS1 14080 -0.15 0.19 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 CELL CYCLE.

Figure S6.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG CELL CYCLE, 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 ERK1 ERK2 MAPK PATHWAY

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 SPC24 SPC24 SPC24 57 0.55 0.012 YES
2 CASC5 CASC5 CASC5 80 0.53 0.025 YES
3 CENPI CENPI CENPI 96 0.51 0.038 YES
4 CCNE2 CCNE2 CCNE2 117 0.5 0.05 YES
5 NDC80 NDC80 NDC80 138 0.48 0.062 YES
6 POLA1 POLA1 POLA1 190 0.45 0.071 YES
7 SPC25 SPC25 SPC25 201 0.44 0.083 YES
8 BUB1B BUB1B BUB1B 218 0.43 0.094 YES
9 MCM10 MCM10 MCM10 220 0.43 0.1 YES
10 KIF18A KIF18A KIF18A 222 0.43 0.12 YES
11 CDC25C CDC25C CDC25C 228 0.42 0.13 YES
12 NEK2 NEK2 NEK2 280 0.4 0.14 YES
13 BUB1 BUB1 BUB1 287 0.4 0.15 YES
14 ERCC6L ERCC6L ERCC6L 288 0.4 0.16 YES
15 E2F5 E2F5 E2F5 298 0.4 0.17 YES
16 CENPA CENPA CENPA 306 0.39 0.18 YES
17 KIF20A KIF20A KIF20A 307 0.39 0.19 YES
18 CCNB2 CCNB2 CCNB2 327 0.39 0.2 YES
19 CDK1 CDK1 CDK1 361 0.37 0.21 YES
20 POLE2 POLE2 POLE2 404 0.36 0.21 YES
21 DNA2 DNA2 DNA2 421 0.35 0.22 YES
22 NUF2 NUF2 NUF2 425 0.35 0.23 YES
23 RRM2 RRM2 RRM2 456 0.34 0.24 YES
24 CDC6 CDC6 CDC6 460 0.34 0.25 YES
25 MLF1IP MLF1IP MLF1IP 498 0.33 0.26 YES
26 PLK4 PLK4 PLK4 520 0.33 0.26 YES
27 CCNA2 CCNA2 CCNA2 555 0.32 0.27 YES
28 KIF23 KIF23 KIF23 634 0.3 0.27 YES
29 SKA1 SKA1 SKA1 656 0.3 0.28 YES
30 CENPP CENPP CENPP 694 0.29 0.29 YES
31 TAOK1 TAOK1 TAOK1 795 0.28 0.29 YES
32 CENPJ CENPJ CENPJ 828 0.27 0.29 YES
33 CDC45 CDC45 CDC45 835 0.27 0.3 YES
34 CEP192 CEP192 CEP192 837 0.27 0.31 YES
35 DBF4 DBF4 DBF4 841 0.27 0.32 YES
36 CEP135 CEP135 CEP135 855 0.27 0.32 YES
37 BIRC5 BIRC5 BIRC5 898 0.26 0.33 YES
38 KNTC1 KNTC1 KNTC1 936 0.26 0.33 YES
39 WEE1 WEE1 WEE1 963 0.25 0.34 YES
40 LIN9 LIN9 LIN9 979 0.25 0.34 YES
41 MCM4 MCM4 MCM4 1006 0.25 0.35 YES
42 CENPC1 CENPC1 CENPC1 1033 0.24 0.35 YES
43 CEP72 CEP72 CEP72 1054 0.24 0.36 YES
44 FBXO5 FBXO5 FBXO5 1070 0.24 0.36 YES
45 PLK1 PLK1 PLK1 1074 0.24 0.37 YES
46 RPA4 RPA4 RPA4 1085 0.24 0.38 YES
47 CDC25B CDC25B CDC25B 1086 0.24 0.38 YES
48 AURKA AURKA AURKA 1136 0.23 0.39 YES
49 CENPK CENPK CENPK 1157 0.23 0.39 YES
50 AURKB AURKB AURKB 1172 0.23 0.4 YES
51 RBL1 RBL1 RBL1 1200 0.23 0.4 YES
52 CENPL CENPL CENPL 1250 0.22 0.41 YES
53 SGOL2 SGOL2 SGOL2 1272 0.22 0.41 YES
54 CEP290 CEP290 CEP290 1288 0.22 0.42 YES
55 TYMS TYMS TYMS 1331 0.22 0.42 YES
56 E2F2 E2F2 E2F2 1469 0.21 0.42 YES
57 UBE2C UBE2C UBE2C 1609 0.2 0.41 YES
58 PKMYT1 PKMYT1 PKMYT1 1617 0.19 0.42 YES
59 MAD2L1 MAD2L1 MAD2L1 1626 0.19 0.42 YES
60 APITD1 APITD1 APITD1 1752 0.18 0.42 YES
61 PRIM1 PRIM1 PRIM1 1769 0.18 0.42 YES
62 DSN1 DSN1 DSN1 1809 0.18 0.43 YES
63 GINS1 GINS1 GINS1 1823 0.18 0.43 YES
64 CENPM CENPM CENPM 1848 0.18 0.44 YES
65 AKAP9 AKAP9 AKAP9 1875 0.18 0.44 YES
66 NEDD1 NEDD1 NEDD1 1918 0.17 0.44 YES
67 ANAPC4 ANAPC4 ANAPC4 1923 0.17 0.45 YES
68 CCNB1 CCNB1 CCNB1 1948 0.17 0.45 YES
69 PRKAR2B PRKAR2B PRKAR2B 1969 0.17 0.45 YES
70 PSME4 PSME4 PSME4 1974 0.17 0.46 YES
71 MCM6 MCM6 MCM6 2122 0.16 0.45 YES
72 RAD21 RAD21 RAD21 2208 0.16 0.45 YES
73 CDKN2C CDKN2C CDKN2C 2263 0.15 0.45 YES
74 CDC7 CDC7 CDC7 2430 0.15 0.45 YES
75 CLIP1 CLIP1 CLIP1 2470 0.14 0.45 YES
76 CENPO CENPO CENPO 2476 0.14 0.45 YES
77 KIF2C KIF2C KIF2C 2492 0.14 0.46 YES
78 XPO1 XPO1 XPO1 2516 0.14 0.46 YES
79 CCNH CCNH CCNH 2518 0.14 0.46 YES
80 ANAPC10 ANAPC10 ANAPC10 2559 0.14 0.46 YES
81 ZWINT ZWINT ZWINT 2677 0.14 0.46 YES
82 CDC27 CDC27 CDC27 2696 0.14 0.46 YES
83 CCNA1 CCNA1 CCNA1 2705 0.14 0.47 YES
84 KIF2A KIF2A KIF2A 2793 0.13 0.46 YES
85 PRIM2 PRIM2 PRIM2 2807 0.13 0.47 YES
86 AHCTF1 AHCTF1 AHCTF1 2816 0.13 0.47 YES
87 PSMD14 PSMD14 PSMD14 2847 0.13 0.47 YES
88 CCND2 CCND2 CCND2 2874 0.13 0.48 YES
89 TUBGCP5 TUBGCP5 TUBGCP5 2902 0.13 0.48 YES
90 POLE POLE POLE 2957 0.13 0.48 YES
91 SKP2 SKP2 SKP2 3008 0.12 0.48 YES
92 HAUS2 HAUS2 HAUS2 3018 0.12 0.48 YES
93 MYBL2 MYBL2 MYBL2 3031 0.12 0.48 YES
94 CKS1B CKS1B CKS1B 3045 0.12 0.48 YES
95 PSMA3 PSMA3 PSMA3 3074 0.12 0.49 YES
96 PSMA4 PSMA4 PSMA4 3164 0.12 0.48 YES
97 PTTG1 PTTG1 PTTG1 3220 0.12 0.48 YES
98 LIN54 LIN54 LIN54 3221 0.12 0.49 YES
99 DHFR DHFR DHFR 3230 0.12 0.49 YES
100 CUL1 CUL1 CUL1 3250 0.12 0.49 YES
101 CENPH CENPH CENPH 3259 0.12 0.5 YES
102 CDCA8 CDCA8 CDCA8 3294 0.12 0.5 YES
103 CENPN CENPN CENPN 3299 0.12 0.5 YES
104 CENPQ CENPQ CENPQ 3331 0.11 0.5 YES
105 PSMA8 PSMA8 PSMA8 3350 0.11 0.5 YES
106 NUP37 NUP37 NUP37 3363 0.11 0.51 YES
107 PSMD12 PSMD12 PSMD12 3436 0.11 0.5 YES
108 NUP107 NUP107 NUP107 3439 0.11 0.51 YES
109 ANAPC1 ANAPC1 ANAPC1 3533 0.11 0.5 YES
110 HSP90AA1 HSP90AA1 HSP90AA1 3541 0.11 0.51 YES
111 PSMC6 PSMC6 PSMC6 3542 0.11 0.51 YES
112 CDK6 CDK6 CDK6 3561 0.11 0.51 YES
113 PSMD5 PSMD5 PSMD5 3589 0.1 0.51 YES
114 MNAT1 MNAT1 MNAT1 3606 0.1 0.52 YES
115 SEH1L SEH1L SEH1L 3776 0.099 0.51 NO
116 ZWILCH ZWILCH ZWILCH 3833 0.097 0.51 NO
117 PPP2R5E PPP2R5E PPP2R5E 3847 0.097 0.51 NO
118 MIS12 MIS12 MIS12 3853 0.097 0.51 NO
119 MCM8 MCM8 MCM8 3891 0.096 0.51 NO
120 NUP85 NUP85 NUP85 3894 0.096 0.51 NO
121 CDKN2B CDKN2B CDKN2B 4054 0.092 0.51 NO
122 CDK5RAP2 CDK5RAP2 CDK5RAP2 4082 0.091 0.51 NO
123 CDKN1B CDKN1B CDKN1B 4143 0.09 0.51 NO
124 CDC23 CDC23 CDC23 4184 0.089 0.51 NO
125 PAFAH1B1 PAFAH1B1 PAFAH1B1 4212 0.088 0.51 NO
126 NUP43 NUP43 NUP43 4234 0.088 0.51 NO
127 CDK7 CDK7 CDK7 4285 0.087 0.51 NO
128 CCDC99 CCDC99 CCDC99 4371 0.085 0.51 NO
129 GMNN GMNN GMNN 4400 0.084 0.51 NO
130 B9D2 B9D2 B9D2 4466 0.082 0.5 NO
131 RFC5 RFC5 RFC5 4472 0.082 0.51 NO
132 PSMD11 PSMD11 PSMD11 4512 0.082 0.51 NO
133 PSMA7 PSMA7 PSMA7 4620 0.079 0.5 NO
134 STAG2 STAG2 STAG2 4650 0.078 0.5 NO
135 CDT1 CDT1 CDT1 4667 0.078 0.5 NO
136 PPP2R5C PPP2R5C PPP2R5C 4675 0.078 0.51 NO
137 OFD1 OFD1 OFD1 4763 0.076 0.5 NO
138 SGOL1 SGOL1 SGOL1 4765 0.076 0.5 NO
139 PSMA6 PSMA6 PSMA6 4794 0.075 0.51 NO
140 PCNT PCNT PCNT 4850 0.074 0.5 NO
141 PSMC1 PSMC1 PSMC1 4855 0.074 0.51 NO
142 ANAPC7 ANAPC7 ANAPC7 4873 0.073 0.51 NO
143 PCNA PCNA PCNA 4947 0.072 0.5 NO
144 SMC3 SMC3 SMC3 4951 0.071 0.51 NO
145 RANBP2 RANBP2 RANBP2 5001 0.07 0.51 NO
146 CDKN1A CDKN1A CDKN1A 5019 0.07 0.51 NO
147 TUBGCP3 TUBGCP3 TUBGCP3 5169 0.066 0.5 NO
148 CKAP5 CKAP5 CKAP5 5203 0.066 0.5 NO
149 PSMC2 PSMC2 PSMC2 5251 0.064 0.5 NO
150 CCNE1 CCNE1 CCNE1 5281 0.063 0.5 NO
151 RFC2 RFC2 RFC2 5387 0.061 0.49 NO
152 POLA2 POLA2 POLA2 5411 0.061 0.5 NO
153 PSMA2 PSMA2 PSMA2 5436 0.06 0.5 NO
154 NSL1 NSL1 NSL1 5510 0.059 0.49 NO
155 POLD3 POLD3 POLD3 5553 0.058 0.49 NO
156 DYNLL1 DYNLL1 DYNLL1 5588 0.057 0.49 NO
157 FEN1 FEN1 FEN1 5732 0.054 0.48 NO
158 FGFR1OP FGFR1OP FGFR1OP 5742 0.054 0.48 NO
159 SMC1A SMC1A SMC1A 5788 0.053 0.48 NO
160 RFC3 RFC3 RFC3 5799 0.053 0.48 NO
161 DYRK1A DYRK1A DYRK1A 5889 0.051 0.48 NO
162 CEP76 CEP76 CEP76 5904 0.05 0.48 NO
163 E2F1 E2F1 E2F1 6018 0.048 0.48 NO
164 PSMA1 PSMA1 PSMA1 6020 0.048 0.48 NO
165 LIG1 LIG1 LIG1 6084 0.046 0.48 NO
166 ZW10 ZW10 ZW10 6095 0.046 0.48 NO
167 DYNC1I2 DYNC1I2 DYNC1I2 6116 0.046 0.48 NO
168 CSNK1E CSNK1E CSNK1E 6158 0.044 0.47 NO
169 PPP2CA PPP2CA PPP2CA 6163 0.044 0.48 NO
170 PSMD7 PSMD7 PSMD7 6233 0.043 0.47 NO
171 BUB3 BUB3 BUB3 6236 0.043 0.47 NO
172 TFDP1 TFDP1 TFDP1 6311 0.042 0.47 NO
173 YWHAG YWHAG YWHAG 6341 0.041 0.47 NO
174 NDEL1 NDEL1 NDEL1 6370 0.041 0.47 NO
175 PSMD10 PSMD10 PSMD10 6489 0.038 0.46 NO
176 SKP1 SKP1 SKP1 6534 0.037 0.46 NO
177 CDC20 CDC20 CDC20 6536 0.037 0.46 NO
178 MYC MYC MYC 6556 0.036 0.46 NO
179 SDCCAG8 SDCCAG8 SDCCAG8 6811 0.031 0.45 NO
180 MAD1L1 MAD1L1 MAD1L1 6863 0.03 0.45 NO
181 PSMB3 PSMB3 PSMB3 6892 0.03 0.45 NO
182 NUP133 NUP133 NUP133 6911 0.03 0.44 NO
183 CEP57 CEP57 CEP57 7119 0.026 0.43 NO
184 PSMC3 PSMC3 PSMC3 7136 0.026 0.43 NO
185 DYNC1H1 DYNC1H1 DYNC1H1 7138 0.026 0.43 NO
186 CCND1 CCND1 CCND1 7202 0.025 0.43 NO
187 PSMB5 PSMB5 PSMB5 7309 0.023 0.43 NO
188 PSMC4 PSMC4 PSMC4 7439 0.02 0.42 NO
189 ANAPC5 ANAPC5 ANAPC5 7468 0.02 0.42 NO
190 YWHAE YWHAE YWHAE 7564 0.018 0.41 NO
191 PSMC5 PSMC5 PSMC5 7612 0.017 0.41 NO
192 MCM3 MCM3 MCM3 7719 0.015 0.4 NO
193 RB1 RB1 RB1 7743 0.015 0.4 NO
194 RBL2 RBL2 RBL2 7781 0.014 0.4 NO
195 PSMD1 PSMD1 PSMD1 7784 0.014 0.4 NO
196 GINS2 GINS2 GINS2 7813 0.014 0.4 NO
197 PPP2R5A PPP2R5A PPP2R5A 7835 0.013 0.4 NO
198 PSMD8 PSMD8 PSMD8 7894 0.012 0.4 NO
199 STAG1 STAG1 STAG1 7913 0.012 0.4 NO
200 CDC16 CDC16 CDC16 7947 0.011 0.39 NO
201 SKA2 SKA2 SKA2 7965 0.011 0.39 NO
202 PSMB1 PSMB1 PSMB1 8003 0.0099 0.39 NO
203 PSMD3 PSMD3 PSMD3 8060 0.0089 0.39 NO
204 TUBG2 TUBG2 TUBG2 8210 0.0063 0.38 NO
205 CLASP1 CLASP1 CLASP1 8279 0.0051 0.38 NO
206 CDC26 CDC26 CDC26 8386 0.003 0.37 NO
207 MCM7 MCM7 MCM7 8411 0.0025 0.37 NO
208 CDC14A CDC14A CDC14A 8453 0.0017 0.37 NO
209 PPP1CC PPP1CC PPP1CC 8520 0.00057 0.36 NO
210 PCM1 PCM1 PCM1 8527 0.00035 0.36 NO
211 ANAPC11 ANAPC11 ANAPC11 8556 -0.00018 0.36 NO
212 PSMD4 PSMD4 PSMD4 8706 -0.003 0.35 NO
213 PSMB4 PSMB4 PSMB4 8711 -0.0031 0.35 NO
214 NUMA1 NUMA1 NUMA1 8809 -0.0052 0.35 NO
215 POLD2 POLD2 POLD2 8863 -0.0059 0.34 NO
216 CDKN2A CDKN2A CDKN2A 8910 -0.0065 0.34 NO
217 PSMB8 PSMB8 PSMB8 8972 -0.0079 0.34 NO
218 PSMB6 PSMB6 PSMB6 8984 -0.008 0.34 NO
219 PPP2R2A PPP2R2A PPP2R2A 9083 -0.0098 0.33 NO
220 PSMB7 PSMB7 PSMB7 9116 -0.01 0.33 NO
221 GINS4 GINS4 GINS4 9142 -0.011 0.33 NO
222 PSMD13 PSMD13 PSMD13 9144 -0.011 0.33 NO
223 PPP2R1A PPP2R1A PPP2R1A 9229 -0.013 0.32 NO
224 ALMS1 ALMS1 ALMS1 9249 -0.013 0.32 NO
225 HDAC1 HDAC1 HDAC1 9272 -0.013 0.32 NO
226 TUBGCP6 TUBGCP6 TUBGCP6 9365 -0.015 0.32 NO
227 RPA3 RPA3 RPA3 9426 -0.017 0.32 NO
228 SSNA1 SSNA1 SSNA1 9474 -0.018 0.31 NO
229 TUBG1 TUBG1 TUBG1 9494 -0.018 0.31 NO
230 PRKACA PRKACA PRKACA 9522 -0.018 0.31 NO
231 TUBGCP2 TUBGCP2 TUBGCP2 9541 -0.019 0.31 NO
232 RCC2 RCC2 RCC2 9559 -0.019 0.31 NO
233 DCTN2 DCTN2 DCTN2 9574 -0.019 0.31 NO
234 CEP70 CEP70 CEP70 9644 -0.02 0.31 NO
235 RBBP4 RBBP4 RBBP4 9694 -0.021 0.3 NO
236 PPP2R1B PPP2R1B PPP2R1B 9717 -0.021 0.3 NO
237 TUBA1A TUBA1A TUBA1A 9763 -0.022 0.3 NO
238 TK2 TK2 TK2 9801 -0.023 0.3 NO
239 PSMD9 PSMD9 PSMD9 9851 -0.024 0.3 NO
240 POLD4 POLD4 POLD4 9901 -0.024 0.3 NO
241 RPA1 RPA1 RPA1 9955 -0.026 0.29 NO
242 PMF1 PMF1 PMF1 9986 -0.026 0.29 NO
243 CDK4 CDK4 CDK4 9990 -0.026 0.29 NO
244 MAPRE1 MAPRE1 MAPRE1 10032 -0.027 0.29 NO
245 PSMA5 PSMA5 PSMA5 10040 -0.027 0.29 NO
246 BTRC BTRC BTRC 10246 -0.031 0.28 NO
247 RANGAP1 RANGAP1 RANGAP1 10460 -0.035 0.27 NO
248 CSNK1D CSNK1D CSNK1D 10605 -0.038 0.26 NO
249 RFC4 RFC4 RFC4 10688 -0.04 0.26 NO
250 DCTN1 DCTN1 DCTN1 10690 -0.04 0.26 NO
251 RPS27A RPS27A RPS27A 10731 -0.041 0.26 NO
252 PPP2CB PPP2CB PPP2CB 10746 -0.041 0.26 NO
253 ACTR1A ACTR1A ACTR1A 10806 -0.042 0.26 NO
254 MAX MAX MAX 10860 -0.043 0.25 NO
255 CEP63 CEP63 CEP63 11105 -0.048 0.24 NO
256 CEP250 CEP250 CEP250 11135 -0.049 0.24 NO
257 NINL NINL NINL 11228 -0.051 0.24 NO
258 ANAPC2 ANAPC2 ANAPC2 11403 -0.055 0.23 NO
259 E2F4 E2F4 E2F4 11454 -0.056 0.22 NO
260 CENPT CENPT CENPT 11458 -0.056 0.23 NO
261 PSMB2 PSMB2 PSMB2 11561 -0.058 0.22 NO
262 CDKN2D CDKN2D CDKN2D 11571 -0.059 0.22 NO
263 POLD1 POLD1 POLD1 11686 -0.062 0.22 NO
264 PSMD6 PSMD6 PSMD6 11712 -0.062 0.22 NO
265 LIN52 LIN52 LIN52 11727 -0.062 0.22 NO
266 UBE2D1 UBE2D1 UBE2D1 11834 -0.065 0.22 NO
267 PSMF1 PSMF1 PSMF1 11995 -0.069 0.21 NO
268 RPA2 RPA2 RPA2 12077 -0.072 0.2 NO
269 E2F3 E2F3 E2F3 12094 -0.072 0.21 NO
270 UBA52 UBA52 UBA52 12103 -0.072 0.21 NO
271 CEP164 CEP164 CEP164 12110 -0.073 0.21 NO
272 PPP2R5D PPP2R5D PPP2R5D 12148 -0.074 0.21 NO
273 INCENP INCENP INCENP 12234 -0.076 0.21 NO
274 PSME2 PSME2 PSME2 12288 -0.077 0.2 NO
275 ITGB3BP ITGB3BP ITGB3BP 12334 -0.079 0.2 NO
276 PSME1 PSME1 PSME1 12477 -0.083 0.2 NO
277 PSMB10 PSMB10 PSMB10 12523 -0.084 0.2 NO
278 MCM5 MCM5 MCM5 12601 -0.088 0.2 NO
279 TUBB TUBB TUBB 12653 -0.09 0.2 NO
280 NUDC NUDC NUDC 12655 -0.09 0.2 NO
281 CCND3 CCND3 CCND3 13035 -0.1 0.18 NO
282 DCTN3 DCTN3 DCTN3 13069 -0.1 0.18 NO
283 PSMD2 PSMD2 PSMD2 13080 -0.1 0.18 NO
284 CETN2 CETN2 CETN2 13381 -0.12 0.17 NO
285 UBE2E1 UBE2E1 UBE2E1 13436 -0.12 0.17 NO
286 SEC13 SEC13 SEC13 13781 -0.13 0.15 NO
287 LIN37 LIN37 LIN37 13786 -0.13 0.15 NO
288 CDK2 CDK2 CDK2 14017 -0.14 0.14 NO
289 AZI1 AZI1 AZI1 14148 -0.15 0.14 NO
290 RPS27 RPS27 RPS27 14306 -0.16 0.14 NO
291 PSMB9 PSMB9 PSMB9 14551 -0.17 0.13 NO
292 GORASP1 GORASP1 GORASP1 15006 -0.2 0.1 NO
293 MCM2 MCM2 MCM2 15091 -0.2 0.11 NO
294 PPP2R3B PPP2R3B PPP2R3B 15224 -0.21 0.1 NO
295 PPP2R5B PPP2R5B PPP2R5B 15278 -0.22 0.11 NO
296 CDC25A CDC25A CDC25A 15383 -0.23 0.11 NO
297 TUBA4A TUBA4A TUBA4A 16175 -0.3 0.069 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: ST ERK1 ERK2 MAPK PATHWAY.

Figure S8.  Get High-res Image For the top 5 core enriched genes in the pathway: ST ERK1 ERK2 MAPK 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 NECTIN PATHWAY

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 CCNE2 CCNE2 CCNE2 117 0.5 0.03 YES
2 POLA1 POLA1 POLA1 190 0.45 0.058 YES
3 MCM10 MCM10 MCM10 220 0.43 0.088 YES
4 E2F5 E2F5 E2F5 298 0.4 0.11 YES
5 CDK1 CDK1 CDK1 361 0.37 0.14 YES
6 POLE2 POLE2 POLE2 404 0.36 0.16 YES
7 RRM2 RRM2 RRM2 456 0.34 0.18 YES
8 CDC6 CDC6 CDC6 460 0.34 0.21 YES
9 CCNA2 CCNA2 CCNA2 555 0.32 0.23 YES
10 CDC45 CDC45 CDC45 835 0.27 0.23 YES
11 DBF4 DBF4 DBF4 841 0.27 0.25 YES
12 WEE1 WEE1 WEE1 963 0.25 0.26 YES
13 LIN9 LIN9 LIN9 979 0.25 0.28 YES
14 MCM4 MCM4 MCM4 1006 0.25 0.3 YES
15 FBXO5 FBXO5 FBXO5 1070 0.24 0.31 YES
16 RPA4 RPA4 RPA4 1085 0.24 0.33 YES
17 RBL1 RBL1 RBL1 1200 0.23 0.34 YES
18 TYMS TYMS TYMS 1331 0.22 0.34 YES
19 E2F2 E2F2 E2F2 1469 0.21 0.35 YES
20 PKMYT1 PKMYT1 PKMYT1 1617 0.19 0.36 YES
21 PRIM1 PRIM1 PRIM1 1769 0.18 0.36 YES
22 CCNB1 CCNB1 CCNB1 1948 0.17 0.36 YES
23 MCM6 MCM6 MCM6 2122 0.16 0.37 YES
24 CDKN2C CDKN2C CDKN2C 2263 0.15 0.37 YES
25 CDC7 CDC7 CDC7 2430 0.15 0.37 YES
26 CCNH CCNH CCNH 2518 0.14 0.38 YES
27 CCNA1 CCNA1 CCNA1 2705 0.14 0.38 YES
28 PRIM2 PRIM2 PRIM2 2807 0.13 0.38 YES
29 PSMD14 PSMD14 PSMD14 2847 0.13 0.39 YES
30 CCND2 CCND2 CCND2 2874 0.13 0.39 YES
31 POLE POLE POLE 2957 0.13 0.4 YES
32 SKP2 SKP2 SKP2 3008 0.12 0.4 YES
33 MYBL2 MYBL2 MYBL2 3031 0.12 0.41 YES
34 CKS1B CKS1B CKS1B 3045 0.12 0.42 YES
35 PSMA3 PSMA3 PSMA3 3074 0.12 0.43 YES
36 PSMA4 PSMA4 PSMA4 3164 0.12 0.43 YES
37 LIN54 LIN54 LIN54 3221 0.12 0.44 YES
38 DHFR DHFR DHFR 3230 0.12 0.45 YES
39 CUL1 CUL1 CUL1 3250 0.12 0.45 YES
40 PSMD12 PSMD12 PSMD12 3436 0.11 0.45 YES
41 PSMC6 PSMC6 PSMC6 3542 0.11 0.45 YES
42 CDK6 CDK6 CDK6 3561 0.11 0.46 YES
43 PSMD5 PSMD5 PSMD5 3589 0.1 0.46 YES
44 MNAT1 MNAT1 MNAT1 3606 0.1 0.47 YES
45 MCM8 MCM8 MCM8 3891 0.096 0.46 NO
46 CDKN2B CDKN2B CDKN2B 4054 0.092 0.46 NO
47 CDKN1B CDKN1B CDKN1B 4143 0.09 0.46 NO
48 CDK7 CDK7 CDK7 4285 0.087 0.46 NO
49 PSMD11 PSMD11 PSMD11 4512 0.082 0.45 NO
50 PSMA7 PSMA7 PSMA7 4620 0.079 0.45 NO
51 CDT1 CDT1 CDT1 4667 0.078 0.46 NO
52 PSMA6 PSMA6 PSMA6 4794 0.075 0.45 NO
53 PSMC1 PSMC1 PSMC1 4855 0.074 0.46 NO
54 PCNA PCNA PCNA 4947 0.072 0.46 NO
55 CDKN1A CDKN1A CDKN1A 5019 0.07 0.46 NO
56 PSMC2 PSMC2 PSMC2 5251 0.064 0.45 NO
57 CCNE1 CCNE1 CCNE1 5281 0.063 0.45 NO
58 POLA2 POLA2 POLA2 5411 0.061 0.45 NO
59 PSMA2 PSMA2 PSMA2 5436 0.06 0.45 NO
60 DYRK1A DYRK1A DYRK1A 5889 0.051 0.43 NO
61 E2F1 E2F1 E2F1 6018 0.048 0.42 NO
62 PSMA1 PSMA1 PSMA1 6020 0.048 0.43 NO
63 PPP2CA PPP2CA PPP2CA 6163 0.044 0.42 NO
64 PSMD7 PSMD7 PSMD7 6233 0.043 0.42 NO
65 TFDP1 TFDP1 TFDP1 6311 0.042 0.42 NO
66 PSMD10 PSMD10 PSMD10 6489 0.038 0.41 NO
67 SKP1 SKP1 SKP1 6534 0.037 0.41 NO
68 MYC MYC MYC 6556 0.036 0.41 NO
69 PSMB3 PSMB3 PSMB3 6892 0.03 0.4 NO
70 PSMC3 PSMC3 PSMC3 7136 0.026 0.38 NO
71 CCND1 CCND1 CCND1 7202 0.025 0.38 NO
72 PSMB5 PSMB5 PSMB5 7309 0.023 0.38 NO
73 PSMC4 PSMC4 PSMC4 7439 0.02 0.37 NO
74 PSMC5 PSMC5 PSMC5 7612 0.017 0.36 NO
75 MCM3 MCM3 MCM3 7719 0.015 0.36 NO
76 RB1 RB1 RB1 7743 0.015 0.36 NO
77 RBL2 RBL2 RBL2 7781 0.014 0.36 NO
78 PSMD1 PSMD1 PSMD1 7784 0.014 0.36 NO
79 PSMD8 PSMD8 PSMD8 7894 0.012 0.35 NO
80 PSMB1 PSMB1 PSMB1 8003 0.0099 0.35 NO
81 PSMD3 PSMD3 PSMD3 8060 0.0089 0.34 NO
82 MCM7 MCM7 MCM7 8411 0.0025 0.32 NO
83 PSMD4 PSMD4 PSMD4 8706 -0.003 0.31 NO
84 PSMB4 PSMB4 PSMB4 8711 -0.0031 0.31 NO
85 CDKN2A CDKN2A CDKN2A 8910 -0.0065 0.3 NO
86 PSMB8 PSMB8 PSMB8 8972 -0.0079 0.29 NO
87 PSMB6 PSMB6 PSMB6 8984 -0.008 0.29 NO
88 PPP2R2A PPP2R2A PPP2R2A 9083 -0.0098 0.29 NO
89 PSMB7 PSMB7 PSMB7 9116 -0.01 0.29 NO
90 PSMD13 PSMD13 PSMD13 9144 -0.011 0.29 NO
91 PPP2R1A PPP2R1A PPP2R1A 9229 -0.013 0.28 NO
92 HDAC1 HDAC1 HDAC1 9272 -0.013 0.28 NO
93 RPA3 RPA3 RPA3 9426 -0.017 0.27 NO
94 RBBP4 RBBP4 RBBP4 9694 -0.021 0.26 NO
95 PPP2R1B PPP2R1B PPP2R1B 9717 -0.021 0.26 NO
96 TK2 TK2 TK2 9801 -0.023 0.26 NO
97 PSMD9 PSMD9 PSMD9 9851 -0.024 0.26 NO
98 RPA1 RPA1 RPA1 9955 -0.026 0.25 NO
99 CDK4 CDK4 CDK4 9990 -0.026 0.25 NO
100 PSMA5 PSMA5 PSMA5 10040 -0.027 0.25 NO
101 RPS27A RPS27A RPS27A 10731 -0.041 0.21 NO
102 PPP2CB PPP2CB PPP2CB 10746 -0.041 0.22 NO
103 MAX MAX MAX 10860 -0.043 0.21 NO
104 E2F4 E2F4 E2F4 11454 -0.056 0.18 NO
105 PSMB2 PSMB2 PSMB2 11561 -0.058 0.18 NO
106 CDKN2D CDKN2D CDKN2D 11571 -0.059 0.18 NO
107 PSMD6 PSMD6 PSMD6 11712 -0.062 0.18 NO
108 LIN52 LIN52 LIN52 11727 -0.062 0.18 NO
109 PSMF1 PSMF1 PSMF1 11995 -0.069 0.17 NO
110 RPA2 RPA2 RPA2 12077 -0.072 0.18 NO
111 E2F3 E2F3 E2F3 12094 -0.072 0.18 NO
112 UBA52 UBA52 UBA52 12103 -0.072 0.18 NO
113 PSME2 PSME2 PSME2 12288 -0.077 0.18 NO
114 PSME1 PSME1 PSME1 12477 -0.083 0.17 NO
115 PSMB10 PSMB10 PSMB10 12523 -0.084 0.18 NO
116 MCM5 MCM5 MCM5 12601 -0.088 0.18 NO
117 CCND3 CCND3 CCND3 13035 -0.1 0.16 NO
118 PSMD2 PSMD2 PSMD2 13080 -0.1 0.17 NO
119 LIN37 LIN37 LIN37 13786 -0.13 0.14 NO
120 CDK2 CDK2 CDK2 14017 -0.14 0.13 NO
121 PSMB9 PSMB9 PSMB9 14551 -0.17 0.12 NO
122 MCM2 MCM2 MCM2 15091 -0.2 0.098 NO
123 PPP2R3B PPP2R3B PPP2R3B 15224 -0.21 0.11 NO
124 CDC25A CDC25A CDC25A 15383 -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: PID NECTIN PATHWAY.

Figure S10.  Get High-res Image For the top 5 core enriched genes in the pathway: PID NECTIN 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 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 CCNE2 CCNE2 CCNE2 117 0.5 0.028 YES
2 BUB1B BUB1B BUB1B 218 0.43 0.052 YES
3 CDC25C CDC25C CDC25C 228 0.42 0.081 YES
4 BUB1 BUB1 BUB1 287 0.4 0.1 YES
5 E2F5 E2F5 E2F5 298 0.4 0.13 YES
6 CCNB2 CCNB2 CCNB2 327 0.39 0.16 YES
7 CDK1 CDK1 CDK1 361 0.37 0.18 YES
8 TTK TTK TTK 408 0.36 0.2 YES
9 CDC6 CDC6 CDC6 460 0.34 0.22 YES
10 CCNA2 CCNA2 CCNA2 555 0.32 0.24 YES
11 GADD45G GADD45G GADD45G 666 0.3 0.26 YES
12 ESPL1 ESPL1 ESPL1 774 0.28 0.27 YES
13 CDC45 CDC45 CDC45 835 0.27 0.28 YES
14 DBF4 DBF4 DBF4 841 0.27 0.3 YES
15 PTTG2 PTTG2 PTTG2 938 0.26 0.32 YES
16 WEE1 WEE1 WEE1 963 0.25 0.33 YES
17 ATM ATM ATM 1001 0.25 0.35 YES
18 MCM4 MCM4 MCM4 1006 0.25 0.36 YES
19 PRKDC PRKDC PRKDC 1065 0.24 0.38 YES
20 PLK1 PLK1 PLK1 1074 0.24 0.39 YES
21 CDC25B CDC25B CDC25B 1086 0.24 0.41 YES
22 RBL1 RBL1 RBL1 1200 0.23 0.42 YES
23 CHEK2 CHEK2 CHEK2 1419 0.21 0.42 YES
24 E2F2 E2F2 E2F2 1469 0.21 0.43 YES
25 PKMYT1 PKMYT1 PKMYT1 1617 0.19 0.44 YES
26 MAD2L1 MAD2L1 MAD2L1 1626 0.19 0.45 YES
27 ANAPC4 ANAPC4 ANAPC4 1923 0.17 0.44 YES
28 CCNB1 CCNB1 CCNB1 1948 0.17 0.46 YES
29 MCM6 MCM6 MCM6 2122 0.16 0.46 YES
30 RAD21 RAD21 RAD21 2208 0.16 0.46 YES
31 CDKN2C CDKN2C CDKN2C 2263 0.15 0.47 YES
32 CDC7 CDC7 CDC7 2430 0.15 0.47 YES
33 CCNH CCNH CCNH 2518 0.14 0.48 YES
34 ANAPC10 ANAPC10 ANAPC10 2559 0.14 0.48 YES
35 CDC27 CDC27 CDC27 2696 0.14 0.48 YES
36 CCNA1 CCNA1 CCNA1 2705 0.14 0.49 YES
37 SMC1B SMC1B SMC1B 2721 0.13 0.5 YES
38 CCND2 CCND2 CCND2 2874 0.13 0.5 YES
39 SKP2 SKP2 SKP2 3008 0.12 0.5 YES
40 PTTG1 PTTG1 PTTG1 3220 0.12 0.5 YES
41 CUL1 CUL1 CUL1 3250 0.12 0.5 YES
42 ANAPC1 ANAPC1 ANAPC1 3533 0.11 0.5 YES
43 MDM2 MDM2 MDM2 3538 0.11 0.5 YES
44 CDK6 CDK6 CDK6 3561 0.11 0.51 YES
45 YWHAZ YWHAZ YWHAZ 3733 0.1 0.51 YES
46 SFN SFN SFN 3874 0.096 0.5 YES
47 CDKN2B CDKN2B CDKN2B 4054 0.092 0.5 YES
48 CDKN1B CDKN1B CDKN1B 4143 0.09 0.5 YES
49 CDC23 CDC23 CDC23 4184 0.089 0.51 YES
50 CDK7 CDK7 CDK7 4285 0.087 0.51 YES
51 CHEK1 CHEK1 CHEK1 4318 0.086 0.51 YES
52 CDC14B CDC14B CDC14B 4487 0.082 0.51 NO
53 STAG2 STAG2 STAG2 4650 0.078 0.5 NO
54 ANAPC7 ANAPC7 ANAPC7 4873 0.073 0.5 NO
55 PCNA PCNA PCNA 4947 0.072 0.5 NO
56 SMC3 SMC3 SMC3 4951 0.071 0.5 NO
57 CDKN1A CDKN1A CDKN1A 5019 0.07 0.5 NO
58 SMAD4 SMAD4 SMAD4 5126 0.068 0.5 NO
59 YWHAQ YWHAQ YWHAQ 5204 0.066 0.5 NO
60 CCNE1 CCNE1 CCNE1 5281 0.063 0.5 NO
61 YWHAH YWHAH YWHAH 5565 0.058 0.49 NO
62 SMC1A SMC1A SMC1A 5788 0.053 0.48 NO
63 EP300 EP300 EP300 5916 0.05 0.48 NO
64 E2F1 E2F1 E2F1 6018 0.048 0.47 NO
65 HDAC2 HDAC2 HDAC2 6135 0.045 0.47 NO
66 BUB3 BUB3 BUB3 6236 0.043 0.47 NO
67 TGFB2 TGFB2 TGFB2 6310 0.042 0.46 NO
68 TFDP1 TFDP1 TFDP1 6311 0.042 0.47 NO
69 YWHAG YWHAG YWHAG 6341 0.041 0.47 NO
70 YWHAB YWHAB YWHAB 6497 0.038 0.46 NO
71 SKP1 SKP1 SKP1 6534 0.037 0.46 NO
72 CDC20 CDC20 CDC20 6536 0.037 0.46 NO
73 MYC MYC MYC 6556 0.036 0.47 NO
74 RBX1 RBX1 RBX1 6562 0.036 0.47 NO
75 CCNB3 CCNB3 CCNB3 6654 0.034 0.47 NO
76 MAD1L1 MAD1L1 MAD1L1 6863 0.03 0.46 NO
77 CREBBP CREBBP CREBBP 7010 0.028 0.45 NO
78 CCND1 CCND1 CCND1 7202 0.025 0.44 NO
79 ANAPC5 ANAPC5 ANAPC5 7468 0.02 0.43 NO
80 YWHAE YWHAE YWHAE 7564 0.018 0.42 NO
81 MCM3 MCM3 MCM3 7719 0.015 0.41 NO
82 RB1 RB1 RB1 7743 0.015 0.41 NO
83 SMAD3 SMAD3 SMAD3 7764 0.014 0.41 NO
84 RBL2 RBL2 RBL2 7781 0.014 0.41 NO
85 STAG1 STAG1 STAG1 7913 0.012 0.41 NO
86 CDC16 CDC16 CDC16 7947 0.011 0.4 NO
87 TGFB3 TGFB3 TGFB3 8126 0.0079 0.4 NO
88 CDC26 CDC26 CDC26 8386 0.003 0.38 NO
89 MCM7 MCM7 MCM7 8411 0.0025 0.38 NO
90 CDC14A CDC14A CDC14A 8453 0.0017 0.38 NO
91 ABL1 ABL1 ABL1 8529 0.00032 0.37 NO
92 ANAPC11 ANAPC11 ANAPC11 8556 -0.00018 0.37 NO
93 GADD45B GADD45B GADD45B 8577 -0.00055 0.37 NO
94 GADD45A GADD45A GADD45A 8717 -0.0032 0.36 NO
95 SMAD2 SMAD2 SMAD2 8792 -0.0048 0.36 NO
96 TP53 TP53 TP53 8796 -0.0049 0.36 NO
97 CDKN2A CDKN2A CDKN2A 8910 -0.0065 0.35 NO
98 HDAC1 HDAC1 HDAC1 9272 -0.013 0.33 NO
99 CDKN1C CDKN1C CDKN1C 9759 -0.022 0.31 NO
100 WEE2 WEE2 WEE2 9807 -0.023 0.3 NO
101 GSK3B GSK3B GSK3B 9914 -0.025 0.3 NO
102 CDK4 CDK4 CDK4 9990 -0.026 0.3 NO
103 ATR ATR ATR 11220 -0.051 0.23 NO
104 ANAPC2 ANAPC2 ANAPC2 11403 -0.055 0.22 NO
105 E2F4 E2F4 E2F4 11454 -0.056 0.22 NO
106 CDKN2D CDKN2D CDKN2D 11571 -0.059 0.22 NO
107 E2F3 E2F3 E2F3 12094 -0.072 0.2 NO
108 FZR1 FZR1 FZR1 12132 -0.073 0.2 NO
109 MCM5 MCM5 MCM5 12601 -0.088 0.18 NO
110 ZBTB17 ZBTB17 ZBTB17 13012 -0.1 0.16 NO
111 CCND3 CCND3 CCND3 13035 -0.1 0.17 NO
112 TGFB1 TGFB1 TGFB1 13148 -0.11 0.17 NO
113 CDK2 CDK2 CDK2 14017 -0.14 0.13 NO
114 MAD2L2 MAD2L2 MAD2L2 14060 -0.15 0.14 NO
115 ANAPC13 ANAPC13 ANAPC13 14341 -0.16 0.13 NO
116 TFDP2 TFDP2 TFDP2 15026 -0.2 0.1 NO
117 MCM2 MCM2 MCM2 15091 -0.2 0.12 NO
118 CDC25A CDC25A CDC25A 15383 -0.23 0.11 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 PLK1 PATHWAY.

Figure S12.  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

genes ES table in pathway: PID FOXM1PATHWAY

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 PVRL3 PVRL3 PVRL3 130 0.48 0.16 YES
2 ITGB3 ITGB3 ITGB3 806 0.28 0.21 YES
3 CDH1 CDH1 CDH1 1091 0.24 0.27 YES
4 IQGAP1 IQGAP1 IQGAP1 1391 0.21 0.33 YES
5 VAV2 VAV2 VAV2 1705 0.19 0.37 YES
6 PDGFB PDGFB PDGFB 1761 0.18 0.43 YES
7 PVRL1 PVRL1 PVRL1 3035 0.12 0.4 YES
8 ITGAV ITGAV ITGAV 3212 0.12 0.43 YES
9 PTK2 PTK2 PTK2 3270 0.12 0.46 YES
10 RAP1B RAP1B RAP1B 3374 0.11 0.5 YES
11 PIK3R1 PIK3R1 PIK3R1 4226 0.088 0.48 YES
12 PDGFRB PDGFRB PDGFRB 4902 0.073 0.46 YES
13 PTPRM PTPRM PTPRM 4990 0.07 0.48 YES
14 MLLT4 MLLT4 MLLT4 5060 0.069 0.5 YES
15 CTNNA1 CTNNA1 CTNNA1 7110 0.026 0.39 NO
16 PVR PVR PVR 7116 0.026 0.4 NO
17 CRK CRK CRK 7274 0.023 0.4 NO
18 RAPGEF1 RAPGEF1 RAPGEF1 7465 0.02 0.4 NO
19 PIK3CA PIK3CA PIK3CA 7637 0.017 0.39 NO
20 FARP2 FARP2 FARP2 7650 0.017 0.4 NO
21 CLDN1 CLDN1 CLDN1 8409 0.0025 0.35 NO
22 RAC1 RAC1 RAC1 8875 -0.0061 0.33 NO
23 SRC SRC SRC 9507 -0.018 0.3 NO
24 PIP5K1C PIP5K1C PIP5K1C 10554 -0.037 0.25 NO
25 CDC42 CDC42 CDC42 10708 -0.04 0.26 NO
26 TLN1 TLN1 TLN1 10787 -0.042 0.26 NO
27 PVRL2 PVRL2 PVRL2 11445 -0.056 0.24 NO
28 F11R F11R F11R 12458 -0.082 0.21 NO
29 RAP1A RAP1A RAP1A 12671 -0.09 0.23 NO
30 CTNNB1 CTNNB1 CTNNB1 13255 -0.11 0.24 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 FOXM1PATHWAY.

Figure S14.  Get High-res Image For the top 5 core enriched genes in the pathway: PID FOXM1PATHWAY, 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 AURORA A 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 SPC24 SPC24 SPC24 57 0.55 0.06 YES
2 SSPO SSPO SSPO 97 0.51 0.12 YES
3 NDC80 NDC80 NDC80 138 0.48 0.17 YES
4 BUB1B BUB1B BUB1B 218 0.43 0.22 YES
5 CDC25C CDC25C CDC25C 228 0.42 0.26 YES
6 BUB1 BUB1 BUB1 287 0.4 0.31 YES
7 ERCC6L ERCC6L ERCC6L 288 0.4 0.35 YES
8 KIF20A KIF20A KIF20A 307 0.39 0.4 YES
9 CDK1 CDK1 CDK1 361 0.37 0.44 YES
10 CENPE CENPE CENPE 368 0.37 0.48 YES
11 CLSPN CLSPN CLSPN 465 0.34 0.52 YES
12 MLF1IP MLF1IP MLF1IP 498 0.33 0.55 YES
13 WEE1 WEE1 WEE1 963 0.25 0.55 YES
14 FBXO5 FBXO5 FBXO5 1070 0.24 0.58 YES
15 PLK1 PLK1 PLK1 1074 0.24 0.6 YES
16 CDC25B CDC25B CDC25B 1086 0.24 0.63 YES
17 AURKA AURKA AURKA 1136 0.23 0.66 YES
18 PRC1 PRC1 PRC1 1409 0.21 0.66 YES
19 TPX2 TPX2 TPX2 1559 0.2 0.68 YES
20 PPP1R12A PPP1R12A PPP1R12A 1674 0.19 0.69 YES
21 CCNB1 CCNB1 CCNB1 1948 0.17 0.7 YES
22 ROCK2 ROCK2 ROCK2 2639 0.14 0.67 NO
23 KIF2A KIF2A KIF2A 2793 0.13 0.68 NO
24 ECT2 ECT2 ECT2 3810 0.098 0.63 NO
25 CDC14B CDC14B CDC14B 4487 0.082 0.6 NO
26 STAG2 STAG2 STAG2 4650 0.078 0.6 NO
27 SGOL1 SGOL1 SGOL1 4765 0.076 0.61 NO
28 RAB1A RAB1A RAB1A 5825 0.052 0.55 NO
29 PPP2CA PPP2CA PPP2CA 6163 0.044 0.54 NO
30 CDC20 CDC20 CDC20 6536 0.037 0.52 NO
31 ODF2 ODF2 ODF2 7346 0.022 0.48 NO
32 PPP1CB PPP1CB PPP1CB 7507 0.019 0.47 NO
33 FBXW11 FBXW11 FBXW11 7901 0.012 0.45 NO
34 PPP2R1A PPP2R1A PPP2R1A 9229 -0.013 0.37 NO
35 GOLGA2 GOLGA2 GOLGA2 9261 -0.013 0.37 NO
36 TUBG1 TUBG1 TUBG1 9494 -0.018 0.36 NO
37 TPT1 TPT1 TPT1 10633 -0.039 0.3 NO
38 NINL NINL NINL 11228 -0.051 0.27 NO
39 RHOA RHOA RHOA 11828 -0.065 0.24 NO
40 FZR1 FZR1 FZR1 12132 -0.073 0.23 NO
41 INCENP INCENP INCENP 12234 -0.076 0.24 NO
42 NUDC NUDC NUDC 12655 -0.09 0.22 NO
43 PAK1 PAK1 PAK1 13110 -0.1 0.21 NO
44 PLK1S1 PLK1S1 PLK1S1 13234 -0.11 0.22 NO
45 GORASP1 GORASP1 GORASP1 15006 -0.2 0.14 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 AURORA A PATHWAY.

Figure S16.  Get High-res Image For the top 5 core enriched genes in the pathway: PID AURORA A 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 METABOLISM OF NON CODING RNA

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 TPR TPR TPR 2115 0.16 -0.051 YES
2 NUPL2 NUPL2 NUPL2 2301 0.15 0.0059 YES
3 SLC25A4 SLC25A4 SLC25A4 2885 0.13 0.029 YES
4 NUP88 NUP88 NUP88 2909 0.13 0.084 YES
5 NUP155 NUP155 NUP155 2914 0.13 0.14 YES
6 NUP205 NUP205 NUP205 3052 0.12 0.19 YES
7 NUP37 NUP37 NUP37 3363 0.11 0.22 YES
8 NUP107 NUP107 NUP107 3439 0.11 0.26 YES
9 NUP35 NUP35 NUP35 3766 0.099 0.29 YES
10 SEH1L SEH1L SEH1L 3776 0.099 0.33 YES
11 NUP85 NUP85 NUP85 3894 0.096 0.37 YES
12 NUP43 NUP43 NUP43 4234 0.088 0.39 YES
13 PSIP1 PSIP1 PSIP1 4257 0.087 0.42 YES
14 NUP50 NUP50 NUP50 4271 0.087 0.46 YES
15 RANBP2 RANBP2 RANBP2 5001 0.07 0.45 YES
16 NUPL1 NUPL1 NUPL1 5140 0.067 0.47 YES
17 POM121 POM121 POM121 6081 0.046 0.44 NO
18 NUP54 NUP54 NUP54 6841 0.031 0.41 NO
19 NUP133 NUP133 NUP133 6911 0.03 0.42 NO
20 NUP188 NUP188 NUP188 7250 0.024 0.41 NO
21 SLC25A5 SLC25A5 SLC25A5 7312 0.022 0.41 NO
22 NUP210 NUP210 NUP210 7551 0.019 0.41 NO
23 AAAS AAAS AAAS 8199 0.0064 0.37 NO
24 NUP153 NUP153 NUP153 8518 0.00058 0.36 NO
25 NUP62 NUP62 NUP62 8950 -0.0074 0.33 NO
26 RAE1 RAE1 RAE1 9695 -0.021 0.3 NO
27 NUP214 NUP214 NUP214 10180 -0.03 0.29 NO
28 BANF1 BANF1 BANF1 10521 -0.037 0.28 NO
29 HMGA1 HMGA1 HMGA1 10610 -0.038 0.29 NO
30 KPNA1 KPNA1 KPNA1 11587 -0.059 0.26 NO
31 NUP93 NUP93 NUP93 12256 -0.076 0.26 NO
32 SLC25A6 SLC25A6 SLC25A6 12349 -0.079 0.29 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: REACTOME METABOLISM OF NON CODING RNA.

Figure S18.  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 CELL CYCLE MITOTIC

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 SMN1 SMN1 SMN1 612 0.31 0.054 YES
2 TGS1 TGS1 TGS1 1035 0.24 0.1 YES
3 TPR TPR TPR 2115 0.16 0.085 YES
4 NUPL2 NUPL2 NUPL2 2301 0.15 0.12 YES
5 NCBP1 NCBP1 NCBP1 2821 0.13 0.13 YES
6 PHAX PHAX PHAX 2857 0.13 0.16 YES
7 NUP88 NUP88 NUP88 2909 0.13 0.2 YES
8 NUP155 NUP155 NUP155 2914 0.13 0.23 YES
9 NUP205 NUP205 NUP205 3052 0.12 0.26 YES
10 NUP37 NUP37 NUP37 3363 0.11 0.28 YES
11 NUP107 NUP107 NUP107 3439 0.11 0.3 YES
12 SNUPN SNUPN SNUPN 3638 0.1 0.32 YES
13 NUP35 NUP35 NUP35 3766 0.099 0.34 YES
14 SEH1L SEH1L SEH1L 3776 0.099 0.37 YES
15 NUP85 NUP85 NUP85 3894 0.096 0.39 YES
16 SNRPG SNRPG SNRPG 4133 0.09 0.4 YES
17 NUP43 NUP43 NUP43 4234 0.088 0.42 YES
18 NUP50 NUP50 NUP50 4271 0.087 0.45 YES
19 SNRPD1 SNRPD1 SNRPD1 4616 0.079 0.45 YES
20 RANBP2 RANBP2 RANBP2 5001 0.07 0.45 YES
21 NUPL1 NUPL1 NUPL1 5140 0.067 0.46 YES
22 GEMIN6 GEMIN6 GEMIN6 5468 0.06 0.46 YES
23 SMN2 SMN2 SMN2 5836 0.052 0.45 YES
24 CLNS1A CLNS1A CLNS1A 5928 0.05 0.46 YES
25 POM121 POM121 POM121 6081 0.046 0.46 YES
26 PRMT5 PRMT5 PRMT5 6293 0.042 0.46 NO
27 GEMIN5 GEMIN5 GEMIN5 6650 0.035 0.46 NO
28 NUP54 NUP54 NUP54 6841 0.031 0.45 NO
29 NUP133 NUP133 NUP133 6911 0.03 0.46 NO
30 NUP188 NUP188 NUP188 7250 0.024 0.44 NO
31 NUP210 NUP210 NUP210 7551 0.019 0.43 NO
32 DDX20 DDX20 DDX20 7959 0.011 0.41 NO
33 AAAS AAAS AAAS 8199 0.0064 0.4 NO
34 SNRPD3 SNRPD3 SNRPD3 8372 0.0033 0.39 NO
35 SNRPB SNRPB SNRPB 8442 0.0019 0.39 NO
36 NUP153 NUP153 NUP153 8518 0.00058 0.38 NO
37 GEMIN4 GEMIN4 GEMIN4 8560 -0.00026 0.38 NO
38 NUP62 NUP62 NUP62 8950 -0.0074 0.36 NO
39 SNRPD2 SNRPD2 SNRPD2 9438 -0.017 0.34 NO
40 SNRPE SNRPE SNRPE 9464 -0.018 0.34 NO
41 RAE1 RAE1 RAE1 9695 -0.021 0.33 NO
42 SNRPF SNRPF SNRPF 10118 -0.028 0.32 NO
43 NUP214 NUP214 NUP214 10180 -0.03 0.32 NO
44 GEMIN7 GEMIN7 GEMIN7 11185 -0.05 0.28 NO
45 NUP93 NUP93 NUP93 12256 -0.076 0.24 NO
46 WDR77 WDR77 WDR77 12703 -0.091 0.24 NO
47 NCBP2 NCBP2 NCBP2 12868 -0.096 0.26 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 CELL CYCLE MITOTIC.

Figure S20.  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

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 GLYCOLYSIS GLUCONEOGENESIS 55 genes.ES.table 0.43 1.4 0.042 0.21 0.97 0.58 0.38 0.36 0.14 0.008
KEGG STEROID HORMONE BIOSYNTHESIS 27 genes.ES.table 0.55 1.4 0.041 0.23 0.97 0.37 0.13 0.32 0.16 0.01
KEGG PURINE METABOLISM 151 genes.ES.table 0.36 1.5 0.019 0.19 0.95 0.19 0.19 0.16 0.12 0.006
KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM 31 genes.ES.table 0.5 1.5 0.063 0.19 0.95 0.42 0.23 0.32 0.12 0.006
KEGG GLYCINE SERINE AND THREONINE METABOLISM 30 genes.ES.table 0.68 1.7 0.0022 0.14 0.66 0.43 0.16 0.36 0.046 0.026
KEGG ARGININE AND PROLINE METABOLISM 50 genes.ES.table 0.5 1.7 0.0086 0.15 0.62 0.36 0.23 0.28 0.041 0.028
KEGG HISTIDINE METABOLISM 29 genes.ES.table 0.57 1.5 0.044 0.18 0.94 0.28 0.14 0.24 0.11 0.007
KEGG TYROSINE METABOLISM 36 genes.ES.table 0.64 1.6 0.018 0.14 0.79 0.44 0.21 0.35 0.059 0.01
KEGG TRYPTOPHAN METABOLISM 36 genes.ES.table 0.57 1.6 0.0087 0.14 0.81 0.31 0.13 0.27 0.061 0.01
KEGG GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE 25 genes.ES.table 0.63 1.7 0.011 0.13 0.71 0.32 0.12 0.28 0.046 0.015
genes ES table in pathway: KEGG GLYCOLYSIS GLUCONEOGENESIS

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 NGFR NGFR NGFR 24 1.1 0.24 YES
2 GNGT1 GNGT1 GNGT1 181 0.79 0.4 YES
3 PDGFRA PDGFRA PDGFRA 670 0.53 0.49 YES
4 NGF NGF NGF 987 0.43 0.56 YES
5 EGFR EGFR EGFR 1150 0.39 0.64 YES
6 HRAS HRAS HRAS 4025 0.12 0.5 NO
7 MAPK3 MAPK3 MAPK3 4278 0.1 0.51 NO
8 SHC1 SHC1 SHC1 4812 0.088 0.5 NO
9 PTPRR PTPRR PTPRR 5870 0.063 0.45 NO
10 GNB1 GNB1 GNB1 6207 0.056 0.44 NO
11 MAP2K2 MAP2K2 MAP2K2 6504 0.05 0.44 NO
12 RPS6KA1 RPS6KA1 RPS6KA1 6520 0.05 0.44 NO
13 SRC SRC SRC 7184 0.038 0.41 NO
14 GNAS GNAS GNAS 8149 0.021 0.36 NO
15 STAT3 STAT3 STAT3 8169 0.02 0.37 NO
16 MKNK2 MKNK2 MKNK2 8421 0.016 0.36 NO
17 GRB2 GRB2 GRB2 9277 0.0032 0.31 NO
18 ELK1 ELK1 ELK1 9538 -0.0014 0.29 NO
19 MAPK1 MAPK1 MAPK1 9982 -0.009 0.27 NO
20 SOS1 SOS1 SOS1 10603 -0.02 0.24 NO
21 RAF1 RAF1 RAF1 10852 -0.025 0.23 NO
22 IGF1R IGF1R IGF1R 11440 -0.037 0.2 NO
23 PPP2CA PPP2CA PPP2CA 11621 -0.041 0.2 NO
24 ITGB1 ITGB1 ITGB1 11681 -0.042 0.21 NO
25 MAP2K1 MAP2K1 MAP2K1 11793 -0.045 0.21 NO
26 MKNK1 MKNK1 MKNK1 12757 -0.065 0.17 NO
27 MYC MYC MYC 13488 -0.085 0.15 NO
28 RPS6KA5 RPS6KA5 RPS6KA5 17228 -0.35 0.0068 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 GLYCOLYSIS GLUCONEOGENESIS.

Figure S22.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GLYCOLYSIS GLUCONEOGENESIS, 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 STEROID HORMONE BIOSYNTHESIS

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 APC2 APC2 APC2 44 1 0.046 YES
2 SFRP5 SFRP5 SFRP5 56 0.97 0.092 YES
3 SFRP2 SFRP2 SFRP2 64 0.95 0.14 YES
4 WNT5B WNT5B WNT5B 96 0.89 0.18 YES
5 WIF1 WIF1 WIF1 162 0.8 0.22 YES
6 WNT2B WNT2B WNT2B 235 0.75 0.25 YES
7 MAPK10 MAPK10 MAPK10 390 0.65 0.27 YES
8 FZD2 FZD2 FZD2 523 0.59 0.29 YES
9 SFRP4 SFRP4 SFRP4 572 0.57 0.32 YES
10 PRKCG PRKCG PRKCG 796 0.49 0.33 YES
11 WNT9B WNT9B WNT9B 858 0.47 0.34 YES
12 CAMK2B CAMK2B CAMK2B 885 0.46 0.37 YES
13 WNT2 WNT2 WNT2 966 0.44 0.38 YES
14 NFATC4 NFATC4 NFATC4 986 0.43 0.4 YES
15 DKK1 DKK1 DKK1 1089 0.41 0.42 YES
16 PRKCB PRKCB PRKCB 1424 0.34 0.41 YES
17 WNT5A WNT5A WNT5A 1484 0.34 0.43 YES
18 WNT10A WNT10A WNT10A 1650 0.31 0.43 YES
19 WNT6 WNT6 WNT6 1810 0.29 0.44 YES
20 FZD7 FZD7 FZD7 1937 0.27 0.44 YES
21 FOSL1 FOSL1 FOSL1 1953 0.27 0.46 YES
22 SOX17 SOX17 SOX17 1986 0.27 0.47 YES
23 CCND2 CCND2 CCND2 1994 0.27 0.48 YES
24 FZD8 FZD8 FZD8 2049 0.26 0.49 YES
25 LEF1 LEF1 LEF1 2562 0.21 0.47 YES
26 FZD5 FZD5 FZD5 2631 0.2 0.48 YES
27 WNT3A WNT3A WNT3A 2632 0.2 0.48 YES
28 PLCB1 PLCB1 PLCB1 2722 0.2 0.49 YES
29 NKD2 NKD2 NKD2 2815 0.19 0.49 YES
30 CXXC4 CXXC4 CXXC4 2835 0.19 0.5 YES
31 AXIN2 AXIN2 AXIN2 2907 0.18 0.51 YES
32 FZD10 FZD10 FZD10 2997 0.18 0.51 YES
33 SFRP1 SFRP1 SFRP1 3039 0.17 0.52 YES
34 WNT1 WNT1 WNT1 3172 0.16 0.52 YES
35 MMP7 MMP7 MMP7 3264 0.16 0.52 YES
36 PLCB2 PLCB2 PLCB2 3594 0.14 0.51 NO
37 PPP2R5B PPP2R5B PPP2R5B 3629 0.13 0.51 NO
38 CAMK2A CAMK2A CAMK2A 3920 0.12 0.5 NO
39 WNT7B WNT7B WNT7B 3975 0.12 0.5 NO
40 JUN JUN JUN 4120 0.11 0.5 NO
41 NFATC2 NFATC2 NFATC2 4461 0.098 0.48 NO
42 PORCN PORCN PORCN 4478 0.098 0.49 NO
43 FZD3 FZD3 FZD3 4542 0.096 0.49 NO
44 DKK2 DKK2 DKK2 4553 0.095 0.49 NO
45 SMAD3 SMAD3 SMAD3 4695 0.091 0.49 NO
46 VANGL2 VANGL2 VANGL2 4716 0.091 0.49 NO
47 TCF7L1 TCF7L1 TCF7L1 4919 0.085 0.48 NO
48 PRKACA PRKACA PRKACA 4951 0.084 0.49 NO
49 FZD4 FZD4 FZD4 4993 0.083 0.49 NO
50 PRICKLE1 PRICKLE1 PRICKLE1 5139 0.079 0.48 NO
51 NFATC3 NFATC3 NFATC3 5153 0.079 0.49 NO
52 WNT9A WNT9A WNT9A 5204 0.078 0.49 NO
53 CHP2 CHP2 CHP2 5617 0.068 0.47 NO
54 RAC2 RAC2 RAC2 5651 0.067 0.47 NO
55 DVL3 DVL3 DVL3 5749 0.066 0.47 NO
56 RAC3 RAC3 RAC3 5938 0.062 0.46 NO
57 CSNK1A1L CSNK1A1L CSNK1A1L 6108 0.058 0.45 NO
58 PPP2R1A PPP2R1A PPP2R1A 6201 0.056 0.45 NO
59 WNT3 WNT3 WNT3 6351 0.053 0.44 NO
60 TCF7 TCF7 TCF7 6353 0.053 0.44 NO
61 TP53 TP53 TP53 6479 0.05 0.44 NO
62 CSNK1E CSNK1E CSNK1E 6805 0.044 0.42 NO
63 PPP2R5A PPP2R5A PPP2R5A 6835 0.044 0.42 NO
64 DVL1 DVL1 DVL1 6988 0.041 0.42 NO
65 PPARD PPARD PPARD 7055 0.04 0.42 NO
66 PLCB3 PLCB3 PLCB3 7288 0.036 0.4 NO
67 CTNNBIP1 CTNNBIP1 CTNNBIP1 7597 0.03 0.39 NO
68 RBX1 RBX1 RBX1 7673 0.029 0.38 NO
69 RAC1 RAC1 RAC1 7831 0.026 0.38 NO
70 DVL2 DVL2 DVL2 7880 0.025 0.38 NO
71 CCND1 CCND1 CCND1 8012 0.023 0.37 NO
72 CHD8 CHD8 CHD8 8259 0.019 0.36 NO
73 LRP5 LRP5 LRP5 8296 0.018 0.35 NO
74 PRKX PRKX PRKX 8318 0.018 0.35 NO
75 TBL1X TBL1X TBL1X 8536 0.015 0.34 NO
76 PPP2CB PPP2CB PPP2CB 8582 0.014 0.34 NO
77 CTBP1 CTBP1 CTBP1 8614 0.014 0.34 NO
78 CAMK2G CAMK2G CAMK2G 8715 0.012 0.33 NO
79 NKD1 NKD1 NKD1 8793 0.011 0.33 NO
80 CREBBP CREBBP CREBBP 8844 0.01 0.33 NO
81 PPP3CB PPP3CB PPP3CB 8892 0.0093 0.32 NO
82 PPP3R1 PPP3R1 PPP3R1 9101 0.006 0.31 NO
83 WNT11 WNT11 WNT11 9218 0.0041 0.31 NO
84 CSNK2A1 CSNK2A1 CSNK2A1 9296 0.0029 0.3 NO
85 CAMK2D CAMK2D CAMK2D 9316 0.0026 0.3 NO
86 WNT10B WNT10B WNT10B 9343 0.0019 0.3 NO
87 PPP2R5D PPP2R5D PPP2R5D 9421 0.0006 0.3 NO
88 AXIN1 AXIN1 AXIN1 9428 0.00044 0.3 NO
89 RHOA RHOA RHOA 9478 -0.00042 0.29 NO
90 EP300 EP300 EP300 9541 -0.0014 0.29 NO
91 SMAD2 SMAD2 SMAD2 9560 -0.0017 0.29 NO
92 NFATC1 NFATC1 NFATC1 9568 -0.0019 0.29 NO
93 FZD1 FZD1 FZD1 9601 -0.0025 0.28 NO
94 CSNK2B CSNK2B CSNK2B 9633 -0.0029 0.28 NO
95 CSNK2A2 CSNK2A2 CSNK2A2 9635 -0.003 0.28 NO
96 CHP CHP CHP 9642 -0.0031 0.28 NO
97 PSEN1 PSEN1 PSEN1 9669 -0.0036 0.28 NO
98 PRKCA PRKCA PRKCA 9761 -0.0051 0.28 NO
99 CCND3 CCND3 CCND3 9845 -0.0066 0.27 NO
100 CUL1 CUL1 CUL1 10111 -0.011 0.26 NO
101 PRICKLE2 PRICKLE2 PRICKLE2 10133 -0.012 0.26 NO
102 PPP3CC PPP3CC PPP3CC 10145 -0.012 0.26 NO
103 FRAT2 FRAT2 FRAT2 10156 -0.012 0.26 NO
104 FRAT1 FRAT1 FRAT1 10269 -0.014 0.25 NO
105 BTRC BTRC BTRC 10302 -0.015 0.25 NO
106 RUVBL1 RUVBL1 RUVBL1 10562 -0.02 0.24 NO
107 NLK NLK NLK 10876 -0.026 0.22 NO
108 NFAT5 NFAT5 NFAT5 10899 -0.026 0.22 NO
109 PPP2R5C PPP2R5C PPP2R5C 11063 -0.029 0.21 NO
110 SKP1 SKP1 SKP1 11109 -0.03 0.21 NO
111 CACYBP CACYBP CACYBP 11461 -0.038 0.19 NO
112 CTBP2 CTBP2 CTBP2 11608 -0.041 0.18 NO
113 MAP3K7 MAP3K7 MAP3K7 11614 -0.041 0.19 NO
114 PPP2CA PPP2CA PPP2CA 11621 -0.041 0.19 NO
115 GSK3B GSK3B GSK3B 11850 -0.046 0.18 NO
116 CSNK1A1 CSNK1A1 CSNK1A1 11885 -0.046 0.18 NO
117 TBL1XR1 TBL1XR1 TBL1XR1 11990 -0.049 0.17 NO
118 WNT16 WNT16 WNT16 12038 -0.05 0.17 NO
119 FBXW11 FBXW11 FBXW11 12045 -0.05 0.18 NO
120 VANGL1 VANGL1 VANGL1 12080 -0.051 0.18 NO
121 SENP2 SENP2 SENP2 12431 -0.058 0.16 NO
122 MAPK9 MAPK9 MAPK9 12634 -0.063 0.15 NO
123 TCF7L2 TCF7L2 TCF7L2 12845 -0.068 0.14 NO
124 WNT4 WNT4 WNT4 12995 -0.071 0.14 NO
125 PPP3CA PPP3CA PPP3CA 13280 -0.078 0.12 NO
126 LRP6 LRP6 LRP6 13326 -0.08 0.12 NO
127 MYC MYC MYC 13488 -0.085 0.12 NO
128 PPP2R1B PPP2R1B PPP2R1B 13680 -0.09 0.11 NO
129 CTNNB1 CTNNB1 CTNNB1 13819 -0.094 0.11 NO
130 PPP2R5E PPP2R5E PPP2R5E 13834 -0.094 0.11 NO
131 SMAD4 SMAD4 SMAD4 13949 -0.097 0.11 NO
132 PRKACB PRKACB PRKACB 14001 -0.098 0.11 NO
133 APC APC APC 14501 -0.11 0.089 NO
134 SIAH1 SIAH1 SIAH1 15005 -0.13 0.066 NO
135 DAAM2 DAAM2 DAAM2 15064 -0.13 0.069 NO
136 FZD6 FZD6 FZD6 15087 -0.14 0.074 NO
137 PLCB4 PLCB4 PLCB4 15366 -0.15 0.066 NO
138 ROCK1 ROCK1 ROCK1 15380 -0.15 0.072 NO
139 ROCK2 ROCK2 ROCK2 15535 -0.16 0.071 NO
140 FZD9 FZD9 FZD9 15608 -0.16 0.074 NO
141 DAAM1 DAAM1 DAAM1 15631 -0.16 0.081 NO
142 WNT8B WNT8B WNT8B 16108 -0.19 0.062 NO
143 MAPK8 MAPK8 MAPK8 16177 -0.2 0.068 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 STEROID HORMONE BIOSYNTHESIS.

Figure S24.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG STEROID HORMONE BIOSYNTHESIS, 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 PURINE METABOLISM

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 ACTC1 ACTC1 ACTC1 2 1.4 0.092 YES
2 ATP1A3 ATP1A3 ATP1A3 23 1.1 0.16 YES
3 ATP1A2 ATP1A2 ATP1A2 43 1 0.22 YES
4 CACNG7 CACNG7 CACNG7 190 0.78 0.27 YES
5 CACNG3 CACNG3 CACNG3 239 0.75 0.31 YES
6 CACNA1S CACNA1S CACNA1S 276 0.72 0.36 YES
7 TNNC1 TNNC1 TNNC1 427 0.63 0.39 YES
8 CACNA2D4 CACNA2D4 CACNA2D4 499 0.6 0.42 YES
9 CACNA1C CACNA1C CACNA1C 583 0.56 0.45 YES
10 CACNG4 CACNG4 CACNG4 587 0.56 0.49 YES
11 SLC8A1 SLC8A1 SLC8A1 774 0.49 0.51 YES
12 CACNA1F CACNA1F CACNA1F 812 0.48 0.54 YES
13 CACNA1D CACNA1D CACNA1D 923 0.45 0.56 YES
14 CACNA2D3 CACNA2D3 CACNA2D3 939 0.45 0.59 YES
15 ATP1B2 ATP1B2 ATP1B2 1023 0.42 0.61 YES
16 CACNB1 CACNB1 CACNB1 1244 0.38 0.62 YES
17 COX4I2 COX4I2 COX4I2 1370 0.35 0.64 YES
18 CACNG5 CACNG5 CACNG5 1394 0.35 0.66 YES
19 RYR2 RYR2 RYR2 1510 0.33 0.67 YES
20 CACNB2 CACNB2 CACNB2 1715 0.3 0.68 YES
21 MYH7 MYH7 MYH7 1795 0.29 0.69 YES
22 MYL3 MYL3 MYL3 1846 0.28 0.71 YES
23 COX7A1 COX7A1 COX7A1 2219 0.24 0.7 YES
24 COX8C COX8C COX8C 2342 0.23 0.71 YES
25 CACNA2D2 CACNA2D2 CACNA2D2 2488 0.22 0.72 YES
26 TPM2 TPM2 TPM2 2848 0.19 0.71 NO
27 CACNB4 CACNB4 CACNB4 3340 0.15 0.69 NO
28 TPM1 TPM1 TPM1 4188 0.11 0.65 NO
29 COX6B2 COX6B2 COX6B2 4216 0.11 0.65 NO
30 FXYD2 FXYD2 FXYD2 4264 0.1 0.66 NO
31 CACNB3 CACNB3 CACNB3 4556 0.095 0.65 NO
32 ATP1B1 ATP1B1 ATP1B1 4646 0.093 0.65 NO
33 UQCR10 UQCR10 UQCR10 4682 0.092 0.65 NO
34 MYH6 MYH6 MYH6 4737 0.09 0.65 NO
35 TNNI3 TNNI3 TNNI3 5335 0.075 0.62 NO
36 COX6A1 COX6A1 COX6A1 5481 0.071 0.62 NO
37 SLC9A1 SLC9A1 SLC9A1 5612 0.068 0.62 NO
38 COX8A COX8A COX8A 5659 0.067 0.62 NO
39 COX5B COX5B COX5B 5724 0.066 0.62 NO
40 ATP1A4 ATP1A4 ATP1A4 5755 0.065 0.62 NO
41 COX4I1 COX4I1 COX4I1 5785 0.065 0.62 NO
42 COX6B1 COX6B1 COX6B1 5918 0.062 0.62 NO
43 UQCRC1 UQCRC1 UQCRC1 6533 0.049 0.59 NO
44 COX7A2 COX7A2 COX7A2 7333 0.035 0.54 NO
45 COX5A COX5A COX5A 7642 0.029 0.53 NO
46 TPM4 TPM4 TPM4 7891 0.025 0.52 NO
47 UQCRQ UQCRQ UQCRQ 8140 0.021 0.5 NO
48 CACNA2D1 CACNA2D1 CACNA2D1 8725 0.012 0.47 NO
49 TPM3 TPM3 TPM3 8829 0.01 0.46 NO
50 UQCRH UQCRH UQCRH 9026 0.0073 0.45 NO
51 COX6C COX6C COX6C 9166 0.0049 0.44 NO
52 UQCRHL UQCRHL UQCRHL 9217 0.0041 0.44 NO
53 COX7A2L COX7A2L COX7A2L 9246 0.0037 0.44 NO
54 ATP2A2 ATP2A2 ATP2A2 9658 -0.0033 0.42 NO
55 ATP1A1 ATP1A1 ATP1A1 10050 -0.01 0.4 NO
56 COX7C COX7C COX7C 10081 -0.011 0.39 NO
57 UQCR11 UQCR11 UQCR11 10118 -0.011 0.39 NO
58 CYC1 CYC1 CYC1 10159 -0.012 0.39 NO
59 UQCRB UQCRB UQCRB 11315 -0.034 0.33 NO
60 ATP1B3 ATP1B3 ATP1B3 11415 -0.037 0.32 NO
61 SLC9A6 SLC9A6 SLC9A6 11964 -0.048 0.3 NO
62 UQCRFS1 UQCRFS1 UQCRFS1 12206 -0.054 0.28 NO
63 COX6A2 COX6A2 COX6A2 12245 -0.055 0.28 NO
64 UQCRC2 UQCRC2 UQCRC2 12522 -0.06 0.27 NO
65 COX7B COX7B COX7B 13654 -0.089 0.21 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 PURINE METABOLISM.

Figure S26.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PURINE 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 ALANINE ASPARTATE AND GLUTAMATE METABOLISM

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 GCGR GCGR GCGR 25 1.1 0.052 YES
2 GNB3 GNB3 GNB3 113 0.86 0.089 YES
3 GNG13 GNG13 GNG13 114 0.86 0.13 YES
4 GNGT1 GNGT1 GNGT1 181 0.79 0.17 YES
5 ADCY8 ADCY8 ADCY8 197 0.78 0.2 YES
6 GNG3 GNG3 GNG3 310 0.7 0.23 YES
7 PAX6 PAX6 PAX6 527 0.58 0.25 YES
8 SYT5 SYT5 SYT5 588 0.56 0.27 YES
9 KCNB1 KCNB1 KCNB1 606 0.55 0.3 YES
10 ABCC8 ABCC8 ABCC8 690 0.52 0.32 YES
11 GNG4 GNG4 GNG4 714 0.51 0.34 YES
12 KCNJ11 KCNJ11 KCNJ11 757 0.5 0.37 YES
13 ADCY5 ADCY5 ADCY5 758 0.5 0.39 YES
14 GRP GRP GRP 800 0.49 0.41 YES
15 GNGT2 GNGT2 GNGT2 810 0.48 0.44 YES
16 CHRM3 CHRM3 CHRM3 880 0.46 0.45 YES
17 SNAP25 SNAP25 SNAP25 1027 0.42 0.47 YES
18 ISL1 ISL1 ISL1 1071 0.41 0.48 YES
19 GNA15 GNA15 GNA15 1303 0.36 0.49 YES
20 MLXIPL MLXIPL MLXIPL 1349 0.36 0.5 YES
21 DPP4 DPP4 DPP4 1431 0.34 0.52 YES
22 PRKAA2 PRKAA2 PRKAA2 1656 0.31 0.52 YES
23 GNA14 GNA14 GNA14 1702 0.3 0.53 YES
24 CACNB2 CACNB2 CACNB2 1715 0.3 0.55 YES
25 ADCY1 ADCY1 ADCY1 1723 0.3 0.56 YES
26 ADCY2 ADCY2 ADCY2 1736 0.3 0.57 YES
27 ADCY4 ADCY4 ADCY4 1786 0.29 0.58 YES
28 SLC2A1 SLC2A1 SLC2A1 1924 0.28 0.59 YES
29 ADRA2A ADRA2A ADRA2A 2292 0.23 0.58 NO
30 KCNG2 KCNG2 KCNG2 2659 0.2 0.57 NO
31 PLCB1 PLCB1 PLCB1 2722 0.2 0.58 NO
32 GNB5 GNB5 GNB5 2897 0.18 0.57 NO
33 PCSK1 PCSK1 PCSK1 3011 0.18 0.58 NO
34 GNAO1 GNAO1 GNAO1 3177 0.16 0.57 NO
35 GNG2 GNG2 GNG2 3228 0.16 0.58 NO
36 PLCB2 PLCB2 PLCB2 3594 0.14 0.57 NO
37 RAPGEF4 RAPGEF4 RAPGEF4 3613 0.14 0.57 NO
38 PRKAR2B PRKAR2B PRKAR2B 3661 0.13 0.57 NO
39 ADCY3 ADCY3 ADCY3 3762 0.13 0.58 NO
40 VAMP2 VAMP2 VAMP2 3911 0.12 0.57 NO
41 ACACB ACACB ACACB 4177 0.11 0.56 NO
42 FASN FASN FASN 4402 0.1 0.56 NO
43 STXBP1 STXBP1 STXBP1 4518 0.096 0.55 NO
44 CACNB3 CACNB3 CACNB3 4556 0.095 0.56 NO
45 CACNA1A CACNA1A CACNA1A 4743 0.09 0.55 NO
46 PRKACA PRKACA PRKACA 4951 0.084 0.54 NO
47 GNAI2 GNAI2 GNAI2 5081 0.081 0.54 NO
48 PKLR PKLR PKLR 5203 0.078 0.54 NO
49 SLC25A6 SLC25A6 SLC25A6 5499 0.071 0.52 NO
50 PRKAR1B PRKAR1B PRKAR1B 5771 0.065 0.51 NO
51 GNB2 GNB2 GNB2 5850 0.064 0.51 NO
52 PPP2R1A PPP2R1A PPP2R1A 6201 0.056 0.49 NO
53 GNB1 GNB1 GNB1 6207 0.056 0.49 NO
54 TALDO1 TALDO1 TALDO1 6548 0.049 0.48 NO
55 STX1A STX1A STX1A 6675 0.047 0.47 NO
56 ACACA ACACA ACACA 7159 0.038 0.44 NO
57 ITPR2 ITPR2 ITPR2 7171 0.038 0.44 NO
58 PLCB3 PLCB3 PLCB3 7288 0.036 0.44 NO
59 GNG5 GNG5 GNG5 7451 0.033 0.43 NO
60 GNAS GNAS GNAS 8149 0.021 0.39 NO
61 PPP2CB PPP2CB PPP2CB 8582 0.014 0.37 NO
62 STK11 STK11 STK11 8974 0.0081 0.35 NO
63 ADCY9 ADCY9 ADCY9 9188 0.0046 0.33 NO
64 TKT TKT TKT 9294 0.003 0.33 NO
65 PPP2R5D PPP2R5D PPP2R5D 9421 0.0006 0.32 NO
66 AGPAT1 AGPAT1 AGPAT1 9532 -0.0013 0.32 NO
67 IQGAP1 IQGAP1 IQGAP1 9708 -0.0043 0.3 NO
68 PRKCA PRKCA PRKCA 9761 -0.0051 0.3 NO
69 ACLY ACLY ACLY 9985 -0.0091 0.29 NO
70 LOC653566 LOC653566 LOC653566 10275 -0.014 0.27 NO
71 MLX MLX MLX 10333 -0.015 0.27 NO
72 GNG7 GNG7 GNG7 10458 -0.018 0.26 NO
73 SEC11A SEC11A SEC11A 10465 -0.018 0.26 NO
74 SPCS2 SPCS2 SPCS2 10688 -0.022 0.25 NO
75 ADCY7 ADCY7 ADCY7 11120 -0.03 0.23 NO
76 GNA11 GNA11 GNA11 11500 -0.038 0.21 NO
77 PPP2CA PPP2CA PPP2CA 11621 -0.041 0.2 NO
78 GNAQ GNAQ GNAQ 11651 -0.042 0.2 NO
79 PFKFB1 PFKFB1 PFKFB1 11904 -0.047 0.19 NO
80 SLC25A5 SLC25A5 SLC25A5 11917 -0.047 0.2 NO
81 PRKAB2 PRKAB2 PRKAB2 11926 -0.047 0.2 NO
82 MARCKS MARCKS MARCKS 11993 -0.049 0.2 NO
83 ADCY6 ADCY6 ADCY6 12003 -0.049 0.2 NO
84 RAP1B RAP1B RAP1B 12031 -0.05 0.2 NO
85 SEC11C SEC11C SEC11C 12113 -0.052 0.2 NO
86 SPCS3 SPCS3 SPCS3 12197 -0.053 0.19 NO
87 GNG11 GNG11 GNG11 12239 -0.054 0.19 NO
88 GATA4 GATA4 GATA4 12425 -0.058 0.19 NO
89 ITPR3 ITPR3 ITPR3 12597 -0.062 0.18 NO
90 SPCS1 SPCS1 SPCS1 12680 -0.064 0.18 NO
91 PRKAR1A PRKAR1A PRKAR1A 12993 -0.071 0.16 NO
92 RAP1A RAP1A RAP1A 13018 -0.072 0.16 NO
93 GNAI1 GNAI1 GNAI1 13235 -0.077 0.16 NO
94 GNG12 GNG12 GNG12 13308 -0.079 0.16 NO
95 SLC25A4 SLC25A4 SLC25A4 13319 -0.08 0.16 NO
96 GNG10 GNG10 GNG10 13576 -0.087 0.15 NO
97 PPP2R1B PPP2R1B PPP2R1B 13680 -0.09 0.15 NO
98 CTNNB1 CTNNB1 CTNNB1 13819 -0.094 0.14 NO
99 PRKAG2 PRKAG2 PRKAG2 13848 -0.094 0.15 NO
100 PRKACB PRKACB PRKACB 14001 -0.098 0.14 NO
101 GLP1R GLP1R GLP1R 14246 -0.11 0.13 NO
102 AKAP5 AKAP5 AKAP5 15443 -0.15 0.072 NO
103 KCNS3 KCNS3 KCNS3 15534 -0.16 0.075 NO
104 PRKAR2A PRKAR2A PRKAR2A 16136 -0.19 0.049 NO
105 RAPGEF3 RAPGEF3 RAPGEF3 16264 -0.2 0.052 NO
106 GNB4 GNB4 GNB4 16442 -0.22 0.052 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 ALANINE ASPARTATE AND GLUTAMATE METABOLISM.

Figure S28.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ALANINE ASPARTATE AND GLUTAMATE 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 GLYCINE SERINE AND THREONINE METABOLISM

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 WNT5B WNT5B WNT5B 96 0.89 0.065 YES
2 FRZB FRZB FRZB 132 0.83 0.13 YES
3 WIF1 WIF1 WIF1 162 0.8 0.19 YES
4 WNT2B WNT2B WNT2B 235 0.75 0.24 YES
5 FZD2 FZD2 FZD2 523 0.59 0.27 YES
6 SFRP4 SFRP4 SFRP4 572 0.57 0.32 YES
7 WNT2 WNT2 WNT2 966 0.44 0.33 YES
8 DKK1 DKK1 DKK1 1089 0.41 0.35 YES
9 RHOU RHOU RHOU 1335 0.36 0.37 YES
10 WNT5A WNT5A WNT5A 1484 0.34 0.38 YES
11 WNT10A WNT10A WNT10A 1650 0.31 0.4 YES
12 WNT6 WNT6 WNT6 1810 0.29 0.41 YES
13 FZD7 FZD7 FZD7 1937 0.27 0.43 YES
14 FOSL1 FOSL1 FOSL1 1953 0.27 0.45 YES
15 SOX17 SOX17 SOX17 1986 0.27 0.47 YES
16 CCND2 CCND2 CCND2 1994 0.27 0.49 YES
17 FZD8 FZD8 FZD8 2049 0.26 0.51 YES
18 LEF1 LEF1 LEF1 2562 0.21 0.49 YES
19 FZD5 FZD5 FZD5 2631 0.2 0.5 YES
20 WNT3A WNT3A WNT3A 2632 0.2 0.52 YES
21 PITX2 PITX2 PITX2 2765 0.19 0.53 YES
22 CXXC4 CXXC4 CXXC4 2835 0.19 0.54 YES
23 SFRP1 SFRP1 SFRP1 3039 0.17 0.54 YES
24 WNT1 WNT1 WNT1 3172 0.16 0.55 YES
25 TLE2 TLE2 TLE2 3955 0.12 0.51 NO
26 WNT7B WNT7B WNT7B 3975 0.12 0.52 NO
27 JUN JUN JUN 4120 0.11 0.52 NO
28 TLE1 TLE1 TLE1 4243 0.1 0.52 NO
29 BCL9 BCL9 BCL9 4267 0.1 0.53 NO
30 PORCN PORCN PORCN 4478 0.098 0.52 NO
31 FZD3 FZD3 FZD3 4542 0.096 0.53 NO
32 TCF7L1 TCF7L1 TCF7L1 4919 0.085 0.51 NO
33 FZD4 FZD4 FZD4 4993 0.083 0.51 NO
34 WNT9A WNT9A WNT9A 5204 0.078 0.51 NO
35 GAPDH GAPDH GAPDH 5326 0.075 0.51 NO
36 GSK3A GSK3A GSK3A 5559 0.069 0.5 NO
37 PPP2R1A PPP2R1A PPP2R1A 6201 0.056 0.47 NO
38 WNT3 WNT3 WNT3 6351 0.053 0.46 NO
39 TCF7 TCF7 TCF7 6353 0.053 0.47 NO
40 FBXW4 FBXW4 FBXW4 6493 0.05 0.46 NO
41 ACTB ACTB ACTB 6607 0.048 0.46 NO
42 KREMEN1 KREMEN1 KREMEN1 6743 0.046 0.46 NO
43 DVL1 DVL1 DVL1 6988 0.041 0.44 NO
44 AES AES AES 7009 0.041 0.45 NO
45 SLC9A3R1 SLC9A3R1 SLC9A3R1 7397 0.034 0.43 NO
46 CTNNBIP1 CTNNBIP1 CTNNBIP1 7597 0.03 0.42 NO
47 DVL2 DVL2 DVL2 7880 0.025 0.4 NO
48 CCND1 CCND1 CCND1 8012 0.023 0.4 NO
49 LRP5 LRP5 LRP5 8296 0.018 0.38 NO
50 CTBP1 CTBP1 CTBP1 8614 0.014 0.36 NO
51 RPL13A RPL13A RPL13A 8638 0.013 0.36 NO
52 B2M B2M B2M 8654 0.013 0.36 NO
53 NKD1 NKD1 NKD1 8793 0.011 0.36 NO
54 WNT11 WNT11 WNT11 9218 0.0041 0.33 NO
55 CSNK1D CSNK1D CSNK1D 9229 0.004 0.33 NO
56 CSNK2A1 CSNK2A1 CSNK2A1 9296 0.0029 0.33 NO
57 AXIN1 AXIN1 AXIN1 9428 0.00044 0.32 NO
58 EP300 EP300 EP300 9541 -0.0014 0.32 NO
59 FZD1 FZD1 FZD1 9601 -0.0025 0.31 NO
60 CCND3 CCND3 CCND3 9845 -0.0066 0.3 NO
61 FRAT1 FRAT1 FRAT1 10269 -0.014 0.28 NO
62 BTRC BTRC BTRC 10302 -0.015 0.28 NO
63 CSNK1G1 CSNK1G1 CSNK1G1 10552 -0.02 0.26 NO
64 DIXDC1 DIXDC1 DIXDC1 10712 -0.022 0.25 NO
65 NLK NLK NLK 10876 -0.026 0.25 NO
66 HPRT1 HPRT1 HPRT1 11030 -0.028 0.24 NO
67 CTBP2 CTBP2 CTBP2 11608 -0.041 0.21 NO
68 PPP2CA PPP2CA PPP2CA 11621 -0.041 0.21 NO
69 GSK3B GSK3B GSK3B 11850 -0.046 0.2 NO
70 CSNK1A1 CSNK1A1 CSNK1A1 11885 -0.046 0.2 NO
71 WNT16 WNT16 WNT16 12038 -0.05 0.2 NO
72 FBXW11 FBXW11 FBXW11 12045 -0.05 0.2 NO
73 FBXW2 FBXW2 FBXW2 12218 -0.054 0.2 NO
74 SENP2 SENP2 SENP2 12431 -0.058 0.19 NO
75 WNT4 WNT4 WNT4 12995 -0.071 0.16 NO
76 LRP6 LRP6 LRP6 13326 -0.08 0.15 NO
77 MYC MYC MYC 13488 -0.085 0.15 NO
78 CTNNB1 CTNNB1 CTNNB1 13819 -0.094 0.14 NO
79 APC APC APC 14501 -0.11 0.1 NO
80 FZD6 FZD6 FZD6 15087 -0.14 0.082 NO
81 DAAM1 DAAM1 DAAM1 15631 -0.16 0.063 NO
82 WISP1 WISP1 WISP1 15934 -0.18 0.06 NO
83 PYGO1 PYGO1 PYGO1 16932 -0.28 0.024 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: KEGG GLYCINE SERINE AND THREONINE METABOLISM.

Figure S30.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GLYCINE SERINE AND THREONINE 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 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 ACTC1 ACTC1 ACTC1 2 1.4 0.067 YES
2 CACNG7 CACNG7 CACNG7 190 0.78 0.092 YES
3 ADCY8 ADCY8 ADCY8 197 0.78 0.13 YES
4 CACNG3 CACNG3 CACNG3 239 0.75 0.16 YES
5 CACNA1S CACNA1S CACNA1S 276 0.72 0.19 YES
6 DES DES DES 277 0.72 0.23 YES
7 TGFB2 TGFB2 TGFB2 293 0.71 0.26 YES
8 SGCG SGCG SGCG 403 0.65 0.28 YES
9 TNNC1 TNNC1 TNNC1 427 0.63 0.31 YES
10 ADRB1 ADRB1 ADRB1 471 0.61 0.34 YES
11 CACNA2D4 CACNA2D4 CACNA2D4 499 0.6 0.36 YES
12 CACNA1C CACNA1C CACNA1C 583 0.56 0.38 YES
13 CACNG4 CACNG4 CACNG4 587 0.56 0.41 YES
14 ADCY5 ADCY5 ADCY5 758 0.5 0.42 YES
15 SLC8A1 SLC8A1 SLC8A1 774 0.49 0.44 YES
16 ITGA11 ITGA11 ITGA11 797 0.49 0.47 YES
17 CACNA1F CACNA1F CACNA1F 812 0.48 0.49 YES
18 CACNA1D CACNA1D CACNA1D 923 0.45 0.5 YES
19 CACNA2D3 CACNA2D3 CACNA2D3 939 0.45 0.52 YES
20 SGCA SGCA SGCA 1051 0.42 0.54 YES
21 CACNB1 CACNB1 CACNB1 1244 0.38 0.54 YES
22 ITGA7 ITGA7 ITGA7 1298 0.36 0.56 YES
23 PLN PLN PLN 1377 0.35 0.57 YES
24 CACNG5 CACNG5 CACNG5 1394 0.35 0.58 YES
25 LAMA2 LAMA2 LAMA2 1396 0.35 0.6 YES
26 ITGB4 ITGB4 ITGB4 1486 0.34 0.61 YES
27 RYR2 RYR2 RYR2 1510 0.33 0.62 YES
28 CACNB2 CACNB2 CACNB2 1715 0.3 0.62 YES
29 ITGA2B ITGA2B ITGA2B 1718 0.3 0.64 YES
30 ADCY1 ADCY1 ADCY1 1723 0.3 0.65 YES
31 ADCY2 ADCY2 ADCY2 1736 0.3 0.66 YES
32 ADCY4 ADCY4 ADCY4 1786 0.29 0.68 YES
33 MYH7 MYH7 MYH7 1795 0.29 0.69 YES
34 MYL3 MYL3 MYL3 1846 0.28 0.7 YES
35 ITGA5 ITGA5 ITGA5 1886 0.28 0.71 YES
36 TGFB3 TGFB3 TGFB3 2051 0.26 0.71 YES
37 ITGA2 ITGA2 ITGA2 2060 0.26 0.72 YES
38 TGFB1 TGFB1 TGFB1 2336 0.23 0.72 NO
39 CACNA2D2 CACNA2D2 CACNA2D2 2488 0.22 0.72 NO
40 TPM2 TPM2 TPM2 2848 0.19 0.71 NO
41 ITGB3 ITGB3 ITGB3 3186 0.16 0.7 NO
42 CACNB4 CACNB4 CACNB4 3340 0.15 0.7 NO
43 IGF1 IGF1 IGF1 3505 0.14 0.69 NO
44 ADCY3 ADCY3 ADCY3 3762 0.13 0.68 NO
45 DMD DMD DMD 3980 0.12 0.68 NO
46 TPM1 TPM1 TPM1 4188 0.11 0.67 NO
47 CACNB3 CACNB3 CACNB3 4556 0.095 0.65 NO
48 ITGB7 ITGB7 ITGB7 4661 0.092 0.65 NO
49 MYH6 MYH6 MYH6 4737 0.09 0.65 NO
50 ITGA8 ITGA8 ITGA8 4772 0.089 0.65 NO
51 ITGB8 ITGB8 ITGB8 4788 0.088 0.66 NO
52 PRKACA PRKACA PRKACA 4951 0.084 0.65 NO
53 EMD EMD EMD 5166 0.079 0.64 NO
54 TNNI3 TNNI3 TNNI3 5335 0.075 0.64 NO
55 ITGA3 ITGA3 ITGA3 5554 0.07 0.63 NO
56 ACTB ACTB ACTB 6607 0.048 0.57 NO
57 ITGA4 ITGA4 ITGA4 7253 0.036 0.53 NO
58 ITGA6 ITGA6 ITGA6 7480 0.032 0.52 NO
59 ACTG1 ACTG1 ACTG1 7560 0.03 0.52 NO
60 LMNA LMNA LMNA 7709 0.028 0.51 NO
61 TPM4 TPM4 TPM4 7891 0.025 0.5 NO
62 GNAS GNAS GNAS 8149 0.021 0.49 NO
63 PRKX PRKX PRKX 8318 0.018 0.48 NO
64 CACNA2D1 CACNA2D1 CACNA2D1 8725 0.012 0.45 NO
65 TPM3 TPM3 TPM3 8829 0.01 0.45 NO
66 SGCB SGCB SGCB 8993 0.0078 0.44 NO
67 MYBPC3 MYBPC3 MYBPC3 9067 0.0065 0.44 NO
68 ITGB5 ITGB5 ITGB5 9119 0.0057 0.43 NO
69 ADCY9 ADCY9 ADCY9 9188 0.0046 0.43 NO
70 ATP2A2 ATP2A2 ATP2A2 9658 -0.0033 0.4 NO
71 DAG1 DAG1 DAG1 11095 -0.03 0.32 NO
72 ADCY7 ADCY7 ADCY7 11120 -0.03 0.32 NO
73 TNF TNF TNF 11342 -0.035 0.31 NO
74 ITGA10 ITGA10 ITGA10 11656 -0.042 0.29 NO
75 ITGB1 ITGB1 ITGB1 11681 -0.042 0.29 NO
76 ADCY6 ADCY6 ADCY6 12003 -0.049 0.28 NO
77 SGCD SGCD SGCD 12529 -0.06 0.25 NO
78 ITGA1 ITGA1 ITGA1 12607 -0.062 0.25 NO
79 ITGAV ITGAV ITGAV 13222 -0.077 0.22 NO
80 PRKACB PRKACB PRKACB 14001 -0.098 0.18 NO
81 TTN TTN TTN 14715 -0.12 0.14 NO
82 ITGA9 ITGA9 ITGA9 16815 -0.26 0.031 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: KEGG ARGININE AND PROLINE METABOLISM.

Figure S32.  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 HISTIDINE METABOLISM

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 ACTC1 ACTC1 ACTC1 2 1.4 0.074 YES
2 CACNG7 CACNG7 CACNG7 190 0.78 0.1 YES
3 CACNG3 CACNG3 CACNG3 239 0.75 0.14 YES
4 CACNA1S CACNA1S CACNA1S 276 0.72 0.17 YES
5 DES DES DES 277 0.72 0.21 YES
6 TGFB2 TGFB2 TGFB2 293 0.71 0.25 YES
7 SGCG SGCG SGCG 403 0.65 0.27 YES
8 TNNC1 TNNC1 TNNC1 427 0.63 0.3 YES
9 CACNA2D4 CACNA2D4 CACNA2D4 499 0.6 0.33 YES
10 CACNA1C CACNA1C CACNA1C 583 0.56 0.36 YES
11 CACNG4 CACNG4 CACNG4 587 0.56 0.38 YES
12 ACE ACE ACE 770 0.49 0.4 YES
13 SLC8A1 SLC8A1 SLC8A1 774 0.49 0.42 YES
14 ITGA11 ITGA11 ITGA11 797 0.49 0.45 YES
15 CACNA1F CACNA1F CACNA1F 812 0.48 0.47 YES
16 CACNA1D CACNA1D CACNA1D 923 0.45 0.49 YES
17 CACNA2D3 CACNA2D3 CACNA2D3 939 0.45 0.51 YES
18 SGCA SGCA SGCA 1051 0.42 0.53 YES
19 CACNB1 CACNB1 CACNB1 1244 0.38 0.54 YES
20 ITGA7 ITGA7 ITGA7 1298 0.36 0.55 YES
21 IL6 IL6 IL6 1386 0.35 0.56 YES
22 CACNG5 CACNG5 CACNG5 1394 0.35 0.58 YES
23 LAMA2 LAMA2 LAMA2 1396 0.35 0.6 YES
24 ITGB4 ITGB4 ITGB4 1486 0.34 0.61 YES
25 RYR2 RYR2 RYR2 1510 0.33 0.63 YES
26 PRKAA2 PRKAA2 PRKAA2 1656 0.31 0.63 YES
27 CACNB2 CACNB2 CACNB2 1715 0.3 0.65 YES
28 ITGA2B ITGA2B ITGA2B 1718 0.3 0.66 YES
29 MYH7 MYH7 MYH7 1795 0.29 0.67 YES
30 MYL3 MYL3 MYL3 1846 0.28 0.68 YES
31 ITGA5 ITGA5 ITGA5 1886 0.28 0.7 YES
32 TGFB3 TGFB3 TGFB3 2051 0.26 0.7 YES
33 ITGA2 ITGA2 ITGA2 2060 0.26 0.71 YES
34 TGFB1 TGFB1 TGFB1 2336 0.23 0.71 NO
35 CACNA2D2 CACNA2D2 CACNA2D2 2488 0.22 0.71 NO
36 TPM2 TPM2 TPM2 2848 0.19 0.7 NO
37 ITGB3 ITGB3 ITGB3 3186 0.16 0.69 NO
38 CACNB4 CACNB4 CACNB4 3340 0.15 0.69 NO
39 IGF1 IGF1 IGF1 3505 0.14 0.69 NO
40 DMD DMD DMD 3980 0.12 0.66 NO
41 TPM1 TPM1 TPM1 4188 0.11 0.66 NO
42 CACNB3 CACNB3 CACNB3 4556 0.095 0.64 NO
43 ITGB7 ITGB7 ITGB7 4661 0.092 0.64 NO
44 MYH6 MYH6 MYH6 4737 0.09 0.64 NO
45 ITGA8 ITGA8 ITGA8 4772 0.089 0.64 NO
46 ITGB8 ITGB8 ITGB8 4788 0.088 0.65 NO
47 EMD EMD EMD 5166 0.079 0.63 NO
48 TNNI3 TNNI3 TNNI3 5335 0.075 0.62 NO
49 ITGA3 ITGA3 ITGA3 5554 0.07 0.62 NO
50 ACTB ACTB ACTB 6607 0.048 0.56 NO
51 ITGA4 ITGA4 ITGA4 7253 0.036 0.52 NO
52 ITGA6 ITGA6 ITGA6 7480 0.032 0.51 NO
53 ACTG1 ACTG1 ACTG1 7560 0.03 0.51 NO
54 LMNA LMNA LMNA 7709 0.028 0.5 NO
55 TPM4 TPM4 TPM4 7891 0.025 0.49 NO
56 CACNA2D1 CACNA2D1 CACNA2D1 8725 0.012 0.44 NO
57 TPM3 TPM3 TPM3 8829 0.01 0.44 NO
58 SGCB SGCB SGCB 8993 0.0078 0.43 NO
59 MYBPC3 MYBPC3 MYBPC3 9067 0.0065 0.42 NO
60 ITGB5 ITGB5 ITGB5 9119 0.0057 0.42 NO
61 ATP2A2 ATP2A2 ATP2A2 9658 -0.0033 0.39 NO
62 PRKAB1 PRKAB1 PRKAB1 10185 -0.013 0.36 NO
63 DAG1 DAG1 DAG1 11095 -0.03 0.31 NO
64 TNF TNF TNF 11342 -0.035 0.3 NO
65 ITGA10 ITGA10 ITGA10 11656 -0.042 0.28 NO
66 ITGB1 ITGB1 ITGB1 11681 -0.042 0.28 NO
67 PRKAG1 PRKAG1 PRKAG1 11812 -0.045 0.28 NO
68 PRKAB2 PRKAB2 PRKAB2 11926 -0.047 0.27 NO
69 SGCD SGCD SGCD 12529 -0.06 0.24 NO
70 ITGA1 ITGA1 ITGA1 12607 -0.062 0.24 NO
71 ITGAV ITGAV ITGAV 13222 -0.077 0.21 NO
72 PRKAG2 PRKAG2 PRKAG2 13848 -0.094 0.18 NO
73 PRKAA1 PRKAA1 PRKAA1 14525 -0.12 0.14 NO
74 TTN TTN TTN 14715 -0.12 0.14 NO
75 ITGA9 ITGA9 ITGA9 16815 -0.26 0.031 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: KEGG HISTIDINE METABOLISM.

Figure S34.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG HISTIDINE 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 TYROSINE METABOLISM

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 GNB3 GNB3 GNB3 113 0.86 0.073 YES
2 GNG13 GNG13 GNG13 114 0.86 0.15 YES
3 GNGT1 GNGT1 GNGT1 181 0.79 0.22 YES
4 ADCY8 ADCY8 ADCY8 197 0.78 0.29 YES
5 GNG3 GNG3 GNG3 310 0.7 0.35 YES
6 GNG4 GNG4 GNG4 714 0.51 0.38 YES
7 RGS4 RGS4 RGS4 715 0.51 0.42 YES
8 ADCY5 ADCY5 ADCY5 758 0.5 0.47 YES
9 PRKCG PRKCG PRKCG 796 0.49 0.51 YES
10 GNGT2 GNGT2 GNGT2 810 0.48 0.55 YES
11 GNAZ GNAZ GNAZ 841 0.48 0.6 YES
12 ADRA2B ADRA2B ADRA2B 857 0.47 0.64 YES
13 PRKCB PRKCB PRKCB 1424 0.34 0.64 YES
14 ADCY1 ADCY1 ADCY1 1723 0.3 0.65 YES
15 ADCY2 ADCY2 ADCY2 1736 0.3 0.67 YES
16 ADCY4 ADCY4 ADCY4 1786 0.29 0.7 YES
17 ADRA2A ADRA2A ADRA2A 2292 0.23 0.69 NO
18 GNB5 GNB5 GNB5 2897 0.18 0.67 NO
19 GNG2 GNG2 GNG2 3228 0.16 0.67 NO
20 ADCY3 ADCY3 ADCY3 3762 0.13 0.65 NO
21 GNAI2 GNAI2 GNAI2 5081 0.081 0.58 NO
22 GNB2 GNB2 GNB2 5850 0.064 0.54 NO
23 RGS19 RGS19 RGS19 5979 0.061 0.54 NO
24 GNB1 GNB1 GNB1 6207 0.056 0.53 NO
25 GNG5 GNG5 GNG5 7451 0.033 0.46 NO
26 GNAS GNAS GNAS 8149 0.021 0.42 NO
27 PRKCQ PRKCQ PRKCQ 8664 0.013 0.4 NO
28 RGS20 RGS20 RGS20 9034 0.0072 0.38 NO
29 ADCY9 ADCY9 ADCY9 9188 0.0046 0.37 NO
30 PRKCA PRKCA PRKCA 9761 -0.0051 0.34 NO
31 GNG7 GNG7 GNG7 10458 -0.018 0.3 NO
32 PRKCE PRKCE PRKCE 10787 -0.024 0.28 NO
33 ADCY7 ADCY7 ADCY7 11120 -0.03 0.26 NO
34 GNAI3 GNAI3 GNAI3 11407 -0.036 0.25 NO
35 PRKCD PRKCD PRKCD 11857 -0.046 0.23 NO
36 ADCY6 ADCY6 ADCY6 12003 -0.049 0.22 NO
37 GNG11 GNG11 GNG11 12239 -0.054 0.22 NO
38 GNAI1 GNAI1 GNAI1 13235 -0.077 0.17 NO
39 GNG12 GNG12 GNG12 13308 -0.079 0.17 NO
40 GNG10 GNG10 GNG10 13576 -0.087 0.16 NO
41 PRKCH PRKCH PRKCH 15219 -0.14 0.08 NO
42 GNB4 GNB4 GNB4 16442 -0.22 0.029 NO
43 RGS17 RGS17 RGS17 16715 -0.25 0.036 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: KEGG TYROSINE METABOLISM.

Figure S36.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG TYROSINE 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 TRYPTOPHAN METABOLISM

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 SLC1A7 SLC1A7 SLC1A7 8 1.2 0.03 YES
2 SLC22A8 SLC22A8 SLC22A8 26 1.1 0.055 YES
3 SLC38A3 SLC38A3 SLC38A3 46 0.99 0.078 YES
4 CP CP CP 91 0.9 0.098 YES
5 SLC8A3 SLC8A3 SLC8A3 165 0.8 0.11 YES
6 SLC47A2 SLC47A2 SLC47A2 169 0.8 0.13 YES
7 HEPH HEPH HEPH 172 0.8 0.15 YES
8 SLC6A20 SLC6A20 SLC6A20 248 0.74 0.16 YES
9 SLC27A6 SLC27A6 SLC27A6 261 0.73 0.18 YES
10 SLC17A7 SLC17A7 SLC17A7 275 0.72 0.2 YES
11 SLC13A5 SLC13A5 SLC13A5 291 0.71 0.22 YES
12 SLC34A2 SLC34A2 SLC34A2 341 0.67 0.23 YES
13 SLC12A5 SLC12A5 SLC12A5 355 0.67 0.24 YES
14 SLC30A3 SLC30A3 SLC30A3 429 0.63 0.26 YES
15 SLC15A2 SLC15A2 SLC15A2 451 0.62 0.27 YES
16 SLC4A4 SLC4A4 SLC4A4 465 0.62 0.28 YES
17 SLC6A9 SLC6A9 SLC6A9 474 0.61 0.3 YES
18 SLC1A3 SLC1A3 SLC1A3 512 0.59 0.31 YES
19 SLC1A2 SLC1A2 SLC1A2 522 0.59 0.32 YES
20 SLC4A8 SLC4A8 SLC4A8 536 0.58 0.34 YES
21 SLC30A8 SLC30A8 SLC30A8 547 0.58 0.35 YES
22 SLC22A2 SLC22A2 SLC22A2 551 0.57 0.36 YES
23 GCK GCK GCK 621 0.55 0.37 YES
24 SLC7A10 SLC7A10 SLC7A10 652 0.54 0.38 YES
25 SLC11A1 SLC11A1 SLC11A1 704 0.51 0.39 YES
26 SLC29A4 SLC29A4 SLC29A4 706 0.51 0.41 YES
27 G6PC2 G6PC2 G6PC2 762 0.5 0.42 YES
28 SLC39A2 SLC39A2 SLC39A2 763 0.5 0.43 YES
29 SLC8A1 SLC8A1 SLC8A1 774 0.49 0.44 YES
30 SLC34A1 SLC34A1 SLC34A1 949 0.44 0.44 YES
31 SLC6A12 SLC6A12 SLC6A12 961 0.44 0.45 YES
32 SLC9A7 SLC9A7 SLC9A7 1039 0.42 0.46 YES
33 SLC6A1 SLC6A1 SLC6A1 1124 0.4 0.46 YES
34 SLC4A3 SLC4A3 SLC4A3 1146 0.4 0.47 YES
35 SLC2A6 SLC2A6 SLC2A6 1179 0.39 0.48 YES
36 SLC2A12 SLC2A12 SLC2A12 1350 0.36 0.47 YES
37 SLC2A3 SLC2A3 SLC2A3 1356 0.36 0.48 YES
38 SLC5A5 SLC5A5 SLC5A5 1398 0.35 0.49 YES
39 SLC1A6 SLC1A6 SLC1A6 1506 0.33 0.49 YES
40 SLC16A8 SLC16A8 SLC16A8 1516 0.33 0.5 YES
41 SLC38A4 SLC38A4 SLC38A4 1519 0.33 0.51 YES
42 SLC6A7 SLC6A7 SLC6A7 1550 0.32 0.51 YES
43 SLC47A1 SLC47A1 SLC47A1 1561 0.32 0.52 YES
44 SLC8A2 SLC8A2 SLC8A2 1627 0.31 0.52 YES
45 SLC9A9 SLC9A9 SLC9A9 1679 0.3 0.53 YES
46 SLC39A5 SLC39A5 SLC39A5 1792 0.29 0.53 YES
47 SLCO2A1 SLCO2A1 SLCO2A1 1798 0.29 0.54 YES
48 SLC2A1 SLC2A1 SLC2A1 1924 0.28 0.53 YES
49 RHCG RHCG RHCG 2015 0.27 0.54 YES
50 SLC2A5 SLC2A5 SLC2A5 2041 0.26 0.54 YES
51 SLC22A11 SLC22A11 SLC22A11 2075 0.26 0.55 YES
52 SLC43A2 SLC43A2 SLC43A2 2087 0.26 0.55 YES
53 SLC44A4 SLC44A4 SLC44A4 2210 0.24 0.55 YES
54 SLCO3A1 SLCO3A1 SLCO3A1 2234 0.24 0.55 YES
55 SLC7A3 SLC7A3 SLC7A3 2246 0.24 0.56 YES
56 SLC15A3 SLC15A3 SLC15A3 2248 0.24 0.56 YES
57 SLC7A11 SLC7A11 SLC7A11 2339 0.23 0.56 YES
58 SLC6A11 SLC6A11 SLC6A11 2345 0.23 0.57 YES
59 SLC12A1 SLC12A1 SLC12A1 2389 0.23 0.57 YES
60 SLC22A3 SLC22A3 SLC22A3 2537 0.21 0.57 NO
61 SLC16A3 SLC16A3 SLC16A3 2605 0.21 0.57 NO
62 SLC2A9 SLC2A9 SLC2A9 2742 0.2 0.57 NO
63 SLC38A5 SLC38A5 SLC38A5 2744 0.2 0.57 NO
64 SLC22A4 SLC22A4 SLC22A4 2837 0.19 0.57 NO
65 SLC6A3 SLC6A3 SLC6A3 3026 0.17 0.56 NO
66 SLC9A5 SLC9A5 SLC9A5 3223 0.16 0.56 NO
67 SLCO2B1 SLCO2B1 SLCO2B1 3511 0.14 0.54 NO
68 SLC7A7 SLC7A7 SLC7A7 3561 0.14 0.55 NO
69 SLC15A1 SLC15A1 SLC15A1 3605 0.14 0.55 NO
70 SLC28A1 SLC28A1 SLC28A1 3622 0.14 0.55 NO
71 SLC5A2 SLC5A2 SLC5A2 3713 0.13 0.55 NO
72 SLC22A1 SLC22A1 SLC22A1 3973 0.12 0.53 NO
73 SLC4A5 SLC4A5 SLC4A5 4064 0.11 0.53 NO
74 SLC20A2 SLC20A2 SLC20A2 4072 0.11 0.53 NO
75 SLC38A1 SLC38A1 SLC38A1 4316 0.1 0.52 NO
76 SLC7A2 SLC7A2 SLC7A2 4346 0.1 0.52 NO
77 SLC18A2 SLC18A2 SLC18A2 4424 0.1 0.52 NO
78 SLC6A19 SLC6A19 SLC6A19 4454 0.098 0.52 NO
79 SLC10A6 SLC10A6 SLC10A6 4523 0.096 0.52 NO
80 SLC39A4 SLC39A4 SLC39A4 4536 0.096 0.52 NO
81 SLC24A5 SLC24A5 SLC24A5 4612 0.094 0.52 NO
82 SLC12A4 SLC12A4 SLC12A4 4673 0.092 0.52 NO
83 SLC41A1 SLC41A1 SLC41A1 4715 0.091 0.52 NO
84 G6PC3 G6PC3 G6PC3 4771 0.089 0.52 NO
85 HK1 HK1 HK1 4876 0.086 0.51 NO
86 SLC30A2 SLC30A2 SLC30A2 4931 0.084 0.51 NO
87 SLC14A1 SLC14A1 SLC14A1 5011 0.082 0.51 NO
88 SLC25A10 SLC25A10 SLC25A10 5068 0.081 0.51 NO
89 SLC29A3 SLC29A3 SLC29A3 5109 0.08 0.51 NO
90 SLC6A6 SLC6A6 SLC6A6 5131 0.08 0.51 NO
91 SLC4A2 SLC4A2 SLC4A2 5213 0.078 0.5 NO
92 SLC5A6 SLC5A6 SLC5A6 5262 0.077 0.5 NO
93 SLC29A2 SLC29A2 SLC29A2 5307 0.076 0.5 NO
94 SLC7A8 SLC7A8 SLC7A8 5445 0.072 0.5 NO
95 SLC39A8 SLC39A8 SLC39A8 5500 0.071 0.5 NO
96 SLC7A5 SLC7A5 SLC7A5 5594 0.068 0.49 NO
97 SLC9A1 SLC9A1 SLC9A1 5612 0.068 0.49 NO
98 HK2 HK2 HK2 5642 0.068 0.49 NO
99 SLC2A8 SLC2A8 SLC2A8 5644 0.068 0.49 NO
100 SLC3A2 SLC3A2 SLC3A2 5647 0.067 0.5 NO
101 AAAS AAAS AAAS 5653 0.067 0.5 NO
102 SLC22A18 SLC22A18 SLC22A18 5722 0.066 0.49 NO
103 SLC41A2 SLC41A2 SLC41A2 5747 0.066 0.5 NO
104 SLC2A10 SLC2A10 SLC2A10 5759 0.065 0.5 NO
105 SLC27A4 SLC27A4 SLC27A4 6076 0.058 0.48 NO
106 HK3 HK3 HK3 6095 0.058 0.48 NO
107 SLC24A6 SLC24A6 SLC24A6 6191 0.056 0.48 NO
108 SLC2A4 SLC2A4 SLC2A4 6283 0.054 0.47 NO
109 RAE1 RAE1 RAE1 6594 0.048 0.45 NO
110 NUP93 NUP93 NUP93 6609 0.048 0.45 NO
111 SLC35C1 SLC35C1 SLC35C1 6636 0.048 0.45 NO
112 NUP214 NUP214 NUP214 6686 0.047 0.45 NO
113 SLC24A1 SLC24A1 SLC24A1 6690 0.046 0.45 NO
114 SLC39A3 SLC39A3 SLC39A3 6981 0.041 0.44 NO
115 SLC16A7 SLC16A7 SLC16A7 7164 0.038 0.43 NO
116 SLC36A1 SLC36A1 SLC36A1 7269 0.036 0.42 NO
117 POM121 POM121 POM121 7465 0.032 0.41 NO
118 SLC39A1 SLC39A1 SLC39A1 7639 0.029 0.4 NO
119 SLC1A4 SLC1A4 SLC1A4 7643 0.029 0.4 NO
120 SLC1A5 SLC1A5 SLC1A5 7925 0.024 0.39 NO
121 SLC37A4 SLC37A4 SLC37A4 7997 0.023 0.38 NO
122 SLC44A2 SLC44A2 SLC44A2 8040 0.022 0.38 NO
123 NUP188 NUP188 NUP188 8212 0.02 0.37 NO
124 SLC7A1 SLC7A1 SLC7A1 8365 0.017 0.36 NO
125 SLC26A4 SLC26A4 SLC26A4 8544 0.015 0.35 NO
126 SLC7A6 SLC7A6 SLC7A6 8569 0.014 0.35 NO
127 SLC35A2 SLC35A2 SLC35A2 8616 0.014 0.35 NO
128 SLC12A6 SLC12A6 SLC12A6 8628 0.014 0.35 NO
129 SLC20A1 SLC20A1 SLC20A1 8856 0.0099 0.34 NO
130 TPR TPR TPR 8977 0.008 0.33 NO
131 SLCO1C1 SLCO1C1 SLCO1C1 9000 0.0077 0.33 NO
132 SLC22A16 SLC22A16 SLC22A16 9005 0.0076 0.33 NO
133 NUP62 NUP62 NUP62 9121 0.0057 0.32 NO
134 SLC35B4 SLC35B4 SLC35B4 9190 0.0046 0.32 NO
135 SLC9A8 SLC9A8 SLC9A8 9244 0.0037 0.32 NO
136 SLC12A7 SLC12A7 SLC12A7 9306 0.0028 0.31 NO
137 SLC27A1 SLC27A1 SLC27A1 9364 0.0016 0.31 NO
138 SLC7A9 SLC7A9 SLC7A9 9786 -0.0056 0.28 NO
139 NUP88 NUP88 NUP88 9804 -0.0059 0.28 NO
140 SLC13A3 SLC13A3 SLC13A3 9893 -0.0075 0.28 NO
141 SLC24A3 SLC24A3 SLC24A3 9948 -0.0084 0.28 NO
142 SLC26A7 SLC26A7 SLC26A7 9961 -0.0087 0.28 NO
143 SLC39A7 SLC39A7 SLC39A7 10038 -0.01 0.27 NO
144 NUP85 NUP85 NUP85 10165 -0.012 0.26 NO
145 SLC2A11 SLC2A11 SLC2A11 10220 -0.013 0.26 NO
146 SLC40A1 SLC40A1 SLC40A1 10267 -0.014 0.26 NO
147 SLC24A4 SLC24A4 SLC24A4 10594 -0.02 0.24 NO
148 SLC35B2 SLC35B2 SLC35B2 10729 -0.023 0.23 NO
149 NUP205 NUP205 NUP205 10808 -0.024 0.23 NO
150 SLC35D1 SLC35D1 SLC35D1 10822 -0.024 0.23 NO
151 SLC43A1 SLC43A1 SLC43A1 11076 -0.029 0.22 NO
152 NUPL1 NUPL1 NUPL1 11140 -0.031 0.21 NO
153 SLC17A5 SLC17A5 SLC17A5 11287 -0.034 0.2 NO
154 SLC35D2 SLC35D2 SLC35D2 11562 -0.04 0.19 NO
155 SLC22A5 SLC22A5 SLC22A5 11731 -0.044 0.18 NO
156 SLC39A6 SLC39A6 SLC39A6 11766 -0.044 0.18 NO
157 NUP133 NUP133 NUP133 11825 -0.045 0.18 NO
158 SLC15A4 SLC15A4 SLC15A4 11837 -0.046 0.18 NO
159 SLC9A6 SLC9A6 SLC9A6 11964 -0.048 0.17 NO
160 NUP50 NUP50 NUP50 12024 -0.049 0.17 NO
161 SLC1A1 SLC1A1 SLC1A1 12094 -0.051 0.17 NO
162 ALB ALB ALB 12150 -0.052 0.16 NO
163 NUP43 NUP43 NUP43 12297 -0.056 0.16 NO
164 SLC4A9 SLC4A9 SLC4A9 12325 -0.056 0.16 NO
165 RANBP2 RANBP2 RANBP2 12440 -0.059 0.15 NO
166 SLC39A10 SLC39A10 SLC39A10 12526 -0.06 0.15 NO
167 SLC31A1 SLC31A1 SLC31A1 12576 -0.061 0.15 NO
168 NUP155 NUP155 NUP155 12768 -0.066 0.14 NO
169 SLC12A2 SLC12A2 SLC12A2 12786 -0.066 0.14 NO
170 NUP37 NUP37 NUP37 12881 -0.068 0.13 NO
171 SLC44A5 SLC44A5 SLC44A5 12958 -0.07 0.13 NO
172 SLC29A1 SLC29A1 SLC29A1 13055 -0.073 0.13 NO
173 NUP210 NUP210 NUP210 13108 -0.074 0.13 NO
174 SEH1L SEH1L SEH1L 13263 -0.078 0.12 NO
175 NUP35 NUP35 NUP35 13536 -0.086 0.1 NO
176 SLC38A2 SLC38A2 SLC38A2 13704 -0.09 0.098 NO
177 SLC30A1 SLC30A1 SLC30A1 13789 -0.092 0.095 NO
178 SLC5A3 SLC5A3 SLC5A3 14208 -0.1 0.073 NO
179 SLCO4A1 SLCO4A1 SLCO4A1 14265 -0.11 0.073 NO
180 NUP107 NUP107 NUP107 14303 -0.11 0.073 NO
181 SLC26A6 SLC26A6 SLC26A6 14438 -0.11 0.068 NO
182 SLC30A7 SLC30A7 SLC30A7 14534 -0.12 0.065 NO
183 SLC22A15 SLC22A15 SLC22A15 14599 -0.12 0.064 NO
184 SLC35A1 SLC35A1 SLC35A1 14738 -0.12 0.059 NO
185 SLC26A2 SLC26A2 SLC26A2 14769 -0.12 0.061 NO
186 NUP153 NUP153 NUP153 14774 -0.12 0.063 NO
187 SLC16A10 SLC16A10 SLC16A10 14852 -0.13 0.062 NO
188 SLC16A1 SLC16A1 SLC16A1 14867 -0.13 0.064 NO
189 SLC30A5 SLC30A5 SLC30A5 15121 -0.14 0.053 NO
190 SLC3A1 SLC3A1 SLC3A1 15187 -0.14 0.052 NO
191 SLC33A1 SLC33A1 SLC33A1 15209 -0.14 0.055 NO
192 SLCO4C1 SLCO4C1 SLCO4C1 15231 -0.14 0.057 NO
193 NUP54 NUP54 NUP54 15248 -0.14 0.059 NO
194 SLC5A11 SLC5A11 SLC5A11 15299 -0.14 0.06 NO
195 SLC6A15 SLC6A15 SLC6A15 15323 -0.15 0.062 NO
196 SLC2A13 SLC2A13 SLC2A13 15822 -0.17 0.037 NO
197 SLC44A1 SLC44A1 SLC44A1 15866 -0.18 0.039 NO
198 SLC26A1 SLC26A1 SLC26A1 15900 -0.18 0.041 NO
199 SLCO1A2 SLCO1A2 SLCO1A2 16011 -0.18 0.039 NO
200 NUPL2 NUPL2 NUPL2 16031 -0.19 0.043 NO
201 SLC44A3 SLC44A3 SLC44A3 16373 -0.21 0.028 NO
202 SLC34A3 SLC34A3 SLC34A3 16592 -0.23 0.021 NO
203 SLC4A7 SLC4A7 SLC4A7 16681 -0.24 0.022 NO
204 SLC35A3 SLC35A3 SLC35A3 17198 -0.34 -0.000065 NO
205 SLC9A3 SLC9A3 SLC9A3 17231 -0.36 0.0067 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: KEGG TRYPTOPHAN METABOLISM.

Figure S38.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG TRYPTOPHAN 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 GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE

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 GCGR GCGR GCGR 25 1.1 0.064 YES
2 GNB3 GNB3 GNB3 113 0.86 0.11 YES
3 GNG13 GNG13 GNG13 114 0.86 0.16 YES
4 GNGT1 GNGT1 GNGT1 181 0.79 0.21 YES
5 WNT2B WNT2B WNT2B 235 0.75 0.25 YES
6 GNG3 GNG3 GNG3 310 0.7 0.29 YES
7 FZD2 FZD2 FZD2 523 0.59 0.31 YES
8 GNG4 GNG4 GNG4 714 0.51 0.33 YES
9 GNGT2 GNGT2 GNGT2 810 0.48 0.35 YES
10 WNT9B WNT9B WNT9B 858 0.47 0.38 YES
11 CRHR2 CRHR2 CRHR2 946 0.44 0.4 YES
12 WNT2 WNT2 WNT2 966 0.44 0.43 YES
13 PTH2R PTH2R PTH2R 1167 0.39 0.44 YES
14 ADCYAP1 ADCYAP1 ADCYAP1 1417 0.34 0.44 YES
15 WNT5A WNT5A WNT5A 1484 0.34 0.46 YES
16 VIPR2 VIPR2 VIPR2 1540 0.33 0.48 YES
17 PTH1R PTH1R PTH1R 1579 0.32 0.5 YES
18 EMR1 EMR1 EMR1 1580 0.32 0.52 YES
19 WNT10A WNT10A WNT10A 1650 0.31 0.53 YES
20 VIPR1 VIPR1 VIPR1 1661 0.31 0.55 YES
21 DHH DHH DHH 1678 0.3 0.56 YES
22 WNT6 WNT6 WNT6 1810 0.29 0.57 YES
23 FZD7 FZD7 FZD7 1937 0.27 0.58 YES
24 FZD8 FZD8 FZD8 2049 0.26 0.59 YES
25 RAMP3 RAMP3 RAMP3 2056 0.26 0.61 YES
26 ADM2 ADM2 ADM2 2500 0.22 0.6 YES
27 PTCH2 PTCH2 PTCH2 2512 0.22 0.61 YES
28 FZD5 FZD5 FZD5 2631 0.2 0.61 YES
29 WNT3A WNT3A WNT3A 2632 0.2 0.63 YES
30 GNB5 GNB5 GNB5 2897 0.18 0.62 YES
31 FZD10 FZD10 FZD10 2997 0.18 0.63 YES
32 IHH IHH IHH 3162 0.16 0.63 YES
33 WNT1 WNT1 WNT1 3172 0.16 0.64 YES
34 GNG2 GNG2 GNG2 3228 0.16 0.64 YES
35 RAMP2 RAMP2 RAMP2 3240 0.16 0.65 YES
36 PTHLH PTHLH PTHLH 3556 0.14 0.64 NO
37 ADM ADM ADM 3788 0.13 0.64 NO
38 WNT7B WNT7B WNT7B 3975 0.12 0.63 NO
39 FZD3 FZD3 FZD3 4542 0.096 0.61 NO
40 FZD4 FZD4 FZD4 4993 0.083 0.59 NO
41 SMO SMO SMO 5144 0.079 0.58 NO
42 WNT9A WNT9A WNT9A 5204 0.078 0.58 NO
43 GNB2 GNB2 GNB2 5850 0.064 0.55 NO
44 GNB1 GNB1 GNB1 6207 0.056 0.53 NO
45 WNT3 WNT3 WNT3 6351 0.053 0.53 NO
46 EMR3 EMR3 EMR3 6531 0.049 0.52 NO
47 GNG5 GNG5 GNG5 7451 0.033 0.47 NO
48 RAMP1 RAMP1 RAMP1 8061 0.022 0.44 NO
49 GNAS GNAS GNAS 8149 0.021 0.43 NO
50 WNT11 WNT11 WNT11 9218 0.0041 0.37 NO
51 WNT10B WNT10B WNT10B 9343 0.0019 0.36 NO
52 FZD1 FZD1 FZD1 9601 -0.0025 0.35 NO
53 CD97 CD97 CD97 9854 -0.0068 0.33 NO
54 GNG7 GNG7 GNG7 10458 -0.018 0.3 NO
55 VIP VIP VIP 10538 -0.019 0.3 NO
56 SCT SCT SCT 11282 -0.034 0.26 NO
57 PTCH1 PTCH1 PTCH1 11815 -0.045 0.23 NO
58 WNT16 WNT16 WNT16 12038 -0.05 0.22 NO
59 GNG11 GNG11 GNG11 12239 -0.054 0.21 NO
60 GIPR GIPR GIPR 12630 -0.063 0.19 NO
61 WNT4 WNT4 WNT4 12995 -0.071 0.17 NO
62 EMR2 EMR2 EMR2 13029 -0.072 0.18 NO
63 GNG12 GNG12 GNG12 13308 -0.079 0.16 NO
64 GNG10 GNG10 GNG10 13576 -0.087 0.16 NO
65 GLP1R GLP1R GLP1R 14246 -0.11 0.12 NO
66 CD55 CD55 CD55 14370 -0.11 0.12 NO
67 CALCRL CALCRL CALCRL 14877 -0.13 0.1 NO
68 FZD6 FZD6 FZD6 15087 -0.14 0.096 NO
69 FZD9 FZD9 FZD9 15608 -0.16 0.076 NO
70 WNT8B WNT8B WNT8B 16108 -0.19 0.058 NO
71 GNB4 GNB4 GNB4 16442 -0.22 0.052 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: KEGG GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE.

Figure S40.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE, 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
KEGG RIBOSOME 86 genes.ES.table 0.67 1.7 0.051 0.16 0.78 0.84 0.25 0.63 0.061 0.024
KEGG RNA POLYMERASE 29 genes.ES.table 0.28 1.2 0.23 1 1 1 0.72 0.28 0.99 0.49
KEGG SPLICEOSOME 114 genes.ES.table 0.25 1.2 0.2 1 1 0.22 0.26 0.16 0.9 0.44
PID MYC PATHWAY 25 genes.ES.table 0.54 2.2 0 0.028 0.04 0.36 0.23 0.28 0 0.008
PID RXR VDR PATHWAY 26 genes.ES.table 0.39 1.2 0.22 1 1 0.23 0.15 0.2 0.91 0.44
PID P53REGULATIONPATHWAY 58 genes.ES.table 0.37 1.4 0.15 0.55 0.98 0.33 0.25 0.25 0.4 0.16
REACTOME TRANSLATION 147 genes.ES.table 0.57 1.8 0.028 0.16 0.39 0.63 0.25 0.47 0 0.044
REACTOME FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX 49 genes.ES.table 0.66 1.8 0.032 0.13 0.55 0.74 0.24 0.56 0.029 0.023
REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE 110 genes.ES.table 0.59 1.7 0.048 0.12 0.6 0.72 0.25 0.54 0.034 0.019
REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S 57 genes.ES.table 0.65 1.8 0.011 0.12 0.4 0.68 0.24 0.52 0 0.022
genes ES table in pathway: KEGG RIBOSOME

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 SUPT3H SUPT3H SUPT3H 1067 0.3 0.1 YES
2 ACTL6A ACTL6A ACTL6A 1725 0.21 0.18 YES
3 RUVBL1 RUVBL1 RUVBL1 1821 0.2 0.28 YES
4 SKP2 SKP2 SKP2 2347 0.16 0.34 YES
5 PML PML PML 2458 0.15 0.42 YES
6 MYC MYC MYC 3283 0.1 0.43 YES
7 HBP1 HBP1 HBP1 3404 0.1 0.48 YES
8 PAK2 PAK2 PAK2 3930 0.08 0.49 YES
9 GSK3B GSK3B GSK3B 3956 0.079 0.54 YES
10 PIN1 PIN1 PIN1 4784 0.054 0.52 NO
11 AXIN1 AXIN1 AXIN1 5834 0.028 0.47 NO
12 KAT5 KAT5 KAT5 6559 0.014 0.44 NO
13 MAX MAX MAX 7495 -0.0044 0.39 NO
14 TAF12 TAF12 TAF12 7525 -0.0048 0.39 NO
15 TAF10 TAF10 TAF10 7908 -0.012 0.37 NO
16 TAF9 TAF9 TAF9 7934 -0.012 0.38 NO
17 ZBTB17 ZBTB17 ZBTB17 8196 -0.017 0.37 NO
18 KAT2A KAT2A KAT2A 8258 -0.018 0.38 NO
19 FBXW7 FBXW7 FBXW7 8624 -0.024 0.37 NO
20 TRRAP TRRAP TRRAP 8787 -0.027 0.38 NO
21 RUVBL2 RUVBL2 RUVBL2 8840 -0.028 0.39 NO
22 PPP2CA PPP2CA PPP2CA 9348 -0.038 0.38 NO
23 SUPT7L SUPT7L SUPT7L 9527 -0.041 0.4 NO
24 CDKN2A CDKN2A CDKN2A 9572 -0.042 0.42 NO
25 PPP2R5A PPP2R5A PPP2R5A 10406 -0.06 0.4 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: KEGG RIBOSOME.

Figure S42.  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 RNA POLYMERASE

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 RPSAP9 RPSAP9 RPSAP9 285 0.54 0.03 YES
2 RPL21 RPL21 RPL21 463 0.45 0.059 YES
3 RPL3L RPL3L RPL3L 657 0.38 0.082 YES
4 RPL35A RPL35A RPL35A 1174 0.28 0.076 YES
5 FAM153A FAM153A FAM153A 1234 0.27 0.095 YES
6 RPSA RPSA RPSA 1418 0.24 0.11 YES
7 RPL15 RPL15 RPL15 1540 0.22 0.12 YES
8 RPL24 RPL24 RPL24 1552 0.22 0.14 YES
9 RPL32 RPL32 RPL32 1562 0.22 0.16 YES
10 RPL14 RPL14 RPL14 1705 0.21 0.16 YES
11 RPS10 RPS10 RPS10 1819 0.2 0.18 YES
12 RPS18 RPS18 RPS18 1977 0.18 0.18 YES
13 RPL29 RPL29 RPL29 2047 0.18 0.19 YES
14 RPL10A RPL10A RPL10A 2067 0.18 0.21 YES
15 RPS4Y1 RPS4Y1 RPS4Y1 2186 0.17 0.22 YES
16 RPS12 RPS12 RPS12 2210 0.16 0.23 YES
17 RPS3A RPS3A RPS3A 2436 0.15 0.23 YES
18 RPL36A RPL36A RPL36A 2449 0.15 0.24 YES
19 RPL39 RPL39 RPL39 2560 0.14 0.25 YES
20 RPL5 RPL5 RPL5 2664 0.14 0.25 YES
21 NCBP2 NCBP2 NCBP2 2723 0.13 0.26 YES
22 RPL22 RPL22 RPL22 2735 0.13 0.27 YES
23 EIF4G1 EIF4G1 EIF4G1 2783 0.13 0.28 YES
24 RPL18A RPL18A RPL18A 2817 0.13 0.29 YES
25 RPL9 RPL9 RPL9 2860 0.12 0.3 YES
26 RPS29 RPS29 RPS29 2911 0.12 0.31 YES
27 RPL34 RPL34 RPL34 2939 0.12 0.32 YES
28 RPL12 RPL12 RPL12 2966 0.12 0.32 YES
29 RPS3 RPS3 RPS3 3004 0.12 0.33 YES
30 RPS8 RPS8 RPS8 3015 0.12 0.34 YES
31 RPL3 RPL3 RPL3 3042 0.12 0.35 YES
32 RPS6 RPS6 RPS6 3073 0.12 0.36 YES
33 RPL26 RPL26 RPL26 3081 0.12 0.37 YES
34 RPS19 RPS19 RPS19 3095 0.11 0.38 YES
35 RPS23 RPS23 RPS23 3113 0.11 0.39 YES
36 RPS27A RPS27A RPS27A 3116 0.11 0.4 YES
37 RPL11 RPL11 RPL11 3123 0.11 0.4 YES
38 RPS9 RPS9 RPS9 3124 0.11 0.42 YES
39 RPL17 RPL17 RPL17 3125 0.11 0.42 YES
40 RPS15A RPS15A RPS15A 3142 0.11 0.43 YES
41 RPS17 RPS17 RPS17 3196 0.11 0.44 YES
42 RPL10 RPL10 RPL10 3221 0.11 0.45 YES
43 RPS5 RPS5 RPS5 3224 0.11 0.46 YES
44 RPL13A RPL13A RPL13A 3259 0.11 0.46 YES
45 RPL23 RPL23 RPL23 3268 0.11 0.47 YES
46 RPL18 RPL18 RPL18 3306 0.1 0.48 YES
47 RPS2 RPS2 RPS2 3308 0.1 0.49 YES
48 RPS7 RPS7 RPS7 3312 0.1 0.5 YES
49 RPLP1 RPLP1 RPLP1 3338 0.1 0.5 YES
50 RPL31 RPL31 RPL31 3342 0.1 0.51 YES
51 RPL38 RPL38 RPL38 3346 0.1 0.52 YES
52 RPS25 RPS25 RPS25 3371 0.1 0.53 YES
53 RPL7A RPL7A RPL7A 3486 0.097 0.53 YES
54 RPS24 RPS24 RPS24 3506 0.096 0.54 YES
55 RPS4X RPS4X RPS4X 3510 0.096 0.55 YES
56 RPS13 RPS13 RPS13 3530 0.095 0.55 YES
57 RPL35 RPL35 RPL35 3563 0.093 0.56 YES
58 RPS14 RPS14 RPS14 3611 0.091 0.57 YES
59 RPLP2 RPLP2 RPLP2 3696 0.088 0.57 YES
60 RPL41 RPL41 RPL41 3706 0.088 0.58 YES
61 RPS15 RPS15 RPS15 3765 0.086 0.58 YES
62 PPP2R2A PPP2R2A PPP2R2A 3881 0.081 0.58 YES
63 RPL37 RPL37 RPL37 3908 0.081 0.59 YES
64 RPL37A RPL37A RPL37A 3941 0.079 0.59 YES
65 RPS21 RPS21 RPS21 3978 0.078 0.6 YES
66 RPL27 RPL27 RPL27 3990 0.078 0.6 YES
67 RPL13 RPL13 RPL13 4036 0.076 0.61 YES
68 RPL27A RPL27A RPL27A 4077 0.075 0.61 YES
69 RPL36 RPL36 RPL36 4104 0.074 0.62 YES
70 FAU FAU FAU 4118 0.073 0.62 YES
71 RPS16 RPS16 RPS16 4124 0.073 0.63 YES
72 RPS27 RPS27 RPS27 4214 0.071 0.63 YES
73 UBA52 UBA52 UBA52 4217 0.07 0.63 YES
74 RPS11 RPS11 RPS11 4236 0.07 0.64 YES
75 RPLP0 RPLP0 RPLP0 4284 0.068 0.64 YES
76 RPL6 RPL6 RPL6 4309 0.068 0.65 YES
77 RPL4 RPL4 RPL4 4527 0.062 0.64 NO
78 RPL23A RPL23A RPL23A 4664 0.058 0.64 NO
79 RPL28 RPL28 RPL28 4827 0.053 0.63 NO
80 RPS28 RPS28 RPS28 4875 0.052 0.63 NO
81 RPL19 RPL19 RPL19 5067 0.047 0.63 NO
82 RPL8 RPL8 RPL8 5149 0.044 0.62 NO
83 RPS26 RPS26 RPS26 5210 0.043 0.63 NO
84 RPL30 RPL30 RPL30 5498 0.036 0.61 NO
85 RBM8A RBM8A RBM8A 5727 0.03 0.6 NO
86 RNPS1 RNPS1 RNPS1 5998 0.024 0.59 NO
87 RPL7 RPL7 RPL7 6065 0.023 0.59 NO
88 PABPC1 PABPC1 PABPC1 6153 0.021 0.58 NO
89 SMG6 SMG6 SMG6 6918 0.0064 0.54 NO
90 SMG1 SMG1 SMG1 7016 0.0044 0.53 NO
91 PPP2R1A PPP2R1A PPP2R1A 7085 0.003 0.53 NO
92 SMG7 SMG7 SMG7 7954 -0.012 0.48 NO
93 RPS20 RPS20 RPS20 8236 -0.017 0.47 NO
94 CASC3 CASC3 CASC3 8793 -0.027 0.44 NO
95 MAGOH MAGOH MAGOH 8857 -0.029 0.44 NO
96 ETF1 ETF1 ETF1 8959 -0.03 0.43 NO
97 PPP2CA PPP2CA PPP2CA 9348 -0.038 0.41 NO
98 SMG5 SMG5 SMG5 9539 -0.041 0.4 NO
99 GSPT2 GSPT2 GSPT2 9562 -0.042 0.41 NO
100 EIF4A3 EIF4A3 EIF4A3 9897 -0.049 0.39 NO
101 UPF3A UPF3A UPF3A 10617 -0.064 0.36 NO
102 UPF2 UPF2 UPF2 10674 -0.066 0.36 NO
103 NCBP1 NCBP1 NCBP1 11936 -0.1 0.29 NO
104 UPF3B UPF3B UPF3B 12070 -0.1 0.3 NO
105 RPL26L1 RPL26L1 RPL26L1 12337 -0.12 0.29 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: KEGG RNA POLYMERASE.

Figure S44.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG RNA POLYMERASE, 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 SPLICEOSOME

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 RPSAP9 RPSAP9 RPSAP9 285 0.54 0.021 YES
2 RPL21 RPL21 RPL21 463 0.45 0.042 YES
3 RPL3L RPL3L RPL3L 657 0.38 0.057 YES
4 RPL35A RPL35A RPL35A 1174 0.28 0.046 YES
5 FAM153A FAM153A FAM153A 1234 0.27 0.061 YES
6 EIF4A2 EIF4A2 EIF4A2 1245 0.26 0.079 YES
7 RPSA RPSA RPSA 1418 0.24 0.086 YES
8 RPL15 RPL15 RPL15 1540 0.22 0.094 YES
9 RPL24 RPL24 RPL24 1552 0.22 0.11 YES
10 RPL32 RPL32 RPL32 1562 0.22 0.12 YES
11 RPL14 RPL14 RPL14 1705 0.21 0.13 YES
12 RPS10 RPS10 RPS10 1819 0.2 0.14 YES
13 RPS18 RPS18 RPS18 1977 0.18 0.14 YES
14 RPL29 RPL29 RPL29 2047 0.18 0.15 YES
15 RPL10A RPL10A RPL10A 2067 0.18 0.16 YES
16 RPS4Y1 RPS4Y1 RPS4Y1 2186 0.17 0.16 YES
17 RPS12 RPS12 RPS12 2210 0.16 0.17 YES
18 EIF2B5 EIF2B5 EIF2B5 2305 0.16 0.18 YES
19 RPS3A RPS3A RPS3A 2436 0.15 0.18 YES
20 RPL36A RPL36A RPL36A 2449 0.15 0.19 YES
21 RPL39 RPL39 RPL39 2560 0.14 0.2 YES
22 RPL5 RPL5 RPL5 2664 0.14 0.2 YES
23 RPL22 RPL22 RPL22 2735 0.13 0.2 YES
24 EEF1A1 EEF1A1 EEF1A1 2751 0.13 0.21 YES
25 EIF4G1 EIF4G1 EIF4G1 2783 0.13 0.22 YES
26 RPL18A RPL18A RPL18A 2817 0.13 0.23 YES
27 RPL9 RPL9 RPL9 2860 0.12 0.23 YES
28 RPS29 RPS29 RPS29 2911 0.12 0.24 YES
29 RPL34 RPL34 RPL34 2939 0.12 0.24 YES
30 RPL12 RPL12 RPL12 2966 0.12 0.25 YES
31 RPS3 RPS3 RPS3 3004 0.12 0.26 YES
32 RPS8 RPS8 RPS8 3015 0.12 0.27 YES
33 RPL3 RPL3 RPL3 3042 0.12 0.27 YES
34 RPS6 RPS6 RPS6 3073 0.12 0.28 YES
35 RPL26 RPL26 RPL26 3081 0.12 0.29 YES
36 EIF2S3 EIF2S3 EIF2S3 3089 0.11 0.29 YES
37 RPS19 RPS19 RPS19 3095 0.11 0.3 YES
38 RPS23 RPS23 RPS23 3113 0.11 0.31 YES
39 RPS27A RPS27A RPS27A 3116 0.11 0.32 YES
40 RPL11 RPL11 RPL11 3123 0.11 0.32 YES
41 RPS9 RPS9 RPS9 3124 0.11 0.33 YES
42 RPL17 RPL17 RPL17 3125 0.11 0.34 YES
43 RPS15A RPS15A RPS15A 3142 0.11 0.34 YES
44 RPS17 RPS17 RPS17 3196 0.11 0.35 YES
45 RPL10 RPL10 RPL10 3221 0.11 0.36 YES
46 RPS5 RPS5 RPS5 3224 0.11 0.36 YES
47 RPL13A RPL13A RPL13A 3259 0.11 0.37 YES
48 RPL23 RPL23 RPL23 3268 0.11 0.38 YES
49 RPL18 RPL18 RPL18 3306 0.1 0.38 YES
50 RPS2 RPS2 RPS2 3308 0.1 0.39 YES
51 EIF3G EIF3G EIF3G 3311 0.1 0.4 YES
52 RPS7 RPS7 RPS7 3312 0.1 0.4 YES
53 RPLP1 RPLP1 RPLP1 3338 0.1 0.41 YES
54 RPL31 RPL31 RPL31 3342 0.1 0.42 YES
55 RPL38 RPL38 RPL38 3346 0.1 0.42 YES
56 SSR3 SSR3 SSR3 3347 0.1 0.43 YES
57 RPS25 RPS25 RPS25 3371 0.1 0.43 YES
58 RPL7A RPL7A RPL7A 3486 0.097 0.43 YES
59 RPS24 RPS24 RPS24 3506 0.096 0.44 YES
60 RPS4X RPS4X RPS4X 3510 0.096 0.45 YES
61 RPS13 RPS13 RPS13 3530 0.095 0.45 YES
62 EEF1G EEF1G EEF1G 3536 0.094 0.46 YES
63 RPL35 RPL35 RPL35 3563 0.093 0.46 YES
64 SPCS1 SPCS1 SPCS1 3570 0.093 0.47 YES
65 EIF4B EIF4B EIF4B 3598 0.092 0.47 YES
66 RPS14 RPS14 RPS14 3611 0.091 0.48 YES
67 RPLP2 RPLP2 RPLP2 3696 0.088 0.48 YES
68 RPL41 RPL41 RPL41 3706 0.088 0.49 YES
69 RPS15 RPS15 RPS15 3765 0.086 0.49 YES
70 EEF2 EEF2 EEF2 3901 0.081 0.49 YES
71 RPL37 RPL37 RPL37 3908 0.081 0.49 YES
72 EIF3F EIF3F EIF3F 3920 0.08 0.5 YES
73 EIF3C EIF3C EIF3C 3928 0.08 0.5 YES
74 RPL37A RPL37A RPL37A 3941 0.079 0.51 YES
75 RPS21 RPS21 RPS21 3978 0.078 0.51 YES
76 RPL27 RPL27 RPL27 3990 0.078 0.52 YES
77 RPL13 RPL13 RPL13 4036 0.076 0.52 YES
78 RPL27A RPL27A RPL27A 4077 0.075 0.52 YES
79 RPL36 RPL36 RPL36 4104 0.074 0.52 YES
80 SEC11A SEC11A SEC11A 4105 0.074 0.53 YES
81 SRPRB SRPRB SRPRB 4107 0.074 0.53 YES
82 FAU FAU FAU 4118 0.073 0.54 YES
83 RPS16 RPS16 RPS16 4124 0.073 0.54 YES
84 EIF3D EIF3D EIF3D 4147 0.073 0.55 YES
85 RPS27 RPS27 RPS27 4214 0.071 0.55 YES
86 UBA52 UBA52 UBA52 4217 0.07 0.55 YES
87 EEF1B2 EEF1B2 EEF1B2 4235 0.07 0.56 YES
88 RPS11 RPS11 RPS11 4236 0.07 0.56 YES
89 RPLP0 RPLP0 RPLP0 4284 0.068 0.56 YES
90 RPL6 RPL6 RPL6 4309 0.068 0.57 YES
91 SSR2 SSR2 SSR2 4371 0.066 0.57 YES
92 RPN1 RPN1 RPN1 4399 0.065 0.57 YES
93 RPL4 RPL4 RPL4 4527 0.062 0.57 NO
94 RPL23A RPL23A RPL23A 4664 0.058 0.56 NO
95 RPL28 RPL28 RPL28 4827 0.053 0.56 NO
96 RPS28 RPS28 RPS28 4875 0.052 0.56 NO
97 EIF3K EIF3K EIF3K 4919 0.05 0.56 NO
98 RPL19 RPL19 RPL19 5067 0.047 0.55 NO
99 SEC61A1 SEC61A1 SEC61A1 5140 0.045 0.55 NO
100 RPL8 RPL8 RPL8 5149 0.044 0.56 NO
101 RPS26 RPS26 RPS26 5210 0.043 0.56 NO
102 SSR1 SSR1 SSR1 5216 0.043 0.56 NO
103 EIF3H EIF3H EIF3H 5245 0.042 0.56 NO
104 RPL30 RPL30 RPL30 5498 0.036 0.55 NO
105 DDOST DDOST DDOST 5884 0.027 0.53 NO
106 RPL7 RPL7 RPL7 6065 0.023 0.52 NO
107 PABPC1 PABPC1 PABPC1 6153 0.021 0.51 NO
108 SEC61B SEC61B SEC61B 6196 0.02 0.51 NO
109 EIF1AX EIF1AX EIF1AX 6253 0.019 0.51 NO
110 SSR4 SSR4 SSR4 6272 0.019 0.51 NO
111 EIF3E EIF3E EIF3E 6612 0.013 0.49 NO
112 EIF3A EIF3A EIF3A 6750 0.01 0.48 NO
113 EIF4H EIF4H EIF4H 6880 0.0073 0.48 NO
114 EIF2B1 EIF2B1 EIF2B1 7434 -0.0032 0.45 NO
115 EIF4A1 EIF4A1 EIF4A1 7438 -0.0033 0.45 NO
116 EEF1D EEF1D EEF1D 7476 -0.0039 0.44 NO
117 EIF3I EIF3I EIF3I 7580 -0.0058 0.44 NO
118 EIF2B2 EIF2B2 EIF2B2 7998 -0.013 0.42 NO
119 EIF2B3 EIF2B3 EIF2B3 8088 -0.015 0.41 NO
120 RPS20 RPS20 RPS20 8236 -0.017 0.4 NO
121 EIF5 EIF5 EIF5 8267 -0.018 0.4 NO
122 EIF5B EIF5B EIF5B 8466 -0.021 0.39 NO
123 SRP68 SRP68 SRP68 8488 -0.022 0.39 NO
124 EIF4EBP1 EIF4EBP1 EIF4EBP1 8572 -0.024 0.39 NO
125 SEC61G SEC61G SEC61G 8688 -0.026 0.39 NO
126 SRP72 SRP72 SRP72 8736 -0.026 0.38 NO
127 EIF2S2 EIF2S2 EIF2S2 8924 -0.03 0.38 NO
128 ETF1 ETF1 ETF1 8959 -0.03 0.38 NO
129 EIF3B EIF3B EIF3B 9162 -0.034 0.37 NO
130 SRPR SRPR SRPR 9460 -0.04 0.35 NO
131 GSPT2 GSPT2 GSPT2 9562 -0.042 0.35 NO
132 EIF2B4 EIF2B4 EIF2B4 9579 -0.042 0.35 NO
133 SRP19 SRP19 SRP19 9696 -0.045 0.35 NO
134 SRP9 SRP9 SRP9 9862 -0.048 0.34 NO
135 SRP14 SRP14 SRP14 9875 -0.048 0.34 NO
136 EIF4E EIF4E EIF4E 10079 -0.053 0.34 NO
137 EIF3J EIF3J EIF3J 10693 -0.066 0.3 NO
138 SRP54 SRP54 SRP54 10740 -0.068 0.31 NO
139 RPN2 RPN2 RPN2 11199 -0.079 0.29 NO
140 EIF2S1 EIF2S1 EIF2S1 11660 -0.092 0.26 NO
141 SEC11C SEC11C SEC11C 11816 -0.097 0.26 NO
142 SPCS3 SPCS3 SPCS3 11881 -0.1 0.27 NO
143 RPL26L1 RPL26L1 RPL26L1 12337 -0.12 0.25 NO
144 LOC653566 LOC653566 LOC653566 12591 -0.13 0.24 NO
145 SPCS2 SPCS2 SPCS2 12805 -0.14 0.24 NO
146 TRAM1 TRAM1 TRAM1 13315 -0.16 0.22 NO
147 SEC61A2 SEC61A2 SEC61A2 13781 -0.2 0.21 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: KEGG SPLICEOSOME.

Figure S46.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG SPLICEOSOME, 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 MYC 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 RPSAP9 RPSAP9 RPSAP9 285 0.54 0.081 YES
2 EIF4A2 EIF4A2 EIF4A2 1245 0.26 0.073 YES
3 RPSA RPSA RPSA 1418 0.24 0.11 YES
4 RPS10 RPS10 RPS10 1819 0.2 0.12 YES
5 RPS18 RPS18 RPS18 1977 0.18 0.14 YES
6 RPS4Y1 RPS4Y1 RPS4Y1 2186 0.17 0.16 YES
7 RPS12 RPS12 RPS12 2210 0.16 0.19 YES
8 RPS3A RPS3A RPS3A 2436 0.15 0.2 YES
9 EIF4G1 EIF4G1 EIF4G1 2783 0.13 0.21 YES
10 RPS29 RPS29 RPS29 2911 0.12 0.22 YES
11 RPS3 RPS3 RPS3 3004 0.12 0.24 YES
12 RPS8 RPS8 RPS8 3015 0.12 0.26 YES
13 RPS6 RPS6 RPS6 3073 0.12 0.28 YES
14 EIF2S3 EIF2S3 EIF2S3 3089 0.11 0.3 YES
15 RPS19 RPS19 RPS19 3095 0.11 0.32 YES
16 RPS23 RPS23 RPS23 3113 0.11 0.33 YES
17 RPS27A RPS27A RPS27A 3116 0.11 0.35 YES
18 RPS9 RPS9 RPS9 3124 0.11 0.37 YES
19 RPS15A RPS15A RPS15A 3142 0.11 0.39 YES
20 RPS17 RPS17 RPS17 3196 0.11 0.41 YES
21 RPS5 RPS5 RPS5 3224 0.11 0.43 YES
22 RPS2 RPS2 RPS2 3308 0.1 0.44 YES
23 EIF3G EIF3G EIF3G 3311 0.1 0.46 YES
24 RPS7 RPS7 RPS7 3312 0.1 0.48 YES
25 RPS25 RPS25 RPS25 3371 0.1 0.49 YES
26 RPS24 RPS24 RPS24 3506 0.096 0.5 YES
27 RPS4X RPS4X RPS4X 3510 0.096 0.52 YES
28 RPS13 RPS13 RPS13 3530 0.095 0.54 YES
29 EIF4B EIF4B EIF4B 3598 0.092 0.55 YES
30 RPS14 RPS14 RPS14 3611 0.091 0.56 YES
31 RPS15 RPS15 RPS15 3765 0.086 0.57 YES
32 EIF3F EIF3F EIF3F 3920 0.08 0.58 YES
33 EIF3C EIF3C EIF3C 3928 0.08 0.59 YES
34 RPS21 RPS21 RPS21 3978 0.078 0.6 YES
35 FAU FAU FAU 4118 0.073 0.61 YES
36 RPS16 RPS16 RPS16 4124 0.073 0.62 YES
37 EIF3D EIF3D EIF3D 4147 0.073 0.63 YES
38 RPS27 RPS27 RPS27 4214 0.071 0.64 YES
39 RPS11 RPS11 RPS11 4236 0.07 0.65 YES
40 RPS28 RPS28 RPS28 4875 0.052 0.62 NO
41 EIF3K EIF3K EIF3K 4919 0.05 0.63 NO
42 RPS26 RPS26 RPS26 5210 0.043 0.62 NO
43 EIF3H EIF3H EIF3H 5245 0.042 0.63 NO
44 PABPC1 PABPC1 PABPC1 6153 0.021 0.58 NO
45 EIF1AX EIF1AX EIF1AX 6253 0.019 0.58 NO
46 EIF3E EIF3E EIF3E 6612 0.013 0.56 NO
47 EIF3A EIF3A EIF3A 6750 0.01 0.55 NO
48 EIF4H EIF4H EIF4H 6880 0.0073 0.55 NO
49 EIF4A1 EIF4A1 EIF4A1 7438 -0.0033 0.52 NO
50 EIF3I EIF3I EIF3I 7580 -0.0058 0.51 NO
51 RPS20 RPS20 RPS20 8236 -0.017 0.47 NO
52 EIF4EBP1 EIF4EBP1 EIF4EBP1 8572 -0.024 0.46 NO
53 EIF2S2 EIF2S2 EIF2S2 8924 -0.03 0.44 NO
54 EIF3B EIF3B EIF3B 9162 -0.034 0.44 NO
55 EIF4E EIF4E EIF4E 10079 -0.053 0.39 NO
56 EIF3J EIF3J EIF3J 10693 -0.066 0.37 NO
57 EIF2S1 EIF2S1 EIF2S1 11660 -0.092 0.33 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 MYC PATHWAY.

Figure S48.  Get High-res Image For the top 5 core enriched genes in the pathway: PID MYC 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 RXR VDR PATHWAY

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 RPSAP9 RPSAP9 RPSAP9 285 0.54 0.029 YES
2 RPL21 RPL21 RPL21 463 0.45 0.057 YES
3 RPL3L RPL3L RPL3L 657 0.38 0.078 YES
4 RPL35A RPL35A RPL35A 1174 0.28 0.071 YES
5 FAM153A FAM153A FAM153A 1234 0.27 0.09 YES
6 EIF4A2 EIF4A2 EIF4A2 1245 0.26 0.11 YES
7 RPSA RPSA RPSA 1418 0.24 0.12 YES
8 RPL15 RPL15 RPL15 1540 0.22 0.13 YES
9 RPL24 RPL24 RPL24 1552 0.22 0.15 YES
10 RPL32 RPL32 RPL32 1562 0.22 0.17 YES
11 RPL14 RPL14 RPL14 1705 0.21 0.18 YES
12 RPS10 RPS10 RPS10 1819 0.2 0.19 YES
13 RPS18 RPS18 RPS18 1977 0.18 0.2 YES
14 RPL29 RPL29 RPL29 2047 0.18 0.21 YES
15 RPL10A RPL10A RPL10A 2067 0.18 0.22 YES
16 RPS4Y1 RPS4Y1 RPS4Y1 2186 0.17 0.23 YES
17 RPS12 RPS12 RPS12 2210 0.16 0.24 YES
18 RPS3A RPS3A RPS3A 2436 0.15 0.24 YES
19 RPL36A RPL36A RPL36A 2449 0.15 0.25 YES
20 RPL39 RPL39 RPL39 2560 0.14 0.26 YES
21 RPL5 RPL5 RPL5 2664 0.14 0.26 YES
22 RPL22 RPL22 RPL22 2735 0.13 0.27 YES
23 EIF4G1 EIF4G1 EIF4G1 2783 0.13 0.28 YES
24 RPL18A RPL18A RPL18A 2817 0.13 0.29 YES
25 RPL9 RPL9 RPL9 2860 0.12 0.3 YES
26 RPS29 RPS29 RPS29 2911 0.12 0.3 YES
27 RPL34 RPL34 RPL34 2939 0.12 0.31 YES
28 RPL12 RPL12 RPL12 2966 0.12 0.32 YES
29 RPS3 RPS3 RPS3 3004 0.12 0.33 YES
30 RPS8 RPS8 RPS8 3015 0.12 0.34 YES
31 RPL3 RPL3 RPL3 3042 0.12 0.35 YES
32 RPS6 RPS6 RPS6 3073 0.12 0.35 YES
33 RPL26 RPL26 RPL26 3081 0.12 0.36 YES
34 EIF2S3 EIF2S3 EIF2S3 3089 0.11 0.37 YES
35 RPS19 RPS19 RPS19 3095 0.11 0.38 YES
36 RPS23 RPS23 RPS23 3113 0.11 0.39 YES
37 RPS27A RPS27A RPS27A 3116 0.11 0.4 YES
38 RPL11 RPL11 RPL11 3123 0.11 0.41 YES
39 RPS9 RPS9 RPS9 3124 0.11 0.42 YES
40 RPL17 RPL17 RPL17 3125 0.11 0.43 YES
41 RPS15A RPS15A RPS15A 3142 0.11 0.44 YES
42 RPS17 RPS17 RPS17 3196 0.11 0.44 YES
43 RPL10 RPL10 RPL10 3221 0.11 0.45 YES
44 RPS5 RPS5 RPS5 3224 0.11 0.46 YES
45 RPL13A RPL13A RPL13A 3259 0.11 0.47 YES
46 RPL23 RPL23 RPL23 3268 0.11 0.48 YES
47 RPL18 RPL18 RPL18 3306 0.1 0.48 YES
48 RPS2 RPS2 RPS2 3308 0.1 0.49 YES
49 EIF3G EIF3G EIF3G 3311 0.1 0.5 YES
50 RPS7 RPS7 RPS7 3312 0.1 0.51 YES
51 RPLP1 RPLP1 RPLP1 3338 0.1 0.52 YES
52 RPL31 RPL31 RPL31 3342 0.1 0.52 YES
53 RPL38 RPL38 RPL38 3346 0.1 0.53 YES
54 RPS25 RPS25 RPS25 3371 0.1 0.54 YES
55 RPL7A RPL7A RPL7A 3486 0.097 0.54 YES
56 RPS24 RPS24 RPS24 3506 0.096 0.55 YES
57 RPS4X RPS4X RPS4X 3510 0.096 0.56 YES
58 RPS13 RPS13 RPS13 3530 0.095 0.56 YES
59 RPL35 RPL35 RPL35 3563 0.093 0.57 YES
60 EIF4B EIF4B EIF4B 3598 0.092 0.57 YES
61 RPS14 RPS14 RPS14 3611 0.091 0.58 YES
62 RPLP2 RPLP2 RPLP2 3696 0.088 0.58 YES
63 RPL41 RPL41 RPL41 3706 0.088 0.59 YES
64 RPS15 RPS15 RPS15 3765 0.086 0.59 YES
65 RPL37 RPL37 RPL37 3908 0.081 0.59 YES
66 EIF3F EIF3F EIF3F 3920 0.08 0.6 YES
67 EIF3C EIF3C EIF3C 3928 0.08 0.6 YES
68 RPL37A RPL37A RPL37A 3941 0.079 0.61 YES
69 RPS21 RPS21 RPS21 3978 0.078 0.62 YES
70 RPL27 RPL27 RPL27 3990 0.078 0.62 YES
71 RPL13 RPL13 RPL13 4036 0.076 0.62 YES
72 RPL27A RPL27A RPL27A 4077 0.075 0.63 YES
73 RPL36 RPL36 RPL36 4104 0.074 0.63 YES
74 FAU FAU FAU 4118 0.073 0.64 YES
75 RPS16 RPS16 RPS16 4124 0.073 0.65 YES
76 EIF3D EIF3D EIF3D 4147 0.073 0.65 YES
77 RPS27 RPS27 RPS27 4214 0.071 0.65 YES
78 UBA52 UBA52 UBA52 4217 0.07 0.66 YES
79 RPS11 RPS11 RPS11 4236 0.07 0.66 YES
80 RPLP0 RPLP0 RPLP0 4284 0.068 0.67 YES
81 RPL6 RPL6 RPL6 4309 0.068 0.67 YES
82 RPL4 RPL4 RPL4 4527 0.062 0.66 NO
83 RPL23A RPL23A RPL23A 4664 0.058 0.66 NO
84 RPL28 RPL28 RPL28 4827 0.053 0.66 NO
85 RPS28 RPS28 RPS28 4875 0.052 0.66 NO
86 EIF3K EIF3K EIF3K 4919 0.05 0.66 NO
87 RPL19 RPL19 RPL19 5067 0.047 0.65 NO
88 RPL8 RPL8 RPL8 5149 0.044 0.65 NO
89 RPS26 RPS26 RPS26 5210 0.043 0.65 NO
90 EIF3H EIF3H EIF3H 5245 0.042 0.66 NO
91 RPL30 RPL30 RPL30 5498 0.036 0.64 NO
92 RPL7 RPL7 RPL7 6065 0.023 0.61 NO
93 PABPC1 PABPC1 PABPC1 6153 0.021 0.61 NO
94 EIF1AX EIF1AX EIF1AX 6253 0.019 0.6 NO
95 EIF3E EIF3E EIF3E 6612 0.013 0.58 NO
96 EIF3A EIF3A EIF3A 6750 0.01 0.58 NO
97 EIF4H EIF4H EIF4H 6880 0.0073 0.57 NO
98 EIF4A1 EIF4A1 EIF4A1 7438 -0.0033 0.54 NO
99 EIF3I EIF3I EIF3I 7580 -0.0058 0.53 NO
100 RPS20 RPS20 RPS20 8236 -0.017 0.5 NO
101 EIF2S2 EIF2S2 EIF2S2 8924 -0.03 0.46 NO
102 EIF3B EIF3B EIF3B 9162 -0.034 0.45 NO
103 EIF4E EIF4E EIF4E 10079 -0.053 0.4 NO
104 EIF3J EIF3J EIF3J 10693 -0.066 0.37 NO
105 EIF2S1 EIF2S1 EIF2S1 11660 -0.092 0.32 NO
106 RPL26L1 RPL26L1 RPL26L1 12337 -0.12 0.29 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 RXR VDR PATHWAY.

Figure S50.  Get High-res Image For the top 5 core enriched genes in the pathway: PID RXR VDR 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 P53REGULATIONPATHWAY

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 RPSAP9 RPSAP9 RPSAP9 285 0.54 0.024 YES
2 RPL21 RPL21 RPL21 463 0.45 0.047 YES
3 RPL3L RPL3L RPL3L 657 0.38 0.064 YES
4 RPL35A RPL35A RPL35A 1174 0.28 0.054 YES
5 FAM153A FAM153A FAM153A 1234 0.27 0.07 YES
6 RPSA RPSA RPSA 1418 0.24 0.078 YES
7 RPL15 RPL15 RPL15 1540 0.22 0.087 YES
8 RPL24 RPL24 RPL24 1552 0.22 0.1 YES
9 RPL32 RPL32 RPL32 1562 0.22 0.12 YES
10 RPL14 RPL14 RPL14 1705 0.21 0.13 YES
11 RPS10 RPS10 RPS10 1819 0.2 0.13 YES
12 RPS18 RPS18 RPS18 1977 0.18 0.14 YES
13 RPL29 RPL29 RPL29 2047 0.18 0.15 YES
14 RPL10A RPL10A RPL10A 2067 0.18 0.16 YES
15 RPS4Y1 RPS4Y1 RPS4Y1 2186 0.17 0.16 YES
16 RPS12 RPS12 RPS12 2210 0.16 0.18 YES
17 RPS3A RPS3A RPS3A 2436 0.15 0.17 YES
18 RPL36A RPL36A RPL36A 2449 0.15 0.18 YES
19 POLR2H POLR2H POLR2H 2450 0.15 0.2 YES
20 RPL39 RPL39 RPL39 2560 0.14 0.2 YES
21 RPL5 RPL5 RPL5 2664 0.14 0.2 YES
22 NUP153 NUP153 NUP153 2711 0.13 0.21 YES
23 RPL22 RPL22 RPL22 2735 0.13 0.22 YES
24 RPL18A RPL18A RPL18A 2817 0.13 0.22 YES
25 RPL9 RPL9 RPL9 2860 0.12 0.23 YES
26 RPS29 RPS29 RPS29 2911 0.12 0.24 YES
27 HSPA1B HSPA1B HSPA1B 2925 0.12 0.24 YES
28 RPL34 RPL34 RPL34 2939 0.12 0.25 YES
29 RPL12 RPL12 RPL12 2966 0.12 0.26 YES
30 RPS3 RPS3 RPS3 3004 0.12 0.27 YES
31 RPS8 RPS8 RPS8 3015 0.12 0.28 YES
32 RPL3 RPL3 RPL3 3042 0.12 0.28 YES
33 RPS6 RPS6 RPS6 3073 0.12 0.29 YES
34 RPL26 RPL26 RPL26 3081 0.12 0.3 YES
35 RPS19 RPS19 RPS19 3095 0.11 0.3 YES
36 RPS23 RPS23 RPS23 3113 0.11 0.31 YES
37 RPS27A RPS27A RPS27A 3116 0.11 0.32 YES
38 RPL11 RPL11 RPL11 3123 0.11 0.33 YES
39 RPS9 RPS9 RPS9 3124 0.11 0.34 YES
40 RPL17 RPL17 RPL17 3125 0.11 0.35 YES
41 RPS15A RPS15A RPS15A 3142 0.11 0.35 YES
42 RPS17 RPS17 RPS17 3196 0.11 0.36 YES
43 RPL10 RPL10 RPL10 3221 0.11 0.36 YES
44 RPS5 RPS5 RPS5 3224 0.11 0.37 YES
45 RPL13A RPL13A RPL13A 3259 0.11 0.38 YES
46 RPL23 RPL23 RPL23 3268 0.11 0.39 YES
47 RPL18 RPL18 RPL18 3306 0.1 0.39 YES
48 RPS2 RPS2 RPS2 3308 0.1 0.4 YES
49 RPS7 RPS7 RPS7 3312 0.1 0.41 YES
50 RPLP1 RPLP1 RPLP1 3338 0.1 0.41 YES
51 RPL31 RPL31 RPL31 3342 0.1 0.42 YES
52 RPL38 RPL38 RPL38 3346 0.1 0.43 YES
53 RPS25 RPS25 RPS25 3371 0.1 0.43 YES
54 RPL7A RPL7A RPL7A 3486 0.097 0.43 YES
55 RPS24 RPS24 RPS24 3506 0.096 0.44 YES
56 RPS4X RPS4X RPS4X 3510 0.096 0.45 YES
57 RPS13 RPS13 RPS13 3530 0.095 0.45 YES
58 RPL35 RPL35 RPL35 3563 0.093 0.46 YES
59 RPS14 RPS14 RPS14 3611 0.091 0.46 YES
60 RPLP2 RPLP2 RPLP2 3696 0.088 0.46 YES
61 RPL41 RPL41 RPL41 3706 0.088 0.47 YES
62 RPS15 RPS15 RPS15 3765 0.086 0.47 YES
63 RPL37 RPL37 RPL37 3908 0.081 0.47 YES
64 RPL37A RPL37A RPL37A 3941 0.079 0.47 YES
65 RPS21 RPS21 RPS21 3978 0.078 0.48 YES
66 RPL27 RPL27 RPL27 3990 0.078 0.48 YES
67 RPL13 RPL13 RPL13 4036 0.076 0.49 YES
68 NUP54 NUP54 NUP54 4065 0.076 0.49 YES
69 RPL27A RPL27A RPL27A 4077 0.075 0.5 YES
70 RPL36 RPL36 RPL36 4104 0.074 0.5 YES
71 FAU FAU FAU 4118 0.073 0.5 YES
72 RPS16 RPS16 RPS16 4124 0.073 0.51 YES
73 RPS27 RPS27 RPS27 4214 0.071 0.51 YES
74 UBA52 UBA52 UBA52 4217 0.07 0.51 YES
75 RPS11 RPS11 RPS11 4236 0.07 0.52 YES
76 RPLP0 RPLP0 RPLP0 4284 0.068 0.52 YES
77 RPL6 RPL6 RPL6 4309 0.068 0.52 YES
78 GTF2F1 GTF2F1 GTF2F1 4311 0.068 0.53 YES
79 NUP210 NUP210 NUP210 4373 0.066 0.53 YES
80 GRSF1 GRSF1 GRSF1 4504 0.062 0.53 YES
81 RPL4 RPL4 RPL4 4527 0.062 0.53 YES
82 RPL23A RPL23A RPL23A 4664 0.058 0.53 NO
83 RPL28 RPL28 RPL28 4827 0.053 0.52 NO
84 RPS28 RPS28 RPS28 4875 0.052 0.52 NO
85 GTF2F2 GTF2F2 GTF2F2 5030 0.047 0.52 NO
86 RPL19 RPL19 RPL19 5067 0.047 0.52 NO
87 IPO5 IPO5 IPO5 5109 0.046 0.52 NO
88 NUP93 NUP93 NUP93 5117 0.045 0.52 NO
89 RPL8 RPL8 RPL8 5149 0.044 0.52 NO
90 RPS26 RPS26 RPS26 5210 0.043 0.52 NO
91 RPL30 RPL30 RPL30 5498 0.036 0.51 NO
92 CLTA CLTA CLTA 5515 0.036 0.51 NO
93 NUP214 NUP214 NUP214 5745 0.03 0.5 NO
94 RPL7 RPL7 RPL7 6065 0.023 0.48 NO
95 POLR2G POLR2G POLR2G 6174 0.021 0.48 NO
96 POLR2F POLR2F POLR2F 6214 0.02 0.48 NO
97 NUP133 NUP133 NUP133 6564 0.014 0.46 NO
98 KPNA1 KPNA1 KPNA1 6647 0.012 0.46 NO
99 NUP62 NUP62 NUP62 6782 0.0094 0.45 NO
100 POLR2L POLR2L POLR2L 7404 -0.0028 0.41 NO
101 NUPL2 NUPL2 NUPL2 7568 -0.0057 0.4 NO
102 NUP43 NUP43 NUP43 7603 -0.0062 0.4 NO
103 NUP35 NUP35 NUP35 7635 -0.0068 0.4 NO
104 POLR2C POLR2C POLR2C 7738 -0.0086 0.4 NO
105 NUP107 NUP107 NUP107 8136 -0.016 0.37 NO
106 RAN RAN RAN 8203 -0.017 0.37 NO
107 RPS20 RPS20 RPS20 8236 -0.017 0.37 NO
108 RAE1 RAE1 RAE1 8271 -0.018 0.37 NO
109 SEH1L SEH1L SEH1L 8359 -0.02 0.36 NO
110 RANBP2 RANBP2 RANBP2 8479 -0.021 0.36 NO
111 POM121 POM121 POM121 8640 -0.025 0.35 NO
112 AAAS AAAS AAAS 8674 -0.025 0.35 NO
113 POLR2B POLR2B POLR2B 8897 -0.029 0.34 NO
114 CALR CALR CALR 9017 -0.032 0.34 NO
115 POLR2J POLR2J POLR2J 9295 -0.037 0.32 NO
116 CANX CANX CANX 9327 -0.037 0.32 NO
117 POLR2I POLR2I POLR2I 9369 -0.038 0.32 NO
118 NUPL1 NUPL1 NUPL1 9422 -0.039 0.32 NO
119 NUP188 NUP188 NUP188 9529 -0.041 0.32 NO
120 POLR2E POLR2E POLR2E 9905 -0.049 0.3 NO
121 HSP90AA1 HSP90AA1 HSP90AA1 10298 -0.057 0.28 NO
122 POLR2A POLR2A POLR2A 10389 -0.059 0.28 NO
123 NUP155 NUP155 NUP155 10416 -0.06 0.29 NO
124 NUP37 NUP37 NUP37 10542 -0.063 0.28 NO
125 NUP50 NUP50 NUP50 10846 -0.07 0.27 NO
126 CLTC CLTC CLTC 10888 -0.071 0.28 NO
127 KPNB1 KPNB1 KPNB1 11037 -0.075 0.27 NO
128 NUP205 NUP205 NUP205 11057 -0.076 0.28 NO
129 POLR2D POLR2D POLR2D 11337 -0.082 0.27 NO
130 XPO1 XPO1 XPO1 11940 -0.1 0.24 NO
131 NUP85 NUP85 NUP85 12232 -0.11 0.23 NO
132 RPL26L1 RPL26L1 RPL26L1 12337 -0.12 0.23 NO
133 POLR2K POLR2K POLR2K 12449 -0.12 0.24 NO
134 NUP88 NUP88 NUP88 13407 -0.17 0.19 NO
135 TPR TPR TPR 14097 -0.22 0.17 NO
136 DNAJC3 DNAJC3 DNAJC3 14706 -0.27 0.15 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: PID P53REGULATIONPATHWAY.

Figure S52.  Get High-res Image For the top 5 core enriched genes in the pathway: PID P53REGULATIONPATHWAY, 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 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 RPSAP9 RPSAP9 RPSAP9 285 0.54 0.093 YES
2 RPSA RPSA RPSA 1418 0.24 0.076 YES
3 RPS10 RPS10 RPS10 1819 0.2 0.092 YES
4 RPS18 RPS18 RPS18 1977 0.18 0.12 YES
5 RPS4Y1 RPS4Y1 RPS4Y1 2186 0.17 0.14 YES
6 RPS12 RPS12 RPS12 2210 0.16 0.17 YES
7 RPS3A RPS3A RPS3A 2436 0.15 0.19 YES
8 RPS29 RPS29 RPS29 2911 0.12 0.19 YES
9 RPS3 RPS3 RPS3 3004 0.12 0.21 YES
10 RPS8 RPS8 RPS8 3015 0.12 0.23 YES
11 RPS6 RPS6 RPS6 3073 0.12 0.25 YES
12 EIF2S3 EIF2S3 EIF2S3 3089 0.11 0.27 YES
13 RPS19 RPS19 RPS19 3095 0.11 0.29 YES
14 RPS23 RPS23 RPS23 3113 0.11 0.32 YES
15 RPS27A RPS27A RPS27A 3116 0.11 0.34 YES
16 RPS9 RPS9 RPS9 3124 0.11 0.36 YES
17 RPS15A RPS15A RPS15A 3142 0.11 0.38 YES
18 RPS17 RPS17 RPS17 3196 0.11 0.4 YES
19 RPS5 RPS5 RPS5 3224 0.11 0.42 YES
20 RPS2 RPS2 RPS2 3308 0.1 0.44 YES
21 EIF3G EIF3G EIF3G 3311 0.1 0.46 YES
22 RPS7 RPS7 RPS7 3312 0.1 0.48 YES
23 RPS25 RPS25 RPS25 3371 0.1 0.5 YES
24 RPS24 RPS24 RPS24 3506 0.096 0.51 YES
25 RPS4X RPS4X RPS4X 3510 0.096 0.53 YES
26 RPS13 RPS13 RPS13 3530 0.095 0.55 YES
27 RPS14 RPS14 RPS14 3611 0.091 0.56 YES
28 RPS15 RPS15 RPS15 3765 0.086 0.57 YES
29 EIF3F EIF3F EIF3F 3920 0.08 0.57 YES
30 EIF3C EIF3C EIF3C 3928 0.08 0.59 YES
31 RPS21 RPS21 RPS21 3978 0.078 0.6 YES
32 FAU FAU FAU 4118 0.073 0.61 YES
33 RPS16 RPS16 RPS16 4124 0.073 0.62 YES
34 EIF3D EIF3D EIF3D 4147 0.073 0.64 YES
35 RPS27 RPS27 RPS27 4214 0.071 0.65 YES
36 RPS11 RPS11 RPS11 4236 0.07 0.66 YES
37 RPS28 RPS28 RPS28 4875 0.052 0.64 NO
38 EIF3K EIF3K EIF3K 4919 0.05 0.64 NO
39 RPS26 RPS26 RPS26 5210 0.043 0.63 NO
40 EIF3H EIF3H EIF3H 5245 0.042 0.64 NO
41 EIF1AX EIF1AX EIF1AX 6253 0.019 0.59 NO
42 EIF3E EIF3E EIF3E 6612 0.013 0.57 NO
43 EIF3A EIF3A EIF3A 6750 0.01 0.56 NO
44 EIF3I EIF3I EIF3I 7580 -0.0058 0.52 NO
45 RPS20 RPS20 RPS20 8236 -0.017 0.48 NO
46 EIF2S2 EIF2S2 EIF2S2 8924 -0.03 0.45 NO
47 EIF3B EIF3B EIF3B 9162 -0.034 0.44 NO
48 EIF3J EIF3J EIF3J 10693 -0.066 0.37 NO
49 EIF2S1 EIF2S1 EIF2S1 11660 -0.092 0.33 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 TRANSLATION.

Figure S54.  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 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 RPSAP9 RPSAP9 RPSAP9 285 0.54 0.01 YES
2 RPL21 RPL21 RPL21 463 0.45 0.022 YES
3 RPL3L RPL3L RPL3L 657 0.38 0.03 YES
4 PRKCD PRKCD PRKCD 992 0.31 0.025 YES
5 RPL35A RPL35A RPL35A 1174 0.28 0.028 YES
6 FAM153A FAM153A FAM153A 1234 0.27 0.038 YES
7 DCP1A DCP1A DCP1A 1235 0.27 0.051 YES
8 EIF4A2 EIF4A2 EIF4A2 1245 0.26 0.064 YES
9 RPSA RPSA RPSA 1418 0.24 0.066 YES
10 RPL15 RPL15 RPL15 1540 0.22 0.07 YES
11 RPL24 RPL24 RPL24 1552 0.22 0.08 YES
12 RPL32 RPL32 RPL32 1562 0.22 0.09 YES
13 RPL14 RPL14 RPL14 1705 0.21 0.092 YES
14 RPS10 RPS10 RPS10 1819 0.2 0.095 YES
15 RPS18 RPS18 RPS18 1977 0.18 0.095 YES
16 CNOT10 CNOT10 CNOT10 2023 0.18 0.1 YES
17 LSM3 LSM3 LSM3 2036 0.18 0.11 YES
18 RPL29 RPL29 RPL29 2047 0.18 0.12 YES
19 LSM2 LSM2 LSM2 2066 0.18 0.13 YES
20 RPL10A RPL10A RPL10A 2067 0.18 0.13 YES
21 RPS4Y1 RPS4Y1 RPS4Y1 2186 0.17 0.14 YES
22 RPS12 RPS12 RPS12 2210 0.16 0.14 YES
23 RPS3A RPS3A RPS3A 2436 0.15 0.14 YES
24 RPL36A RPL36A RPL36A 2449 0.15 0.14 YES
25 LSM5 LSM5 LSM5 2457 0.15 0.15 YES
26 RPL39 RPL39 RPL39 2560 0.14 0.15 YES
27 RPL5 RPL5 RPL5 2664 0.14 0.15 YES
28 NCBP2 NCBP2 NCBP2 2723 0.13 0.16 YES
29 RPL22 RPL22 RPL22 2735 0.13 0.16 YES
30 EIF4G1 EIF4G1 EIF4G1 2783 0.13 0.16 YES
31 RPL18A RPL18A RPL18A 2817 0.13 0.17 YES
32 RPL9 RPL9 RPL9 2860 0.12 0.17 YES
33 RPS29 RPS29 RPS29 2911 0.12 0.18 YES
34 HSPA1B HSPA1B HSPA1B 2925 0.12 0.18 YES
35 RPL34 RPL34 RPL34 2939 0.12 0.19 YES
36 RPL12 RPL12 RPL12 2966 0.12 0.19 YES
37 RPS3 RPS3 RPS3 3004 0.12 0.19 YES
38 RPS8 RPS8 RPS8 3015 0.12 0.2 YES
39 RPL3 RPL3 RPL3 3042 0.12 0.2 YES
40 EXOSC7 EXOSC7 EXOSC7 3055 0.12 0.21 YES
41 RPS6 RPS6 RPS6 3073 0.12 0.21 YES
42 RPL26 RPL26 RPL26 3081 0.12 0.22 YES
43 RPS19 RPS19 RPS19 3095 0.11 0.22 YES
44 LSM6 LSM6 LSM6 3104 0.11 0.23 YES
45 RPS23 RPS23 RPS23 3113 0.11 0.23 YES
46 RPS27A RPS27A RPS27A 3116 0.11 0.24 YES
47 RPL11 RPL11 RPL11 3123 0.11 0.24 YES
48 RPS9 RPS9 RPS9 3124 0.11 0.25 YES
49 RPL17 RPL17 RPL17 3125 0.11 0.26 YES
50 PSMD6 PSMD6 PSMD6 3136 0.11 0.26 YES
51 RPS15A RPS15A RPS15A 3142 0.11 0.27 YES
52 RPS17 RPS17 RPS17 3196 0.11 0.27 YES
53 RPL10 RPL10 RPL10 3221 0.11 0.27 YES
54 RPS5 RPS5 RPS5 3224 0.11 0.28 YES
55 RPL13A RPL13A RPL13A 3259 0.11 0.28 YES
56 RPL23 RPL23 RPL23 3268 0.11 0.28 YES
57 RPL18 RPL18 RPL18 3306 0.1 0.29 YES
58 RPS2 RPS2 RPS2 3308 0.1 0.29 YES
59 RPS7 RPS7 RPS7 3312 0.1 0.3 YES
60 RPLP1 RPLP1 RPLP1 3338 0.1 0.3 YES
61 RPL31 RPL31 RPL31 3342 0.1 0.31 YES
62 RPL38 RPL38 RPL38 3346 0.1 0.31 YES
63 RPS25 RPS25 RPS25 3371 0.1 0.32 YES
64 EXOSC5 EXOSC5 EXOSC5 3461 0.097 0.32 YES
65 PSMD2 PSMD2 PSMD2 3483 0.097 0.32 YES
66 RPL7A RPL7A RPL7A 3486 0.097 0.32 YES
67 RPS24 RPS24 RPS24 3506 0.096 0.33 YES
68 RPS4X RPS4X RPS4X 3510 0.096 0.33 YES
69 RPS13 RPS13 RPS13 3530 0.095 0.34 YES
70 RPL35 RPL35 RPL35 3563 0.093 0.34 YES
71 HSPB1 HSPB1 HSPB1 3589 0.092 0.34 YES
72 EIF4B EIF4B EIF4B 3598 0.092 0.34 YES
73 RPS14 RPS14 RPS14 3611 0.091 0.35 YES
74 XRN1 XRN1 XRN1 3685 0.089 0.35 YES
75 RPLP2 RPLP2 RPLP2 3696 0.088 0.35 YES
76 RPL41 RPL41 RPL41 3706 0.088 0.36 YES
77 RPS15 RPS15 RPS15 3765 0.086 0.36 YES
78 TNFSF13 TNFSF13 TNFSF13 3843 0.083 0.36 YES
79 PPP2R2A PPP2R2A PPP2R2A 3881 0.081 0.36 YES
80 RPL37 RPL37 RPL37 3908 0.081 0.36 YES
81 RPL37A RPL37A RPL37A 3941 0.079 0.36 YES
82 RPS21 RPS21 RPS21 3978 0.078 0.36 YES
83 RPL27 RPL27 RPL27 3990 0.078 0.37 YES
84 RPL13 RPL13 RPL13 4036 0.076 0.37 YES
85 RPL27A RPL27A RPL27A 4077 0.075 0.37 YES
86 RPL36 RPL36 RPL36 4104 0.074 0.37 YES
87 FAU FAU FAU 4118 0.073 0.38 YES
88 RPS16 RPS16 RPS16 4124 0.073 0.38 YES
89 RPS27 RPS27 RPS27 4214 0.071 0.38 YES
90 UBA52 UBA52 UBA52 4217 0.07 0.38 YES
91 RPS11 RPS11 RPS11 4236 0.07 0.38 YES
92 LSM1 LSM1 LSM1 4269 0.069 0.38 YES
93 RPLP0 RPLP0 RPLP0 4284 0.068 0.39 YES
94 RPL6 RPL6 RPL6 4309 0.068 0.39 YES
95 PSMA8 PSMA8 PSMA8 4445 0.064 0.38 NO
96 RPL4 RPL4 RPL4 4527 0.062 0.38 NO
97 RPL23A RPL23A RPL23A 4664 0.058 0.38 NO
98 RPL28 RPL28 RPL28 4827 0.053 0.37 NO
99 RPS28 RPS28 RPS28 4875 0.052 0.37 NO
100 PSMD10 PSMD10 PSMD10 4936 0.05 0.37 NO
101 ZFP36L1 ZFP36L1 ZFP36L1 5045 0.047 0.36 NO
102 RPL19 RPL19 RPL19 5067 0.047 0.37 NO
103 CNOT7 CNOT7 CNOT7 5143 0.045 0.36 NO
104 PSMD9 PSMD9 PSMD9 5145 0.045 0.37 NO
105 RPL8 RPL8 RPL8 5149 0.044 0.37 NO
106 RPS26 RPS26 RPS26 5210 0.043 0.37 NO
107 EDC4 EDC4 EDC4 5350 0.04 0.36 NO
108 DCP2 DCP2 DCP2 5454 0.037 0.36 NO
109 RPL30 RPL30 RPL30 5498 0.036 0.36 NO
110 PAIP1 PAIP1 PAIP1 5571 0.034 0.35 NO
111 PARN PARN PARN 5595 0.034 0.35 NO
112 RBM8A RBM8A RBM8A 5727 0.03 0.35 NO
113 NUP214 NUP214 NUP214 5745 0.03 0.35 NO
114 KHSRP KHSRP KHSRP 5836 0.028 0.34 NO
115 RNPS1 RNPS1 RNPS1 5998 0.024 0.34 NO
116 MAPK14 MAPK14 MAPK14 6017 0.024 0.34 NO
117 RPL7 RPL7 RPL7 6065 0.023 0.34 NO
118 PABPC1 PABPC1 PABPC1 6153 0.021 0.33 NO
119 PSMB7 PSMB7 PSMB7 6194 0.02 0.33 NO
120 HNRNPD HNRNPD HNRNPD 6257 0.019 0.33 NO
121 EDC3 EDC3 EDC3 6266 0.019 0.33 NO
122 PSMF1 PSMF1 PSMF1 6326 0.018 0.32 NO
123 MAPKAPK2 MAPKAPK2 MAPKAPK2 6580 0.014 0.31 NO
124 ELAVL1 ELAVL1 ELAVL1 6600 0.013 0.31 NO
125 PATL1 PATL1 PATL1 6709 0.011 0.3 NO
126 AKT1 AKT1 AKT1 6820 0.0087 0.3 NO
127 DCP1B DCP1B DCP1B 6915 0.0065 0.29 NO
128 SMG6 SMG6 SMG6 6918 0.0064 0.29 NO
129 SMG1 SMG1 SMG1 7016 0.0044 0.29 NO
130 PPP2R1A PPP2R1A PPP2R1A 7085 0.003 0.28 NO
131 CNOT6 CNOT6 CNOT6 7160 0.0017 0.28 NO
132 EIF4A1 EIF4A1 EIF4A1 7438 -0.0033 0.26 NO
133 HSPA8 HSPA8 HSPA8 7570 -0.0057 0.26 NO
134 EXOSC6 EXOSC6 EXOSC6 7669 -0.0072 0.25 NO
135 CNOT8 CNOT8 CNOT8 7773 -0.0092 0.25 NO
136 PSMD5 PSMD5 PSMD5 7778 -0.0092 0.25 NO
137 RQCD1 RQCD1 RQCD1 7897 -0.011 0.24 NO
138 SMG7 SMG7 SMG7 7954 -0.012 0.24 NO
139 RPS20 RPS20 RPS20 8236 -0.017 0.22 NO
140 PSMB4 PSMB4 PSMB4 8265 -0.018 0.22 NO
141 PSMD4 PSMD4 PSMD4 8372 -0.02 0.22 NO
142 PSMD13 PSMD13 PSMD13 8384 -0.02 0.22 NO
143 PSMA2 PSMA2 PSMA2 8652 -0.025 0.2 NO
144 C2orf29 C2orf29 C2orf29 8788 -0.027 0.2 NO
145 CASC3 CASC3 CASC3 8793 -0.027 0.2 NO
146 PSMD1 PSMD1 PSMD1 8800 -0.028 0.2 NO
147 CNOT3 CNOT3 CNOT3 8830 -0.028 0.2 NO
148 MAGOH MAGOH MAGOH 8857 -0.029 0.2 NO
149 EXOSC3 EXOSC3 EXOSC3 8895 -0.029 0.2 NO
150 PSMB2 PSMB2 PSMB2 8929 -0.03 0.2 NO
151 ETF1 ETF1 ETF1 8959 -0.03 0.2 NO
152 PSMA5 PSMA5 PSMA5 9086 -0.033 0.19 NO
153 DDX6 DDX6 DDX6 9098 -0.033 0.19 NO
154 EXOSC2 EXOSC2 EXOSC2 9117 -0.034 0.19 NO
155 LSM4 LSM4 LSM4 9226 -0.036 0.19 NO
156 ANP32A ANP32A ANP32A 9270 -0.037 0.19 NO
157 PPP2CA PPP2CA PPP2CA 9348 -0.038 0.18 NO
158 CNOT2 CNOT2 CNOT2 9439 -0.039 0.18 NO
159 PSMD3 PSMD3 PSMD3 9451 -0.04 0.18 NO
160 SMG5 SMG5 SMG5 9539 -0.041 0.18 NO
161 EXOSC1 EXOSC1 EXOSC1 9551 -0.042 0.18 NO
162 GSPT2 GSPT2 GSPT2 9562 -0.042 0.18 NO
163 PSMB5 PSMB5 PSMB5 9790 -0.047 0.17 NO
164 DIS3 DIS3 DIS3 9848 -0.048 0.17 NO
165 EIF4A3 EIF4A3 EIF4A3 9897 -0.049 0.17 NO
166 PSMA1 PSMA1 PSMA1 9921 -0.049 0.17 NO
167 EIF4E EIF4E EIF4E 10079 -0.053 0.16 NO
168 PSMC6 PSMC6 PSMC6 10082 -0.053 0.17 NO
169 PSME1 PSME1 PSME1 10191 -0.055 0.16 NO
170 MAPK11 MAPK11 MAPK11 10237 -0.056 0.16 NO
171 PSMB1 PSMB1 PSMB1 10330 -0.058 0.16 NO
172 PSMD8 PSMD8 PSMD8 10360 -0.059 0.16 NO
173 YWHAB YWHAB YWHAB 10400 -0.059 0.16 NO
174 PSMB6 PSMB6 PSMB6 10565 -0.063 0.16 NO
175 UPF3A UPF3A UPF3A 10617 -0.064 0.16 NO
176 UPF2 UPF2 UPF2 10674 -0.066 0.16 NO
177 EXOSC9 EXOSC9 EXOSC9 10755 -0.068 0.15 NO
178 DCPS DCPS DCPS 10859 -0.071 0.15 NO
179 PSMD7 PSMD7 PSMD7 10996 -0.074 0.15 NO
180 PSMD11 PSMD11 PSMD11 11219 -0.08 0.14 NO
181 PSMC3 PSMC3 PSMC3 11234 -0.08 0.14 NO
182 PSMC2 PSMC2 PSMC2 11317 -0.082 0.14 NO
183 TNPO1 TNPO1 TNPO1 11338 -0.083 0.14 NO
184 PSMC4 PSMC4 PSMC4 11427 -0.085 0.14 NO
185 PSMC5 PSMC5 PSMC5 11555 -0.089 0.14 NO
186 YWHAZ YWHAZ YWHAZ 11604 -0.09 0.14 NO
187 PSMA7 PSMA7 PSMA7 11685 -0.093 0.14 NO
188 TNKS1BP1 TNKS1BP1 TNKS1BP1 11838 -0.098 0.14 NO
189 CNOT4 CNOT4 CNOT4 11917 -0.1 0.14 NO
190 NCBP1 NCBP1 NCBP1 11936 -0.1 0.14 NO
191 XPO1 XPO1 XPO1 11940 -0.1 0.15 NO
192 ZFP36 ZFP36 ZFP36 11961 -0.1 0.15 NO
193 UPF3B UPF3B UPF3B 12070 -0.1 0.15 NO
194 PSMD12 PSMD12 PSMD12 12119 -0.11 0.15 NO
195 PSMA6 PSMA6 PSMA6 12297 -0.11 0.15 NO
196 RPL26L1 RPL26L1 RPL26L1 12337 -0.12 0.15 NO
197 PSMC1 PSMC1 PSMC1 12423 -0.12 0.15 NO
198 PSMD14 PSMD14 PSMD14 12601 -0.13 0.15 NO
199 PSMB3 PSMB3 PSMB3 12620 -0.13 0.15 NO
200 PSMA4 PSMA4 PSMA4 12636 -0.13 0.16 NO
201 EXOSC8 EXOSC8 EXOSC8 12800 -0.14 0.16 NO
202 PSME2 PSME2 PSME2 13157 -0.16 0.14 NO
203 EXOSC4 EXOSC4 EXOSC4 13256 -0.16 0.14 NO
204 PSMB10 PSMB10 PSMB10 13544 -0.18 0.14 NO
205 PSMA3 PSMA3 PSMA3 13622 -0.18 0.14 NO
206 PSME4 PSME4 PSME4 13815 -0.2 0.14 NO
207 PRKCA PRKCA PRKCA 15098 -0.31 0.08 NO
208 PSMB8 PSMB8 PSMB8 15351 -0.33 0.082 NO
209 PSMB9 PSMB9 PSMB9 17103 -0.71 0.014 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 FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX.

Figure S56.  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 SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE

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 RPSAP9 RPSAP9 RPSAP9 285 0.54 0.027 YES
2 RPL21 RPL21 RPL21 463 0.45 0.054 YES
3 RPL3L RPL3L RPL3L 657 0.38 0.074 YES
4 RPL35A RPL35A RPL35A 1174 0.28 0.066 YES
5 FAM153A FAM153A FAM153A 1234 0.27 0.084 YES
6 RPSA RPSA RPSA 1418 0.24 0.093 YES
7 RPL15 RPL15 RPL15 1540 0.22 0.1 YES
8 RPL24 RPL24 RPL24 1552 0.22 0.12 YES
9 RPL32 RPL32 RPL32 1562 0.22 0.14 YES
10 RPL14 RPL14 RPL14 1705 0.21 0.15 YES
11 RPS10 RPS10 RPS10 1819 0.2 0.16 YES
12 RPS18 RPS18 RPS18 1977 0.18 0.16 YES
13 RPL29 RPL29 RPL29 2047 0.18 0.17 YES
14 RPL10A RPL10A RPL10A 2067 0.18 0.19 YES
15 RPS4Y1 RPS4Y1 RPS4Y1 2186 0.17 0.19 YES
16 RPS12 RPS12 RPS12 2210 0.16 0.2 YES
17 RPS3A RPS3A RPS3A 2436 0.15 0.2 YES
18 RPL36A RPL36A RPL36A 2449 0.15 0.22 YES
19 RPL39 RPL39 RPL39 2560 0.14 0.22 YES
20 RPL5 RPL5 RPL5 2664 0.14 0.23 YES
21 RPL22 RPL22 RPL22 2735 0.13 0.23 YES
22 RPL18A RPL18A RPL18A 2817 0.13 0.24 YES
23 RPL9 RPL9 RPL9 2860 0.12 0.25 YES
24 RPS29 RPS29 RPS29 2911 0.12 0.25 YES
25 RPL34 RPL34 RPL34 2939 0.12 0.26 YES
26 RPL12 RPL12 RPL12 2966 0.12 0.27 YES
27 RPS3 RPS3 RPS3 3004 0.12 0.28 YES
28 RPS8 RPS8 RPS8 3015 0.12 0.29 YES
29 RPL3 RPL3 RPL3 3042 0.12 0.29 YES
30 RPS6 RPS6 RPS6 3073 0.12 0.3 YES
31 RPL26 RPL26 RPL26 3081 0.12 0.31 YES
32 RPS19 RPS19 RPS19 3095 0.11 0.32 YES
33 RPS23 RPS23 RPS23 3113 0.11 0.33 YES
34 RPS27A RPS27A RPS27A 3116 0.11 0.34 YES
35 RPL11 RPL11 RPL11 3123 0.11 0.34 YES
36 RPS9 RPS9 RPS9 3124 0.11 0.35 YES
37 RPL17 RPL17 RPL17 3125 0.11 0.36 YES
38 RPS15A RPS15A RPS15A 3142 0.11 0.37 YES
39 RPS17 RPS17 RPS17 3196 0.11 0.38 YES
40 RPL10 RPL10 RPL10 3221 0.11 0.38 YES
41 RPS5 RPS5 RPS5 3224 0.11 0.39 YES
42 RPL13A RPL13A RPL13A 3259 0.11 0.4 YES
43 RPL23 RPL23 RPL23 3268 0.11 0.41 YES
44 RPL18 RPL18 RPL18 3306 0.1 0.41 YES
45 RPS2 RPS2 RPS2 3308 0.1 0.42 YES
46 RPS7 RPS7 RPS7 3312 0.1 0.43 YES
47 RPLP1 RPLP1 RPLP1 3338 0.1 0.44 YES
48 RPL31 RPL31 RPL31 3342 0.1 0.45 YES
49 RPL38 RPL38 RPL38 3346 0.1 0.45 YES
50 SSR3 SSR3 SSR3 3347 0.1 0.46 YES
51 RPS25 RPS25 RPS25 3371 0.1 0.47 YES
52 RPL7A RPL7A RPL7A 3486 0.097 0.47 YES
53 RPS24 RPS24 RPS24 3506 0.096 0.48 YES
54 RPS4X RPS4X RPS4X 3510 0.096 0.48 YES
55 RPS13 RPS13 RPS13 3530 0.095 0.49 YES
56 RPL35 RPL35 RPL35 3563 0.093 0.5 YES
57 SPCS1 SPCS1 SPCS1 3570 0.093 0.5 YES
58 RPS14 RPS14 RPS14 3611 0.091 0.51 YES
59 RPLP2 RPLP2 RPLP2 3696 0.088 0.51 YES
60 RPL41 RPL41 RPL41 3706 0.088 0.52 YES
61 RPS15 RPS15 RPS15 3765 0.086 0.52 YES
62 RPL37 RPL37 RPL37 3908 0.081 0.52 YES
63 RPL37A RPL37A RPL37A 3941 0.079 0.52 YES
64 RPS21 RPS21 RPS21 3978 0.078 0.53 YES
65 RPL27 RPL27 RPL27 3990 0.078 0.54 YES
66 RPL13 RPL13 RPL13 4036 0.076 0.54 YES
67 RPL27A RPL27A RPL27A 4077 0.075 0.54 YES
68 RPL36 RPL36 RPL36 4104 0.074 0.55 YES
69 SEC11A SEC11A SEC11A 4105 0.074 0.55 YES
70 SRPRB SRPRB SRPRB 4107 0.074 0.56 YES
71 FAU FAU FAU 4118 0.073 0.56 YES
72 RPS16 RPS16 RPS16 4124 0.073 0.57 YES
73 RPS27 RPS27 RPS27 4214 0.071 0.57 YES
74 UBA52 UBA52 UBA52 4217 0.07 0.58 YES
75 RPS11 RPS11 RPS11 4236 0.07 0.58 YES
76 RPLP0 RPLP0 RPLP0 4284 0.068 0.58 YES
77 RPL6 RPL6 RPL6 4309 0.068 0.59 YES
78 SSR2 SSR2 SSR2 4371 0.066 0.59 YES
79 RPN1 RPN1 RPN1 4399 0.065 0.59 YES
80 RPL4 RPL4 RPL4 4527 0.062 0.59 NO
81 RPL23A RPL23A RPL23A 4664 0.058 0.59 NO
82 RPL28 RPL28 RPL28 4827 0.053 0.58 NO
83 RPS28 RPS28 RPS28 4875 0.052 0.58 NO
84 RPL19 RPL19 RPL19 5067 0.047 0.58 NO
85 SEC61A1 SEC61A1 SEC61A1 5140 0.045 0.58 NO
86 RPL8 RPL8 RPL8 5149 0.044 0.58 NO
87 RPS26 RPS26 RPS26 5210 0.043 0.58 NO
88 SSR1 SSR1 SSR1 5216 0.043 0.58 NO
89 RPL30 RPL30 RPL30 5498 0.036 0.57 NO
90 DDOST DDOST DDOST 5884 0.027 0.55 NO
91 RPL7 RPL7 RPL7 6065 0.023 0.54 NO
92 SEC61B SEC61B SEC61B 6196 0.02 0.53 NO
93 SSR4 SSR4 SSR4 6272 0.019 0.53 NO
94 RPS20 RPS20 RPS20 8236 -0.017 0.42 NO
95 SRP68 SRP68 SRP68 8488 -0.022 0.41 NO
96 SEC61G SEC61G SEC61G 8688 -0.026 0.4 NO
97 SRP72 SRP72 SRP72 8736 -0.026 0.4 NO
98 SRPR SRPR SRPR 9460 -0.04 0.36 NO
99 SRP19 SRP19 SRP19 9696 -0.045 0.35 NO
100 SRP9 SRP9 SRP9 9862 -0.048 0.34 NO
101 SRP14 SRP14 SRP14 9875 -0.048 0.34 NO
102 SRP54 SRP54 SRP54 10740 -0.068 0.3 NO
103 RPN2 RPN2 RPN2 11199 -0.079 0.28 NO
104 SEC11C SEC11C SEC11C 11816 -0.097 0.25 NO
105 SPCS3 SPCS3 SPCS3 11881 -0.1 0.26 NO
106 RPL26L1 RPL26L1 RPL26L1 12337 -0.12 0.24 NO
107 LOC653566 LOC653566 LOC653566 12591 -0.13 0.24 NO
108 SPCS2 SPCS2 SPCS2 12805 -0.14 0.23 NO
109 TRAM1 TRAM1 TRAM1 13315 -0.16 0.22 NO
110 SEC61A2 SEC61A2 SEC61A2 13781 -0.2 0.21 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 SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE.

Figure S58.  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 THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S

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 RPSAP9 RPSAP9 RPSAP9 285 0.54 0.03 YES
2 RPL21 RPL21 RPL21 463 0.45 0.058 YES
3 RPL3L RPL3L RPL3L 657 0.38 0.08 YES
4 RPL35A RPL35A RPL35A 1174 0.28 0.074 YES
5 FAM153A FAM153A FAM153A 1234 0.27 0.093 YES
6 RPSA RPSA RPSA 1418 0.24 0.1 YES
7 RPL15 RPL15 RPL15 1540 0.22 0.12 YES
8 RPL24 RPL24 RPL24 1552 0.22 0.13 YES
9 RPL32 RPL32 RPL32 1562 0.22 0.15 YES
10 RPL14 RPL14 RPL14 1705 0.21 0.16 YES
11 RPS10 RPS10 RPS10 1819 0.2 0.17 YES
12 RPS18 RPS18 RPS18 1977 0.18 0.18 YES
13 RPL29 RPL29 RPL29 2047 0.18 0.19 YES
14 RPL10A RPL10A RPL10A 2067 0.18 0.2 YES
15 RPS4Y1 RPS4Y1 RPS4Y1 2186 0.17 0.21 YES
16 RPS12 RPS12 RPS12 2210 0.16 0.22 YES
17 RPS3A RPS3A RPS3A 2436 0.15 0.22 YES
18 RPL36A RPL36A RPL36A 2449 0.15 0.24 YES
19 POLR2H POLR2H POLR2H 2450 0.15 0.25 YES
20 RPL39 RPL39 RPL39 2560 0.14 0.26 YES
21 RPL5 RPL5 RPL5 2664 0.14 0.26 YES
22 RPL22 RPL22 RPL22 2735 0.13 0.27 YES
23 RPL18A RPL18A RPL18A 2817 0.13 0.28 YES
24 RPL9 RPL9 RPL9 2860 0.12 0.28 YES
25 RPS29 RPS29 RPS29 2911 0.12 0.29 YES
26 RPL34 RPL34 RPL34 2939 0.12 0.3 YES
27 RPL12 RPL12 RPL12 2966 0.12 0.31 YES
28 RPS3 RPS3 RPS3 3004 0.12 0.32 YES
29 RPS8 RPS8 RPS8 3015 0.12 0.33 YES
30 RPL3 RPL3 RPL3 3042 0.12 0.34 YES
31 RPS6 RPS6 RPS6 3073 0.12 0.34 YES
32 RPL26 RPL26 RPL26 3081 0.12 0.35 YES
33 RPS19 RPS19 RPS19 3095 0.11 0.36 YES
34 RPS23 RPS23 RPS23 3113 0.11 0.37 YES
35 RPS27A RPS27A RPS27A 3116 0.11 0.38 YES
36 RPL11 RPL11 RPL11 3123 0.11 0.39 YES
37 RPS9 RPS9 RPS9 3124 0.11 0.4 YES
38 RPL17 RPL17 RPL17 3125 0.11 0.41 YES
39 RPS15A RPS15A RPS15A 3142 0.11 0.42 YES
40 RPS17 RPS17 RPS17 3196 0.11 0.42 YES
41 RPL10 RPL10 RPL10 3221 0.11 0.43 YES
42 RPS5 RPS5 RPS5 3224 0.11 0.44 YES
43 RPL13A RPL13A RPL13A 3259 0.11 0.45 YES
44 RPL23 RPL23 RPL23 3268 0.11 0.46 YES
45 RPL18 RPL18 RPL18 3306 0.1 0.46 YES
46 RPS2 RPS2 RPS2 3308 0.1 0.47 YES
47 RPS7 RPS7 RPS7 3312 0.1 0.48 YES
48 RPLP1 RPLP1 RPLP1 3338 0.1 0.49 YES
49 RPL31 RPL31 RPL31 3342 0.1 0.5 YES
50 RPL38 RPL38 RPL38 3346 0.1 0.5 YES
51 RPS25 RPS25 RPS25 3371 0.1 0.51 YES
52 RPL7A RPL7A RPL7A 3486 0.097 0.51 YES
53 RPS24 RPS24 RPS24 3506 0.096 0.52 YES
54 RPS4X RPS4X RPS4X 3510 0.096 0.53 YES
55 RPS13 RPS13 RPS13 3530 0.095 0.54 YES
56 RPL35 RPL35 RPL35 3563 0.093 0.54 YES
57 RPS14 RPS14 RPS14 3611 0.091 0.55 YES
58 RPLP2 RPLP2 RPLP2 3696 0.088 0.55 YES
59 RPL41 RPL41 RPL41 3706 0.088 0.56 YES
60 RPS15 RPS15 RPS15 3765 0.086 0.56 YES
61 RPL37 RPL37 RPL37 3908 0.081 0.56 YES
62 RPL37A RPL37A RPL37A 3941 0.079 0.56 YES
63 RPS21 RPS21 RPS21 3978 0.078 0.57 YES
64 RPL27 RPL27 RPL27 3990 0.078 0.58 YES
65 RPL13 RPL13 RPL13 4036 0.076 0.58 YES
66 RPL27A RPL27A RPL27A 4077 0.075 0.58 YES
67 RPL36 RPL36 RPL36 4104 0.074 0.59 YES
68 FAU FAU FAU 4118 0.073 0.59 YES
69 RPS16 RPS16 RPS16 4124 0.073 0.6 YES
70 RPS27 RPS27 RPS27 4214 0.071 0.6 YES
71 UBA52 UBA52 UBA52 4217 0.07 0.61 YES
72 RPS11 RPS11 RPS11 4236 0.07 0.61 YES
73 RPLP0 RPLP0 RPLP0 4284 0.068 0.62 YES
74 RPL6 RPL6 RPL6 4309 0.068 0.62 YES
75 GTF2F1 GTF2F1 GTF2F1 4311 0.068 0.62 YES
76 GRSF1 GRSF1 GRSF1 4504 0.062 0.62 NO
77 RPL4 RPL4 RPL4 4527 0.062 0.62 NO
78 RPL23A RPL23A RPL23A 4664 0.058 0.62 NO
79 RPL28 RPL28 RPL28 4827 0.053 0.62 NO
80 RPS28 RPS28 RPS28 4875 0.052 0.62 NO
81 GTF2F2 GTF2F2 GTF2F2 5030 0.047 0.61 NO
82 RPL19 RPL19 RPL19 5067 0.047 0.62 NO
83 IPO5 IPO5 IPO5 5109 0.046 0.62 NO
84 RPL8 RPL8 RPL8 5149 0.044 0.62 NO
85 RPS26 RPS26 RPS26 5210 0.043 0.62 NO
86 RPL30 RPL30 RPL30 5498 0.036 0.6 NO
87 RPL7 RPL7 RPL7 6065 0.023 0.57 NO
88 POLR2G POLR2G POLR2G 6174 0.021 0.57 NO
89 POLR2F POLR2F POLR2F 6214 0.02 0.57 NO
90 POLR2L POLR2L POLR2L 7404 -0.0028 0.5 NO
91 POLR2C POLR2C POLR2C 7738 -0.0086 0.48 NO
92 RPS20 RPS20 RPS20 8236 -0.017 0.45 NO
93 POLR2B POLR2B POLR2B 8897 -0.029 0.42 NO
94 POLR2J POLR2J POLR2J 9295 -0.037 0.4 NO
95 POLR2I POLR2I POLR2I 9369 -0.038 0.4 NO
96 POLR2E POLR2E POLR2E 9905 -0.049 0.37 NO
97 HSP90AA1 HSP90AA1 HSP90AA1 10298 -0.057 0.35 NO
98 POLR2A POLR2A POLR2A 10389 -0.059 0.35 NO
99 POLR2D POLR2D POLR2D 11337 -0.082 0.3 NO
100 RPL26L1 RPL26L1 RPL26L1 12337 -0.12 0.26 NO
101 POLR2K POLR2K POLR2K 12449 -0.12 0.26 NO
102 DNAJC3 DNAJC3 DNAJC3 14706 -0.27 0.15 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 ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S.

Figure S60.  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 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 PYRIMIDINE METABOLISM 96 genes.ES.table 0.32 1.5 0.06 0.18 0.96 0.1 0.12 0.092 0.12 0.002
KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM 43 genes.ES.table 0.46 1.8 0.02 0.056 0.57 0.51 0.32 0.35 0.013 0
KEGG INOSITOL PHOSPHATE METABOLISM 51 genes.ES.table 0.42 1.4 0.067 0.19 0.97 0.28 0.19 0.22 0.14 0.002
KEGG DRUG METABOLISM OTHER ENZYMES 25 genes.ES.table 0.51 1.5 0.043 0.16 0.94 0.2 0.07 0.19 0.11 0.001
KEGG PROTEASOME 43 genes.ES.table 0.58 1.8 0.016 0.045 0.4 0.65 0.33 0.44 0 0.003
KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION 209 genes.ES.table 0.74 1.8 0 0.058 0.58 0.57 0.14 0.5 0.014 0
KEGG CHEMOKINE SIGNALING PATHWAY 176 genes.ES.table 0.72 2 0 0.056 0.17 0.4 0.11 0.36 0 0.017
KEGG PHOSPHATIDYLINOSITOL SIGNALING SYSTEM 71 genes.ES.table 0.49 1.5 0.031 0.14 0.92 0.31 0.19 0.25 0.081 0
KEGG LYSOSOME 119 genes.ES.table 0.39 1.7 0.036 0.06 0.6 0.35 0.29 0.25 0.015 0
KEGG ENDOCYTOSIS 178 genes.ES.table 0.39 1.6 0.03 0.1 0.86 0.14 0.12 0.12 0.053 0
genes ES table in pathway: KEGG PYRIMIDINE METABOLISM

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 CD8B CD8B CD8B 8 1.3 0.083 YES
2 LCK LCK LCK 13 1.2 0.16 YES
3 CD247 CD247 CD247 40 1.1 0.23 YES
4 PSMB9 PSMB9 PSMB9 61 1 0.3 YES
5 DOCK2 DOCK2 DOCK2 202 0.82 0.34 YES
6 HCK HCK HCK 424 0.63 0.37 YES
7 CD28 CD28 CD28 464 0.61 0.41 YES
8 ELMO1 ELMO1 ELMO1 618 0.52 0.43 YES
9 PSMB8 PSMB8 PSMB8 688 0.49 0.46 YES
10 B2M B2M B2M 962 0.39 0.47 YES
11 APOBEC3G APOBEC3G APOBEC3G 1018 0.37 0.49 YES
12 CD4 CD4 CD4 1032 0.37 0.51 YES
13 PSMB10 PSMB10 PSMB10 1411 0.3 0.51 YES
14 PSME2 PSME2 PSME2 1542 0.28 0.52 YES
15 HLA-A HLA-A HLA-A 1591 0.27 0.54 YES
16 PSMA3 PSMA3 PSMA3 2092 0.21 0.52 NO
17 PSME1 PSME1 PSME1 2576 0.17 0.5 NO
18 TCEB1 TCEB1 TCEB1 2859 0.15 0.5 NO
19 PSMA4 PSMA4 PSMA4 2986 0.15 0.5 NO
20 PSME4 PSME4 PSME4 3021 0.14 0.51 NO
21 TPR TPR TPR 3028 0.14 0.52 NO
22 PSMA6 PSMA6 PSMA6 3050 0.14 0.52 NO
23 PSMA5 PSMA5 PSMA5 3352 0.13 0.51 NO
24 PSMD14 PSMD14 PSMD14 3355 0.13 0.52 NO
25 NUP88 NUP88 NUP88 3507 0.12 0.52 NO
26 PSMB3 PSMB3 PSMB3 3832 0.11 0.51 NO
27 PSMC1 PSMC1 PSMC1 3934 0.1 0.51 NO
28 PSMB2 PSMB2 PSMB2 4038 0.1 0.51 NO
29 RBX1 RBX1 RBX1 4127 0.098 0.51 NO
30 PSMC6 PSMC6 PSMC6 4144 0.098 0.52 NO
31 PSMA7 PSMA7 PSMA7 4221 0.095 0.52 NO
32 PSMD12 PSMD12 PSMD12 4348 0.091 0.52 NO
33 PSMC2 PSMC2 PSMC2 4564 0.086 0.51 NO
34 PSMD11 PSMD11 PSMD11 4678 0.082 0.51 NO
35 ATP6V1H ATP6V1H ATP6V1H 4743 0.081 0.51 NO
36 NUP85 NUP85 NUP85 4897 0.076 0.51 NO
37 PSMD7 PSMD7 PSMD7 4978 0.074 0.51 NO
38 PSMC4 PSMC4 PSMC4 5002 0.073 0.51 NO
39 XPO1 XPO1 XPO1 5065 0.072 0.51 NO
40 PSMC3 PSMC3 PSMC3 5413 0.064 0.5 NO
41 PSMC5 PSMC5 PSMC5 5505 0.062 0.49 NO
42 PSMB6 PSMB6 PSMB6 5587 0.06 0.49 NO
43 PSMA2 PSMA2 PSMA2 5653 0.059 0.49 NO
44 NUP50 NUP50 NUP50 5674 0.058 0.5 NO
45 PSMB1 PSMB1 PSMB1 6534 0.042 0.45 NO
46 CUL5 CUL5 CUL5 6621 0.04 0.45 NO
47 PSMA1 PSMA1 PSMA1 6784 0.038 0.44 NO
48 PSMD8 PSMD8 PSMD8 6867 0.036 0.44 NO
49 NUP37 NUP37 NUP37 6895 0.036 0.44 NO
50 RCC1 RCC1 RCC1 6962 0.034 0.44 NO
51 PSMD5 PSMD5 PSMD5 6987 0.034 0.44 NO
52 AP1G1 AP1G1 AP1G1 7020 0.033 0.44 NO
53 PSMD13 PSMD13 PSMD13 7204 0.03 0.43 NO
54 KPNB1 KPNB1 KPNB1 7254 0.029 0.43 NO
55 KPNA1 KPNA1 KPNA1 7278 0.029 0.43 NO
56 PSMB5 PSMB5 PSMB5 7390 0.027 0.42 NO
57 PSMD3 PSMD3 PSMD3 7400 0.027 0.42 NO
58 TCEB2 TCEB2 TCEB2 7580 0.024 0.42 NO
59 ARF1 ARF1 ARF1 7589 0.024 0.42 NO
60 AP2A2 AP2A2 AP2A2 7926 0.019 0.4 NO
61 AP2S1 AP2S1 AP2S1 8007 0.018 0.4 NO
62 NUP188 NUP188 NUP188 8013 0.018 0.4 NO
63 AP1M1 AP1M1 AP1M1 8074 0.017 0.39 NO
64 CDK9 CDK9 CDK9 8142 0.016 0.39 NO
65 NUPL1 NUPL1 NUPL1 8214 0.014 0.39 NO
66 NUPL2 NUPL2 NUPL2 8307 0.013 0.38 NO
67 AP2B1 AP2B1 AP2B1 8367 0.012 0.38 NO
68 AP1S1 AP1S1 AP1S1 8444 0.011 0.38 NO
69 RANBP2 RANBP2 RANBP2 8476 0.011 0.38 NO
70 NUP155 NUP155 NUP155 8477 0.011 0.38 NO
71 PSMB4 PSMB4 PSMB4 8551 0.0096 0.37 NO
72 PSMD4 PSMD4 PSMD4 8795 0.0059 0.36 NO
73 PSMB7 PSMB7 PSMB7 8860 0.0051 0.36 NO
74 SKP1 SKP1 SKP1 8868 0.005 0.36 NO
75 AP1B1 AP1B1 AP1B1 8875 0.0049 0.36 NO
76 RAE1 RAE1 RAE1 8925 0.0041 0.35 NO
77 NUP107 NUP107 NUP107 8965 0.0034 0.35 NO
78 PSMF1 PSMF1 PSMF1 9188 0.000016 0.34 NO
79 NUP205 NUP205 NUP205 9190 6.5e-07 0.34 NO
80 SEH1L SEH1L SEH1L 9624 -0.0065 0.31 NO
81 AP1S2 AP1S2 AP1S2 9761 -0.009 0.31 NO
82 PSMD1 PSMD1 PSMD1 9857 -0.01 0.3 NO
83 NUP133 NUP133 NUP133 9889 -0.011 0.3 NO
84 NUP62 NUP62 NUP62 9965 -0.012 0.3 NO
85 PSMD10 PSMD10 PSMD10 9992 -0.012 0.3 NO
86 RAN RAN RAN 10008 -0.013 0.3 NO
87 NUP54 NUP54 NUP54 10129 -0.015 0.29 NO
88 AP2A1 AP2A1 AP2A1 10195 -0.016 0.29 NO
89 PPIA PPIA PPIA 10312 -0.018 0.28 NO
90 NUP35 NUP35 NUP35 10404 -0.019 0.28 NO
91 RAC1 RAC1 RAC1 10537 -0.022 0.27 NO
92 PSIP1 PSIP1 PSIP1 10636 -0.023 0.27 NO
93 SLC25A5 SLC25A5 SLC25A5 10679 -0.024 0.27 NO
94 PAK2 PAK2 PAK2 10946 -0.028 0.25 NO
95 NUP93 NUP93 NUP93 11215 -0.033 0.24 NO
96 AAAS AAAS AAAS 11381 -0.036 0.23 NO
97 NUP43 NUP43 NUP43 11430 -0.037 0.23 NO
98 SLC25A4 SLC25A4 SLC25A4 11441 -0.037 0.23 NO
99 BANF1 BANF1 BANF1 11490 -0.038 0.23 NO
100 POM121 POM121 POM121 11999 -0.048 0.21 NO
101 RANGAP1 RANGAP1 RANGAP1 12000 -0.048 0.21 NO
102 PSMD9 PSMD9 PSMD9 12065 -0.049 0.21 NO
103 AP1M2 AP1M2 AP1M2 12070 -0.049 0.21 NO
104 PSMD6 PSMD6 PSMD6 12120 -0.05 0.21 NO
105 PSMD2 PSMD2 PSMD2 12180 -0.051 0.21 NO
106 NUP210 NUP210 NUP210 12273 -0.052 0.21 NO
107 BTRC BTRC BTRC 12316 -0.053 0.21 NO
108 RANBP1 RANBP1 RANBP1 12395 -0.055 0.21 NO
109 AP2M1 AP2M1 AP2M1 12431 -0.056 0.21 NO
110 NUP214 NUP214 NUP214 12657 -0.06 0.2 NO
111 UBA52 UBA52 UBA52 13271 -0.076 0.17 NO
112 NPM1 NPM1 NPM1 13428 -0.08 0.17 NO
113 FYN FYN FYN 13586 -0.085 0.16 NO
114 NUP153 NUP153 NUP153 13778 -0.091 0.16 NO
115 PACS1 PACS1 PACS1 13860 -0.094 0.16 NO
116 HMGA1 HMGA1 HMGA1 14040 -0.1 0.16 NO
117 RPS27A RPS27A RPS27A 14078 -0.1 0.16 NO
118 SLC25A6 SLC25A6 SLC25A6 14531 -0.12 0.14 NO
119 CCNT1 CCNT1 CCNT1 14792 -0.13 0.14 NO
120 PSMA8 PSMA8 PSMA8 15825 -0.21 0.088 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 PYRIMIDINE METABOLISM.

Figure S62.  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 AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM

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 CD8B CD8B CD8B 8 1.3 0.061 YES
2 LCK LCK LCK 13 1.2 0.12 YES
3 CCR5 CCR5 CCR5 29 1.2 0.17 YES
4 CD247 CD247 CD247 40 1.1 0.22 YES
5 PSMB9 PSMB9 PSMB9 61 1 0.27 YES
6 DOCK2 DOCK2 DOCK2 202 0.82 0.3 YES
7 HCK HCK HCK 424 0.63 0.32 YES
8 CD28 CD28 CD28 464 0.61 0.34 YES
9 ELMO1 ELMO1 ELMO1 618 0.52 0.36 YES
10 PSMB8 PSMB8 PSMB8 688 0.49 0.38 YES
11 B2M B2M B2M 962 0.39 0.38 YES
12 APOBEC3G APOBEC3G APOBEC3G 1018 0.37 0.4 YES
13 CD4 CD4 CD4 1032 0.37 0.41 YES
14 PSMB10 PSMB10 PSMB10 1411 0.3 0.4 YES
15 PSME2 PSME2 PSME2 1542 0.28 0.41 YES
16 HLA-A HLA-A HLA-A 1591 0.27 0.42 YES
17 CXCR4 CXCR4 CXCR4 1879 0.24 0.41 YES
18 PSMA3 PSMA3 PSMA3 2092 0.21 0.41 YES
19 TAF13 TAF13 TAF13 2264 0.2 0.41 YES
20 GTF2H2 GTF2H2 GTF2H2 2450 0.18 0.41 YES
21 TAF5 TAF5 TAF5 2495 0.18 0.42 YES
22 PSME1 PSME1 PSME1 2576 0.17 0.42 YES
23 TCEB1 TCEB1 TCEB1 2859 0.15 0.41 YES
24 GTF2H2B GTF2H2B GTF2H2B 2862 0.15 0.42 YES
25 XRCC4 XRCC4 XRCC4 2914 0.15 0.42 YES
26 PSMA4 PSMA4 PSMA4 2986 0.15 0.42 YES
27 PSME4 PSME4 PSME4 3021 0.14 0.43 YES
28 TPR TPR TPR 3028 0.14 0.43 YES
29 PSMA6 PSMA6 PSMA6 3050 0.14 0.44 YES
30 LIG4 LIG4 LIG4 3277 0.13 0.43 YES
31 PSMA5 PSMA5 PSMA5 3352 0.13 0.43 YES
32 PSMD14 PSMD14 PSMD14 3355 0.13 0.44 YES
33 POLR2K POLR2K POLR2K 3463 0.12 0.44 YES
34 NUP88 NUP88 NUP88 3507 0.12 0.44 YES
35 GTF2B GTF2B GTF2B 3578 0.12 0.44 YES
36 CCNT2 CCNT2 CCNT2 3813 0.11 0.44 YES
37 PSMB3 PSMB3 PSMB3 3832 0.11 0.44 YES
38 GTF2A1 GTF2A1 GTF2A1 3856 0.11 0.44 YES
39 PSMC1 PSMC1 PSMC1 3934 0.1 0.44 YES
40 CCNH CCNH CCNH 3952 0.1 0.45 YES
41 PSMB2 PSMB2 PSMB2 4038 0.1 0.45 YES
42 RBX1 RBX1 RBX1 4127 0.098 0.45 YES
43 PSMC6 PSMC6 PSMC6 4144 0.098 0.45 YES
44 PSMA7 PSMA7 PSMA7 4221 0.095 0.45 YES
45 PSMD12 PSMD12 PSMD12 4348 0.091 0.45 NO
46 PSMC2 PSMC2 PSMC2 4564 0.086 0.44 NO
47 TAF12 TAF12 TAF12 4655 0.083 0.44 NO
48 PSMD11 PSMD11 PSMD11 4678 0.082 0.44 NO
49 ATP6V1H ATP6V1H ATP6V1H 4743 0.081 0.44 NO
50 NUP85 NUP85 NUP85 4897 0.076 0.44 NO
51 TCEB3 TCEB3 TCEB3 4923 0.075 0.44 NO
52 PSMD7 PSMD7 PSMD7 4978 0.074 0.44 NO
53 PSMC4 PSMC4 PSMC4 5002 0.073 0.44 NO
54 XPO1 XPO1 XPO1 5065 0.072 0.44 NO
55 TCEA1 TCEA1 TCEA1 5114 0.071 0.44 NO
56 GTF2F2 GTF2F2 GTF2F2 5118 0.07 0.44 NO
57 NCBP1 NCBP1 NCBP1 5181 0.069 0.44 NO
58 PSMC3 PSMC3 PSMC3 5413 0.064 0.43 NO
59 PSMC5 PSMC5 PSMC5 5505 0.062 0.43 NO
60 XRCC5 XRCC5 XRCC5 5569 0.06 0.43 NO
61 PSMB6 PSMB6 PSMB6 5587 0.06 0.43 NO
62 VPS28 VPS28 VPS28 5633 0.059 0.43 NO
63 PSMA2 PSMA2 PSMA2 5653 0.059 0.43 NO
64 NUP50 NUP50 NUP50 5674 0.058 0.43 NO
65 POLR2D POLR2D POLR2D 6062 0.05 0.41 NO
66 TH1L TH1L TH1L 6119 0.049 0.41 NO
67 NMT1 NMT1 NMT1 6177 0.048 0.41 NO
68 TAF9 TAF9 TAF9 6360 0.045 0.4 NO
69 PSMB1 PSMB1 PSMB1 6534 0.042 0.4 NO
70 SUPT16H SUPT16H SUPT16H 6556 0.041 0.4 NO
71 CUL5 CUL5 CUL5 6621 0.04 0.39 NO
72 PSMA1 PSMA1 PSMA1 6784 0.038 0.39 NO
73 GTF2A2 GTF2A2 GTF2A2 6804 0.037 0.39 NO
74 PSMD8 PSMD8 PSMD8 6867 0.036 0.39 NO
75 NUP37 NUP37 NUP37 6895 0.036 0.39 NO
76 RCC1 RCC1 RCC1 6962 0.034 0.38 NO
77 PSMD5 PSMD5 PSMD5 6987 0.034 0.38 NO
78 AP1G1 AP1G1 AP1G1 7020 0.033 0.38 NO
79 RNGTT RNGTT RNGTT 7109 0.032 0.38 NO
80 PSMD13 PSMD13 PSMD13 7204 0.03 0.38 NO
81 KPNB1 KPNB1 KPNB1 7254 0.029 0.37 NO
82 KPNA1 KPNA1 KPNA1 7278 0.029 0.37 NO
83 POLR2B POLR2B POLR2B 7344 0.028 0.37 NO
84 PSMB5 PSMB5 PSMB5 7390 0.027 0.37 NO
85 PSMD3 PSMD3 PSMD3 7400 0.027 0.37 NO
86 TCEB2 TCEB2 TCEB2 7580 0.024 0.36 NO
87 ARF1 ARF1 ARF1 7589 0.024 0.36 NO
88 AP2A2 AP2A2 AP2A2 7926 0.019 0.34 NO
89 POLR2A POLR2A POLR2A 7963 0.018 0.34 NO
90 AP2S1 AP2S1 AP2S1 8007 0.018 0.34 NO
91 NUP188 NUP188 NUP188 8013 0.018 0.34 NO
92 AP1M1 AP1M1 AP1M1 8074 0.017 0.34 NO
93 CDK9 CDK9 CDK9 8142 0.016 0.34 NO
94 NUPL1 NUPL1 NUPL1 8214 0.014 0.33 NO
95 NUPL2 NUPL2 NUPL2 8307 0.013 0.33 NO
96 RNMT RNMT RNMT 8314 0.013 0.33 NO
97 AP2B1 AP2B1 AP2B1 8367 0.012 0.32 NO
98 POLR2E POLR2E POLR2E 8403 0.012 0.32 NO
99 GTF2E2 GTF2E2 GTF2E2 8425 0.011 0.32 NO
100 AP1S1 AP1S1 AP1S1 8444 0.011 0.32 NO
101 RANBP2 RANBP2 RANBP2 8476 0.011 0.32 NO
102 NUP155 NUP155 NUP155 8477 0.011 0.32 NO
103 PSMB4 PSMB4 PSMB4 8551 0.0096 0.32 NO
104 TAF10 TAF10 TAF10 8612 0.0086 0.32 NO
105 POLR2C POLR2C POLR2C 8740 0.0068 0.31 NO
106 POLR2G POLR2G POLR2G 8762 0.0065 0.31 NO
107 PSMD4 PSMD4 PSMD4 8795 0.0059 0.3 NO
108 PSMB7 PSMB7 PSMB7 8860 0.0051 0.3 NO
109 SKP1 SKP1 SKP1 8868 0.005 0.3 NO
110 AP1B1 AP1B1 AP1B1 8875 0.0049 0.3 NO
111 GTF2H1 GTF2H1 GTF2H1 8889 0.0047 0.3 NO
112 RAE1 RAE1 RAE1 8925 0.0041 0.3 NO
113 ELL ELL ELL 8932 0.004 0.3 NO
114 NUP107 NUP107 NUP107 8965 0.0034 0.3 NO
115 FEN1 FEN1 FEN1 9045 0.0022 0.29 NO
116 POLR2J POLR2J POLR2J 9104 0.0013 0.29 NO
117 PSMF1 PSMF1 PSMF1 9188 0.000016 0.28 NO
118 NUP205 NUP205 NUP205 9190 6.5e-07 0.28 NO
119 POLR2I POLR2I POLR2I 9221 -0.00036 0.28 NO
120 GTF2H3 GTF2H3 GTF2H3 9331 -0.0019 0.28 NO
121 SEH1L SEH1L SEH1L 9624 -0.0065 0.26 NO
122 ERCC3 ERCC3 ERCC3 9632 -0.0066 0.26 NO
123 XRCC6 XRCC6 XRCC6 9697 -0.0078 0.26 NO
124 AP1S2 AP1S2 AP1S2 9761 -0.009 0.25 NO
125 CDK7 CDK7 CDK7 9788 -0.0094 0.25 NO
126 PSMD1 PSMD1 PSMD1 9857 -0.01 0.25 NO
127 NUP133 NUP133 NUP133 9889 -0.011 0.25 NO
128 NUP62 NUP62 NUP62 9965 -0.012 0.24 NO
129 PSMD10 PSMD10 PSMD10 9992 -0.012 0.24 NO
130 RAN RAN RAN 10008 -0.013 0.24 NO
131 NUP54 NUP54 NUP54 10129 -0.015 0.24 NO
132 POLR2F POLR2F POLR2F 10166 -0.016 0.23 NO
133 AP2A1 AP2A1 AP2A1 10195 -0.016 0.23 NO
134 PPIA PPIA PPIA 10312 -0.018 0.23 NO
135 TSG101 TSG101 TSG101 10316 -0.018 0.23 NO
136 CTDP1 CTDP1 CTDP1 10319 -0.018 0.23 NO
137 NUP35 NUP35 NUP35 10404 -0.019 0.22 NO
138 LIG1 LIG1 LIG1 10430 -0.02 0.22 NO
139 MNAT1 MNAT1 MNAT1 10521 -0.021 0.22 NO
140 RAC1 RAC1 RAC1 10537 -0.022 0.22 NO
141 PSIP1 PSIP1 PSIP1 10636 -0.023 0.22 NO
142 SLC25A5 SLC25A5 SLC25A5 10679 -0.024 0.21 NO
143 POLR2L POLR2L POLR2L 10811 -0.026 0.21 NO
144 TAF1 TAF1 TAF1 10819 -0.026 0.21 NO
145 PAK2 PAK2 PAK2 10946 -0.028 0.2 NO
146 VPS37A VPS37A VPS37A 10991 -0.029 0.2 NO
147 TAF4B TAF4B TAF4B 10997 -0.029 0.2 NO
148 SUPT4H1 SUPT4H1 SUPT4H1 11205 -0.033 0.19 NO
149 NUP93 NUP93 NUP93 11215 -0.033 0.19 NO
150 AAAS AAAS AAAS 11381 -0.036 0.18 NO
151 NUP43 NUP43 NUP43 11430 -0.037 0.18 NO
152 SLC25A4 SLC25A4 SLC25A4 11441 -0.037 0.18 NO
153 BANF1 BANF1 BANF1 11490 -0.038 0.18 NO
154 POM121 POM121 POM121 11999 -0.048 0.16 NO
155 RANGAP1 RANGAP1 RANGAP1 12000 -0.048 0.16 NO
156 TAF6 TAF6 TAF6 12029 -0.048 0.16 NO
157 PSMD9 PSMD9 PSMD9 12065 -0.049 0.16 NO
158 AP1M2 AP1M2 AP1M2 12070 -0.049 0.16 NO
159 NCBP2 NCBP2 NCBP2 12103 -0.049 0.16 NO
160 PSMD6 PSMD6 PSMD6 12120 -0.05 0.16 NO
161 PSMD2 PSMD2 PSMD2 12180 -0.051 0.16 NO
162 TAF4 TAF4 TAF4 12265 -0.052 0.16 NO
163 NUP210 NUP210 NUP210 12273 -0.052 0.16 NO
164 BTRC BTRC BTRC 12316 -0.053 0.16 NO
165 RDBP RDBP RDBP 12391 -0.055 0.16 NO
166 RANBP1 RANBP1 RANBP1 12395 -0.055 0.16 NO
167 AP2M1 AP2M1 AP2M1 12431 -0.056 0.16 NO
168 SSRP1 SSRP1 SSRP1 12478 -0.057 0.16 NO
169 NUP214 NUP214 NUP214 12657 -0.06 0.16 NO
170 TAF11 TAF11 TAF11 12870 -0.066 0.15 NO
171 SUPT5H SUPT5H SUPT5H 12916 -0.067 0.15 NO
172 WHSC2 WHSC2 WHSC2 12931 -0.068 0.15 NO
173 TBP TBP TBP 13114 -0.072 0.14 NO
174 VPS37C VPS37C VPS37C 13146 -0.073 0.14 NO
175 COBRA1 COBRA1 COBRA1 13241 -0.076 0.14 NO
176 UBA52 UBA52 UBA52 13271 -0.076 0.14 NO
177 GTF2F1 GTF2F1 GTF2F1 13362 -0.079 0.14 NO
178 NPM1 NPM1 NPM1 13428 -0.08 0.14 NO
179 GTF2E1 GTF2E1 GTF2E1 13533 -0.083 0.14 NO
180 FYN FYN FYN 13586 -0.085 0.14 NO
181 NUP153 NUP153 NUP153 13778 -0.091 0.13 NO
182 PACS1 PACS1 PACS1 13860 -0.094 0.13 NO
183 VPS37B VPS37B VPS37B 13968 -0.098 0.13 NO
184 HMGA1 HMGA1 HMGA1 14040 -0.1 0.13 NO
185 POLR2H POLR2H POLR2H 14053 -0.1 0.14 NO
186 RPS27A RPS27A RPS27A 14078 -0.1 0.14 NO
187 ERCC2 ERCC2 ERCC2 14402 -0.12 0.13 NO
188 SLC25A6 SLC25A6 SLC25A6 14531 -0.12 0.12 NO
189 NMT2 NMT2 NMT2 14580 -0.12 0.13 NO
190 CCNT1 CCNT1 CCNT1 14792 -0.13 0.12 NO
191 GTF2H4 GTF2H4 GTF2H4 15405 -0.17 0.094 NO
192 VPS37D VPS37D VPS37D 15687 -0.2 0.087 NO
193 PSMA8 PSMA8 PSMA8 15825 -0.21 0.089 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: KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM.

Figure S64.  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 INOSITOL PHOSPHATE METABOLISM

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 CXCR3 CXCR3 CXCR3 4 1.3 0.14 YES
2 CXCL9 CXCL9 CXCL9 20 1.2 0.26 YES
3 CXCL13 CXCL13 CXCL13 48 1.1 0.37 YES
4 ITGAL ITGAL ITGAL 59 1.1 0.48 YES
5 CXCL10 CXCL10 CXCL10 72 1 0.58 YES
6 CXCL11 CXCL11 CXCL11 92 0.98 0.68 YES
7 ITGB2 ITGB2 ITGB2 844 0.43 0.68 YES
8 PIK3R3 PIK3R3 PIK3R3 1372 0.3 0.69 YES
9 MAP2K6 MAP2K6 MAP2K6 1547 0.28 0.7 YES
10 GNG2 GNG2 GNG2 2144 0.21 0.69 NO
11 GNAZ GNAZ GNAZ 3528 0.12 0.62 NO
12 NRAS NRAS NRAS 4011 0.1 0.61 NO
13 RICTOR RICTOR RICTOR 4249 0.094 0.6 NO
14 MTOR MTOR MTOR 5420 0.064 0.54 NO
15 GNAI3 GNAI3 GNAI3 5664 0.059 0.53 NO
16 MAPK1 MAPK1 MAPK1 6004 0.052 0.52 NO
17 MAP2K3 MAP2K3 MAP2K3 6042 0.051 0.52 NO
18 PIK3CA PIK3CA PIK3CA 6197 0.048 0.52 NO
19 KRAS KRAS KRAS 6392 0.045 0.51 NO
20 GNB1 GNB1 GNB1 7384 0.027 0.46 NO
21 PIK3R1 PIK3R1 PIK3R1 7416 0.027 0.46 NO
22 HRAS HRAS HRAS 7479 0.026 0.46 NO
23 PIK3CD PIK3CD PIK3CD 7481 0.026 0.46 NO
24 PIK3CB PIK3CB PIK3CB 8010 0.018 0.43 NO
25 MAP2K1 MAP2K1 MAP2K1 8364 0.012 0.41 NO
26 MAPK14 MAPK14 MAPK14 8424 0.011 0.41 NO
27 SRC SRC SRC 8538 0.0098 0.4 NO
28 ARRB1 ARRB1 ARRB1 8599 0.0088 0.4 NO
29 MAPK3 MAPK3 MAPK3 8836 0.0053 0.39 NO
30 MAPK11 MAPK11 MAPK11 9144 0.00055 0.37 NO
31 MLST8 MLST8 MLST8 9467 -0.0042 0.35 NO
32 GNAI2 GNAI2 GNAI2 9478 -0.0044 0.35 NO
33 AKT1 AKT1 AKT1 10764 -0.025 0.28 NO
34 MAP2K2 MAP2K2 MAP2K2 11001 -0.029 0.27 NO
35 MAPKAP1 MAPKAP1 MAPKAP1 11730 -0.042 0.23 NO
36 PIK3R2 PIK3R2 PIK3R2 12192 -0.051 0.21 NO
37 PDPK1 PDPK1 PDPK1 13045 -0.07 0.17 NO
38 DNM1 DNM1 DNM1 13067 -0.071 0.18 NO
39 RAF1 RAF1 RAF1 14416 -0.12 0.11 NO
40 GNAO1 GNAO1 GNAO1 15529 -0.18 0.064 NO
41 GNAI1 GNAI1 GNAI1 16943 -0.4 0.023 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: KEGG INOSITOL PHOSPHATE METABOLISM.

Figure S66.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG INOSITOL PHOSPHATE 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 DRUG METABOLISM OTHER ENZYMES

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 PSMB9 PSMB9 PSMB9 61 1 0.064 YES
2 VAV1 VAV1 VAV1 151 0.87 0.11 YES
3 BLNK BLNK BLNK 254 0.78 0.16 YES
4 RASGRP1 RASGRP1 RASGRP1 314 0.72 0.2 YES
5 CD79A CD79A CD79A 592 0.54 0.22 YES
6 CD19 CD19 CD19 599 0.53 0.25 YES
7 PSMB8 PSMB8 PSMB8 688 0.49 0.28 YES
8 CARD11 CARD11 CARD11 708 0.48 0.31 YES
9 PIK3AP1 PIK3AP1 PIK3AP1 720 0.48 0.34 YES
10 BTK BTK BTK 740 0.47 0.37 YES
11 ITPR2 ITPR2 ITPR2 1158 0.34 0.36 YES
12 CD79B CD79B CD79B 1205 0.33 0.38 YES
13 SYK SYK SYK 1272 0.32 0.4 YES
14 PSMB10 PSMB10 PSMB10 1411 0.3 0.41 YES
15 PRKCB PRKCB PRKCB 1499 0.29 0.42 YES
16 PSME2 PSME2 PSME2 1542 0.28 0.44 YES
17 PLCG2 PLCG2 PLCG2 1739 0.25 0.44 YES
18 CDKN1A CDKN1A CDKN1A 1797 0.24 0.46 YES
19 LYN LYN LYN 1922 0.23 0.46 YES
20 PSMA3 PSMA3 PSMA3 2092 0.21 0.47 YES
21 PSME1 PSME1 PSME1 2576 0.17 0.45 YES
22 BCL10 BCL10 BCL10 2671 0.17 0.46 YES
23 NFKBIA NFKBIA NFKBIA 2752 0.16 0.46 YES
24 MDM2 MDM2 MDM2 2865 0.15 0.46 YES
25 PSMA4 PSMA4 PSMA4 2986 0.15 0.47 YES
26 PSME4 PSME4 PSME4 3021 0.14 0.48 YES
27 BLK BLK BLK 3045 0.14 0.48 YES
28 PSMA6 PSMA6 PSMA6 3050 0.14 0.49 YES
29 SH3KBP1 SH3KBP1 SH3KBP1 3203 0.14 0.49 YES
30 PSMA5 PSMA5 PSMA5 3352 0.13 0.49 YES
31 PSMD14 PSMD14 PSMD14 3355 0.13 0.5 YES
32 PSMB3 PSMB3 PSMB3 3832 0.11 0.48 YES
33 ORAI1 ORAI1 ORAI1 3855 0.11 0.48 YES
34 PSMC1 PSMC1 PSMC1 3934 0.1 0.49 YES
35 NRAS NRAS NRAS 4011 0.1 0.49 YES
36 PSMB2 PSMB2 PSMB2 4038 0.1 0.49 YES
37 PSMC6 PSMC6 PSMC6 4144 0.098 0.49 YES
38 PSMA7 PSMA7 PSMA7 4221 0.095 0.5 YES
39 RICTOR RICTOR RICTOR 4249 0.094 0.5 YES
40 PSMD12 PSMD12 PSMD12 4348 0.091 0.5 YES
41 PSMC2 PSMC2 PSMC2 4564 0.086 0.49 NO
42 CREB1 CREB1 CREB1 4598 0.085 0.5 NO
43 PSMD11 PSMD11 PSMD11 4678 0.082 0.5 NO
44 SHC1 SHC1 SHC1 4802 0.079 0.5 NO
45 PSMD7 PSMD7 PSMD7 4978 0.074 0.49 NO
46 PSMC4 PSMC4 PSMC4 5002 0.073 0.49 NO
47 CALM1 CALM1 CALM1 5047 0.072 0.5 NO
48 CUL1 CUL1 CUL1 5121 0.07 0.5 NO
49 CHUK CHUK CHUK 5335 0.066 0.49 NO
50 PSMC3 PSMC3 PSMC3 5413 0.064 0.49 NO
51 MTOR MTOR MTOR 5420 0.064 0.49 NO
52 SOS1 SOS1 SOS1 5463 0.063 0.49 NO
53 PSMC5 PSMC5 PSMC5 5505 0.062 0.49 NO
54 PSMB6 PSMB6 PSMB6 5587 0.06 0.49 NO
55 PSMA2 PSMA2 PSMA2 5653 0.059 0.49 NO
56 CALM2 CALM2 CALM2 5768 0.056 0.49 NO
57 KRAS KRAS KRAS 6392 0.045 0.46 NO
58 NCK1 NCK1 NCK1 6495 0.043 0.45 NO
59 PSMB1 PSMB1 PSMB1 6534 0.042 0.45 NO
60 NFKBIE NFKBIE NFKBIE 6591 0.041 0.45 NO
61 NFKBIB NFKBIB NFKBIB 6663 0.04 0.45 NO
62 PSMA1 PSMA1 PSMA1 6784 0.038 0.45 NO
63 ITPR3 ITPR3 ITPR3 6820 0.037 0.45 NO
64 PSMD8 PSMD8 PSMD8 6867 0.036 0.45 NO
65 PSMD5 PSMD5 PSMD5 6987 0.034 0.44 NO
66 GRB2 GRB2 GRB2 7036 0.033 0.44 NO
67 PSMD13 PSMD13 PSMD13 7204 0.03 0.43 NO
68 PSMB5 PSMB5 PSMB5 7390 0.027 0.42 NO
69 PSMD3 PSMD3 PSMD3 7400 0.027 0.43 NO
70 PIK3R1 PIK3R1 PIK3R1 7416 0.027 0.43 NO
71 HRAS HRAS HRAS 7479 0.026 0.42 NO
72 PIK3CD PIK3CD PIK3CD 7481 0.026 0.43 NO
73 PTEN PTEN PTEN 7504 0.025 0.43 NO
74 CASP9 CASP9 CASP9 7861 0.02 0.41 NO
75 BAD BAD BAD 8127 0.016 0.39 NO
76 PLCG1 PLCG1 PLCG1 8297 0.013 0.38 NO
77 STIM1 STIM1 STIM1 8317 0.013 0.38 NO
78 PSMB4 PSMB4 PSMB4 8551 0.0096 0.37 NO
79 RASGRP3 RASGRP3 RASGRP3 8704 0.0072 0.36 NO
80 PSMD4 PSMD4 PSMD4 8795 0.0059 0.36 NO
81 CDKN1B CDKN1B CDKN1B 8827 0.0055 0.36 NO
82 PSMB7 PSMB7 PSMB7 8860 0.0051 0.36 NO
83 SKP1 SKP1 SKP1 8868 0.005 0.36 NO
84 PSMF1 PSMF1 PSMF1 9188 0.000016 0.34 NO
85 MAP3K7 MAP3K7 MAP3K7 9223 -0.00039 0.33 NO
86 MLST8 MLST8 MLST8 9467 -0.0042 0.32 NO
87 CALM3 CALM3 CALM3 9719 -0.0082 0.31 NO
88 FOXO4 FOXO4 FOXO4 9767 -0.0091 0.3 NO
89 PSMD1 PSMD1 PSMD1 9857 -0.01 0.3 NO
90 PSMD10 PSMD10 PSMD10 9992 -0.012 0.29 NO
91 AKT1S1 AKT1S1 AKT1S1 9995 -0.013 0.29 NO
92 GSK3A GSK3A GSK3A 10233 -0.017 0.28 NO
93 IKBKB IKBKB IKBKB 10411 -0.02 0.27 NO
94 IKBKG IKBKG IKBKG 10597 -0.023 0.26 NO
95 AKT1 AKT1 AKT1 10764 -0.025 0.25 NO
96 TRIB3 TRIB3 TRIB3 10856 -0.027 0.25 NO
97 FBXW11 FBXW11 FBXW11 10975 -0.029 0.25 NO
98 AKT3 AKT3 AKT3 10986 -0.029 0.25 NO
99 RPS6KB2 RPS6KB2 RPS6KB2 11013 -0.029 0.25 NO
100 CBL CBL CBL 11664 -0.041 0.21 NO
101 CBLB CBLB CBLB 11709 -0.042 0.21 NO
102 MAPKAP1 MAPKAP1 MAPKAP1 11730 -0.042 0.21 NO
103 PHLPP1 PHLPP1 PHLPP1 11841 -0.044 0.21 NO
104 MALT1 MALT1 MALT1 12037 -0.048 0.2 NO
105 PSMD9 PSMD9 PSMD9 12065 -0.049 0.2 NO
106 PSMD6 PSMD6 PSMD6 12120 -0.05 0.2 NO
107 PSMD2 PSMD2 PSMD2 12180 -0.051 0.2 NO
108 BTRC BTRC BTRC 12316 -0.053 0.2 NO
109 AKT2 AKT2 AKT2 12618 -0.06 0.18 NO
110 TSC2 TSC2 TSC2 12803 -0.064 0.18 NO
111 PDPK1 PDPK1 PDPK1 13045 -0.07 0.17 NO
112 THEM4 THEM4 THEM4 13069 -0.071 0.17 NO
113 RELA RELA RELA 13088 -0.071 0.18 NO
114 UBA52 UBA52 UBA52 13271 -0.076 0.17 NO
115 FYN FYN FYN 13586 -0.085 0.16 NO
116 RPS27A RPS27A RPS27A 14078 -0.1 0.14 NO
117 NR4A1 NR4A1 NR4A1 14139 -0.1 0.14 NO
118 FOXO1 FOXO1 FOXO1 15106 -0.15 0.092 NO
119 FOXO3 FOXO3 FOXO3 15484 -0.18 0.082 NO
120 REL REL REL 15764 -0.2 0.078 NO
121 PSMA8 PSMA8 PSMA8 15825 -0.21 0.088 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: KEGG DRUG METABOLISM OTHER ENZYMES.

Figure S68.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG DRUG METABOLISM OTHER ENZYMES, 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 PROTEASOME

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 LCK LCK LCK 13 1.2 0.12 YES
2 GRAP2 GRAP2 GRAP2 28 1.2 0.23 YES
3 VAV1 VAV1 VAV1 151 0.87 0.3 YES
4 PTPN6 PTPN6 PTPN6 318 0.72 0.36 YES
5 STAT1 STAT1 STAT1 647 0.51 0.39 YES
6 MMP9 MMP9 MMP9 788 0.45 0.43 YES
7 PIK3R3 PIK3R3 PIK3R3 1372 0.3 0.42 YES
8 KIT KIT KIT 1515 0.28 0.44 YES
9 JAK2 JAK2 JAK2 1757 0.25 0.45 YES
10 GRAP GRAP GRAP 1787 0.25 0.47 YES
11 CDKN1A CDKN1A CDKN1A 1797 0.24 0.5 YES
12 LYN LYN LYN 1922 0.23 0.51 YES
13 SOCS1 SOCS1 SOCS1 1957 0.23 0.53 YES
14 SH2B3 SH2B3 SH2B3 2538 0.18 0.51 NO
15 PRKCA PRKCA PRKCA 2621 0.17 0.53 NO
16 MDM2 MDM2 MDM2 2865 0.15 0.53 NO
17 SH2B2 SH2B2 SH2B2 3233 0.13 0.52 NO
18 STAT3 STAT3 STAT3 3622 0.12 0.51 NO
19 NRAS NRAS NRAS 4011 0.1 0.49 NO
20 RICTOR RICTOR RICTOR 4249 0.094 0.49 NO
21 CREB1 CREB1 CREB1 4598 0.085 0.48 NO
22 CHUK CHUK CHUK 5335 0.066 0.44 NO
23 MTOR MTOR MTOR 5420 0.064 0.44 NO
24 SOS1 SOS1 SOS1 5463 0.063 0.44 NO
25 YWHAB YWHAB YWHAB 5728 0.057 0.44 NO
26 SOCS6 SOCS6 SOCS6 5814 0.056 0.44 NO
27 KITLG KITLG KITLG 5877 0.054 0.44 NO
28 MAPK1 MAPK1 MAPK1 6004 0.052 0.44 NO
29 PIK3CA PIK3CA PIK3CA 6197 0.048 0.43 NO
30 FES FES FES 6350 0.045 0.42 NO
31 KRAS KRAS KRAS 6392 0.045 0.43 NO
32 GRB2 GRB2 GRB2 7036 0.033 0.39 NO
33 PIK3R1 PIK3R1 PIK3R1 7416 0.027 0.37 NO
34 HRAS HRAS HRAS 7479 0.026 0.37 NO
35 PTEN PTEN PTEN 7504 0.025 0.37 NO
36 CDK1 CDK1 CDK1 7777 0.021 0.36 NO
37 CASP9 CASP9 CASP9 7861 0.02 0.36 NO
38 GRB10 GRB10 GRB10 7918 0.019 0.35 NO
39 STAT5B STAT5B STAT5B 7974 0.018 0.35 NO
40 BAD BAD BAD 8127 0.016 0.35 NO
41 MAP2K1 MAP2K1 MAP2K1 8364 0.012 0.33 NO
42 SRC SRC SRC 8538 0.0098 0.32 NO
43 CDKN1B CDKN1B CDKN1B 8827 0.0055 0.31 NO
44 MAPK3 MAPK3 MAPK3 8836 0.0053 0.31 NO
45 MLST8 MLST8 MLST8 9467 -0.0042 0.27 NO
46 FOXO4 FOXO4 FOXO4 9767 -0.0091 0.26 NO
47 TEC TEC TEC 9806 -0.0096 0.25 NO
48 AKT1S1 AKT1S1 AKT1S1 9995 -0.013 0.24 NO
49 GSK3A GSK3A GSK3A 10233 -0.017 0.23 NO
50 RAC1 RAC1 RAC1 10537 -0.022 0.22 NO
51 AKT1 AKT1 AKT1 10764 -0.025 0.21 NO
52 TRIB3 TRIB3 TRIB3 10856 -0.027 0.2 NO
53 AKT3 AKT3 AKT3 10986 -0.029 0.2 NO
54 MAP2K2 MAP2K2 MAP2K2 11001 -0.029 0.2 NO
55 RPS6KB2 RPS6KB2 RPS6KB2 11013 -0.029 0.2 NO
56 STAT5A STAT5A STAT5A 11033 -0.03 0.2 NO
57 GAB2 GAB2 GAB2 11073 -0.031 0.2 NO
58 CBL CBL CBL 11664 -0.041 0.18 NO
59 MAPKAP1 MAPKAP1 MAPKAP1 11730 -0.042 0.18 NO
60 PHLPP1 PHLPP1 PHLPP1 11841 -0.044 0.17 NO
61 PIK3R2 PIK3R2 PIK3R2 12192 -0.051 0.16 NO
62 AKT2 AKT2 AKT2 12618 -0.06 0.14 NO
63 TSC2 TSC2 TSC2 12803 -0.064 0.13 NO
64 PDPK1 PDPK1 PDPK1 13045 -0.07 0.13 NO
65 THEM4 THEM4 THEM4 13069 -0.071 0.13 NO
66 YES1 YES1 YES1 13070 -0.071 0.14 NO
67 FER FER FER 13298 -0.077 0.13 NO
68 FYN FYN FYN 13586 -0.085 0.12 NO
69 NR4A1 NR4A1 NR4A1 14139 -0.1 0.1 NO
70 CHEK1 CHEK1 CHEK1 14225 -0.11 0.11 NO
71 RAF1 RAF1 RAF1 14416 -0.12 0.11 NO
72 FOXO1 FOXO1 FOXO1 15106 -0.15 0.083 NO
73 FOXO3 FOXO3 FOXO3 15484 -0.18 0.078 NO
74 GRB7 GRB7 GRB7 16554 -0.31 0.046 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: KEGG PROTEASOME.

Figure S70.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PROTEASOME, 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 CYTOKINE CYTOKINE RECEPTOR INTERACTION

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 LCK LCK LCK 13 1.2 0.02 YES
2 GBP5 GBP5 GBP5 41 1.1 0.036 YES
3 IL2RG IL2RG IL2RG 42 1.1 0.054 YES
4 GBP1 GBP1 GBP1 51 1.1 0.072 YES
5 IL2RB IL2RB IL2RB 93 0.98 0.085 YES
6 GBP4 GBP4 GBP4 94 0.97 0.1 YES
7 IL1R2 IL1R2 IL1R2 105 0.94 0.12 YES
8 IRF1 IRF1 IRF1 118 0.91 0.13 YES
9 IRF8 IRF8 IRF8 125 0.9 0.14 YES
10 FCGR1B FCGR1B FCGR1B 127 0.9 0.16 YES
11 FCGR1A FCGR1A FCGR1A 128 0.9 0.17 YES
12 IFI27 IFI27 IFI27 130 0.9 0.19 YES
13 CIITA CIITA CIITA 132 0.9 0.2 YES
14 GBP2 GBP2 GBP2 138 0.89 0.22 YES
15 VAV1 VAV1 VAV1 151 0.87 0.23 YES
16 XAF1 XAF1 XAF1 188 0.83 0.24 YES
17 IFNG IFNG IFNG 216 0.8 0.26 YES
18 NOD2 NOD2 NOD2 234 0.79 0.27 YES
19 BLNK BLNK BLNK 254 0.78 0.28 YES
20 CASP1 CASP1 CASP1 258 0.77 0.29 YES
21 HLA-DRB5 HLA-DRB5 HLA-DRB5 266 0.77 0.3 YES
22 IL18 IL18 IL18 269 0.76 0.32 YES
23 HLA-DQA1 HLA-DQA1 HLA-DQA1 290 0.75 0.33 YES
24 CSF2RB CSF2RB CSF2RB 292 0.74 0.34 YES
25 ISG20 ISG20 ISG20 306 0.73 0.35 YES
26 PTPN6 PTPN6 PTPN6 318 0.72 0.36 YES
27 OASL OASL OASL 324 0.72 0.37 YES
28 IL7R IL7R IL7R 325 0.72 0.38 YES
29 GBP7 GBP7 GBP7 332 0.71 0.4 YES
30 HLA-F HLA-F HLA-F 340 0.7 0.41 YES
31 GBP6 GBP6 GBP6 378 0.67 0.42 YES
32 MX2 MX2 MX2 394 0.66 0.43 YES
33 HLA-DQA2 HLA-DQA2 HLA-DQA2 404 0.65 0.44 YES
34 HCK HCK HCK 424 0.63 0.44 YES
35 IL2RA IL2RA IL2RA 430 0.63 0.46 YES
36 ISG15 ISG15 ISG15 463 0.61 0.46 YES
37 VCAM1 VCAM1 VCAM1 470 0.6 0.47 YES
38 IL1B IL1B IL1B 473 0.6 0.48 YES
39 HLA-DRB1 HLA-DRB1 HLA-DRB1 484 0.6 0.49 YES
40 PTAFR PTAFR PTAFR 514 0.57 0.5 YES
41 UBE2L6 UBE2L6 UBE2L6 554 0.55 0.51 YES
42 IFITM1 IFITM1 IFITM1 567 0.55 0.52 YES
43 CSF2RA CSF2RA CSF2RA 597 0.53 0.52 YES
44 STAT1 STAT1 STAT1 647 0.51 0.53 YES
45 HLA-DPA1 HLA-DPA1 HLA-DPA1 659 0.5 0.54 YES
46 HLA-B HLA-B HLA-B 660 0.5 0.54 YES
47 IL7 IL7 IL7 661 0.5 0.55 YES
48 PSMB8 PSMB8 PSMB8 688 0.49 0.56 YES
49 IL3RA IL3RA IL3RA 699 0.48 0.56 YES
50 OAS2 OAS2 OAS2 722 0.48 0.57 YES
51 OAS1 OAS1 OAS1 736 0.47 0.58 YES
52 IFI6 IFI6 IFI6 771 0.46 0.58 YES
53 IRF5 IRF5 IRF5 818 0.44 0.59 YES
54 HLA-DPB1 HLA-DPB1 HLA-DPB1 832 0.44 0.6 YES
55 JAK3 JAK3 JAK3 840 0.43 0.6 YES
56 IL1RN IL1RN IL1RN 858 0.42 0.61 YES
57 MAP3K8 MAP3K8 MAP3K8 892 0.41 0.61 YES
58 IFIT2 IFIT2 IFIT2 959 0.39 0.62 YES
59 B2M B2M B2M 962 0.39 0.62 YES
60 SOCS2 SOCS2 SOCS2 992 0.38 0.63 YES
61 UBA7 UBA7 UBA7 994 0.38 0.63 YES
62 PELI1 PELI1 PELI1 1015 0.37 0.64 YES
63 IRAK3 IRAK3 IRAK3 1031 0.37 0.64 YES
64 DDX58 DDX58 DDX58 1041 0.37 0.65 YES
65 IFIT1 IFIT1 IFIT1 1054 0.36 0.65 YES
66 HLA-C HLA-C HLA-C 1071 0.36 0.66 YES
67 HLA-G HLA-G HLA-G 1109 0.35 0.66 YES
68 IL1R1 IL1R1 IL1R1 1119 0.35 0.67 YES
69 MX1 MX1 MX1 1181 0.34 0.67 YES
70 SYK SYK SYK 1272 0.32 0.67 YES
71 IRF9 IRF9 IRF9 1284 0.32 0.67 YES
72 IRAK2 IRAK2 IRAK2 1318 0.32 0.68 YES
73 IL6 IL6 IL6 1332 0.31 0.68 YES
74 IFIT3 IFIT3 IFIT3 1371 0.31 0.68 YES
75 PIK3R3 PIK3R3 PIK3R3 1372 0.3 0.69 YES
76 IRF7 IRF7 IRF7 1446 0.29 0.69 YES
77 IFI35 IFI35 IFI35 1457 0.29 0.69 YES
78 IFNAR2 IFNAR2 IFNAR2 1478 0.29 0.7 YES
79 MAP2K6 MAP2K6 MAP2K6 1547 0.28 0.7 YES
80 HLA-A HLA-A HLA-A 1591 0.27 0.7 YES
81 CAMK2A CAMK2A CAMK2A 1632 0.27 0.7 YES
82 PRLR PRLR PRLR 1646 0.26 0.7 YES
83 JAK2 JAK2 JAK2 1757 0.25 0.7 NO
84 LYN LYN LYN 1922 0.23 0.7 NO
85 SOCS1 SOCS1 SOCS1 1957 0.23 0.7 NO
86 MT2A MT2A MT2A 2081 0.21 0.7 NO
87 SOCS3 SOCS3 SOCS3 2083 0.21 0.7 NO
88 USP18 USP18 USP18 2173 0.2 0.7 NO
89 HGF HGF HGF 2265 0.2 0.7 NO
90 IFITM3 IFITM3 IFITM3 2594 0.17 0.68 NO
91 EIF2AK2 EIF2AK2 EIF2AK2 2689 0.16 0.68 NO
92 SP100 SP100 SP100 2785 0.16 0.67 NO
93 TPR TPR TPR 3028 0.14 0.66 NO
94 OAS3 OAS3 OAS3 3389 0.13 0.64 NO
95 NEDD4 NEDD4 NEDD4 3425 0.13 0.64 NO
96 NUP88 NUP88 NUP88 3507 0.12 0.64 NO
97 IFNGR1 IFNGR1 IFNGR1 3611 0.12 0.64 NO
98 STAT3 STAT3 STAT3 3622 0.12 0.64 NO
99 ICAM1 ICAM1 ICAM1 3735 0.11 0.63 NO
100 EIF4G3 EIF4G3 EIF4G3 3799 0.11 0.63 NO
101 KPNA5 KPNA5 KPNA5 3842 0.11 0.63 NO
102 IFNAR1 IFNAR1 IFNAR1 3961 0.1 0.62 NO
103 NRAS NRAS NRAS 4011 0.1 0.62 NO
104 PTPN1 PTPN1 PTPN1 4109 0.099 0.62 NO
105 IFITM2 IFITM2 IFITM2 4113 0.099 0.62 NO
106 PIAS1 PIAS1 PIAS1 4125 0.098 0.62 NO
107 RBX1 RBX1 RBX1 4127 0.098 0.62 NO
108 HERC5 HERC5 HERC5 4329 0.092 0.61 NO
109 PTK2B PTK2B PTK2B 4507 0.087 0.6 NO
110 IRAK4 IRAK4 IRAK4 4581 0.085 0.6 NO
111 ARIH1 ARIH1 ARIH1 4735 0.081 0.59 NO
112 SHC1 SHC1 SHC1 4802 0.079 0.59 NO
113 NUP85 NUP85 NUP85 4897 0.076 0.59 NO
114 STAT2 STAT2 STAT2 4953 0.075 0.58 NO
115 IRF3 IRF3 IRF3 4963 0.074 0.58 NO
116 EIF4E2 EIF4E2 EIF4E2 4996 0.073 0.58 NO
117 CISH CISH CISH 5004 0.073 0.58 NO
118 CUL1 CUL1 CUL1 5121 0.07 0.58 NO
119 IRF4 IRF4 IRF4 5122 0.07 0.58 NO
120 EIF4E EIF4E EIF4E 5163 0.07 0.58 NO
121 MYD88 MYD88 MYD88 5228 0.068 0.58 NO
122 MAP2K4 MAP2K4 MAP2K4 5291 0.067 0.57 NO
123 CHUK CHUK CHUK 5335 0.066 0.57 NO
124 PTPN2 PTPN2 PTPN2 5384 0.064 0.57 NO
125 SOS1 SOS1 SOS1 5463 0.063 0.57 NO
126 YWHAZ YWHAZ YWHAZ 5580 0.06 0.56 NO
127 NUP50 NUP50 NUP50 5674 0.058 0.56 NO
128 ADAM17 ADAM17 ADAM17 5682 0.058 0.56 NO
129 JAK1 JAK1 JAK1 5700 0.058 0.56 NO
130 IRF2 IRF2 IRF2 5707 0.058 0.56 NO
131 YWHAB YWHAB YWHAB 5728 0.057 0.56 NO
132 KPNA3 KPNA3 KPNA3 5921 0.053 0.55 NO
133 IL5RA IL5RA IL5RA 5926 0.053 0.55 NO
134 GH1 GH1 GH1 5934 0.053 0.55 NO
135 MAPK1 MAPK1 MAPK1 6004 0.052 0.55 NO
136 ADAR ADAR ADAR 6007 0.052 0.55 NO
137 RIPK2 RIPK2 RIPK2 6013 0.052 0.55 NO
138 IRAK1 IRAK1 IRAK1 6144 0.049 0.54 NO
139 SUMO1 SUMO1 SUMO1 6170 0.048 0.54 NO
140 PIK3CA PIK3CA PIK3CA 6197 0.048 0.54 NO
141 KRAS KRAS KRAS 6392 0.045 0.53 NO
142 RNASEL RNASEL RNASEL 6398 0.045 0.53 NO
143 NFKB2 NFKB2 NFKB2 6434 0.044 0.53 NO
144 KPNA2 KPNA2 KPNA2 6645 0.04 0.52 NO
145 EIF4G2 EIF4G2 EIF4G2 6755 0.038 0.51 NO
146 SQSTM1 SQSTM1 SQSTM1 6847 0.036 0.5 NO
147 NUP37 NUP37 NUP37 6895 0.036 0.5 NO
148 GRB2 GRB2 GRB2 7036 0.033 0.5 NO
149 CRK CRK CRK 7210 0.03 0.49 NO
150 KPNB1 KPNB1 KPNB1 7254 0.029 0.48 NO
151 KPNA1 KPNA1 KPNA1 7278 0.029 0.48 NO
152 TRAF6 TRAF6 TRAF6 7328 0.028 0.48 NO
153 PIK3R1 PIK3R1 PIK3R1 7416 0.027 0.48 NO
154 IFNGR2 IFNGR2 IFNGR2 7471 0.026 0.47 NO
155 HRAS HRAS HRAS 7479 0.026 0.47 NO
156 PIK3CD PIK3CD PIK3CD 7481 0.026 0.47 NO
157 PRKACB PRKACB PRKACB 7585 0.024 0.47 NO
158 EIF4A3 EIF4A3 EIF4A3 7711 0.022 0.46 NO
159 CDK1 CDK1 CDK1 7777 0.021 0.46 NO
160 UBE2N UBE2N UBE2N 7917 0.019 0.45 NO
161 TYK2 TYK2 TYK2 7947 0.018 0.45 NO
162 STAT5B STAT5B STAT5B 7974 0.018 0.45 NO
163 INPPL1 INPPL1 INPPL1 7982 0.018 0.45 NO
164 PIK3CB PIK3CB PIK3CB 8010 0.018 0.45 NO
165 NUP188 NUP188 NUP188 8013 0.018 0.45 NO
166 TRIM25 TRIM25 TRIM25 8093 0.016 0.44 NO
167 TNIP2 TNIP2 TNIP2 8141 0.016 0.44 NO
168 NUPL1 NUPL1 NUPL1 8214 0.014 0.44 NO
169 PLCG1 PLCG1 PLCG1 8297 0.013 0.43 NO
170 NUPL2 NUPL2 NUPL2 8307 0.013 0.43 NO
171 MAP2K1 MAP2K1 MAP2K1 8364 0.012 0.43 NO
172 RANBP2 RANBP2 RANBP2 8476 0.011 0.42 NO
173 NUP155 NUP155 NUP155 8477 0.011 0.42 NO
174 RAPGEF1 RAPGEF1 RAPGEF1 8568 0.0093 0.42 NO
175 MAPK3 MAPK3 MAPK3 8836 0.0053 0.4 NO
176 SKP1 SKP1 SKP1 8868 0.005 0.4 NO
177 RAE1 RAE1 RAE1 8925 0.0041 0.4 NO
178 NUP107 NUP107 NUP107 8965 0.0034 0.39 NO
179 NUP205 NUP205 NUP205 9190 6.5e-07 0.38 NO
180 MAP3K7 MAP3K7 MAP3K7 9223 -0.00039 0.38 NO
181 SEH1L SEH1L SEH1L 9624 -0.0065 0.36 NO
182 TEC TEC TEC 9806 -0.0096 0.34 NO
183 NUP133 NUP133 NUP133 9889 -0.011 0.34 NO
184 NUP62 NUP62 NUP62 9965 -0.012 0.34 NO
185 TAB1 TAB1 TAB1 9990 -0.012 0.34 NO
186 NUP54 NUP54 NUP54 10129 -0.015 0.33 NO
187 IL6R IL6R IL6R 10250 -0.017 0.32 NO
188 NUP35 NUP35 NUP35 10404 -0.019 0.31 NO
189 IKBKB IKBKB IKBKB 10411 -0.02 0.31 NO
190 TMEM189-UBE2V1 TMEM189-UBE2V1 TMEM189-UBE2V1 10556 -0.022 0.3 NO
191 IKBKG IKBKG IKBKG 10597 -0.023 0.3 NO
192 PIN1 PIN1 PIN1 10869 -0.027 0.29 NO
193 TOLLIP TOLLIP TOLLIP 10906 -0.028 0.28 NO
194 MAP2K2 MAP2K2 MAP2K2 11001 -0.029 0.28 NO
195 STAT5A STAT5A STAT5A 11033 -0.03 0.28 NO
196 PPM1B PPM1B PPM1B 11052 -0.03 0.28 NO
197 GAB2 GAB2 GAB2 11073 -0.031 0.28 NO
198 IL6ST IL6ST IL6ST 11119 -0.032 0.28 NO
199 EIF4A1 EIF4A1 EIF4A1 11193 -0.033 0.27 NO
200 NUP93 NUP93 NUP93 11215 -0.033 0.27 NO
201 AAAS AAAS AAAS 11381 -0.036 0.26 NO
202 TAB2 TAB2 TAB2 11416 -0.036 0.26 NO
203 NUP43 NUP43 NUP43 11430 -0.037 0.26 NO
204 TAB3 TAB3 TAB3 11571 -0.039 0.25 NO
205 CAMK2D CAMK2D CAMK2D 11579 -0.039 0.25 NO
206 CRKL CRKL CRKL 11586 -0.04 0.25 NO
207 CBL CBL CBL 11664 -0.041 0.25 NO
208 NOD1 NOD1 NOD1 11674 -0.041 0.25 NO
209 MAP3K3 MAP3K3 MAP3K3 11782 -0.043 0.24 NO
210 CD44 CD44 CD44 11958 -0.046 0.23 NO
211 POM121 POM121 POM121 11999 -0.048 0.23 NO
212 KPNA4 KPNA4 KPNA4 12010 -0.048 0.23 NO
213 PIK3R2 PIK3R2 PIK3R2 12192 -0.051 0.22 NO
214 NUP210 NUP210 NUP210 12273 -0.052 0.22 NO
215 SH2B1 SH2B1 SH2B1 12300 -0.053 0.22 NO
216 BTRC BTRC BTRC 12316 -0.053 0.22 NO
217 PML PML PML 12383 -0.054 0.22 NO
218 NUP214 NUP214 NUP214 12657 -0.06 0.2 NO
219 YES1 YES1 YES1 13070 -0.071 0.18 NO
220 RELA RELA RELA 13088 -0.071 0.18 NO
221 UBE2E1 UBE2E1 UBE2E1 13178 -0.074 0.17 NO
222 UBA52 UBA52 UBA52 13271 -0.076 0.17 NO
223 IRS2 IRS2 IRS2 13581 -0.085 0.15 NO
224 EIF4E3 EIF4E3 EIF4E3 13582 -0.085 0.15 NO
225 FYN FYN FYN 13586 -0.085 0.16 NO
226 IP6K2 IP6K2 IP6K2 13724 -0.09 0.15 NO
227 NUP153 NUP153 NUP153 13778 -0.091 0.15 NO
228 RPS27A RPS27A RPS27A 14078 -0.1 0.13 NO
229 EIF4G1 EIF4G1 EIF4G1 14152 -0.1 0.13 NO
230 PELI3 PELI3 PELI3 14337 -0.11 0.12 NO
231 RAF1 RAF1 RAF1 14416 -0.12 0.12 NO
232 PRKCD PRKCD PRKCD 14486 -0.12 0.12 NO
233 FLNB FLNB FLNB 14500 -0.12 0.12 NO
234 EIF4A2 EIF4A2 EIF4A2 14760 -0.13 0.1 NO
235 IL1RAP IL1RAP IL1RAP 15233 -0.16 0.079 NO
236 NCAM1 NCAM1 NCAM1 15443 -0.18 0.069 NO
237 PELI2 PELI2 PELI2 15655 -0.19 0.06 NO
238 IRS1 IRS1 IRS1 15864 -0.21 0.051 NO
239 EGR1 EGR1 EGR1 15885 -0.22 0.054 NO
240 GHR GHR GHR 17011 -0.43 -0.005 NO
241 IRF6 IRF6 IRF6 17056 -0.44 -0.00034 NO
242 CAMK2B CAMK2B CAMK2B 17126 -0.47 0.0033 NO
243 PRL PRL PRL 17273 -0.58 0.0043 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: KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION.

Figure S72.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION, 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 CHEMOKINE SIGNALING 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 PSMB9 PSMB9 PSMB9 61 1 0.11 YES
2 RASGRP1 RASGRP1 RASGRP1 314 0.72 0.17 YES
3 PSMB8 PSMB8 PSMB8 688 0.49 0.2 YES
4 CARD11 CARD11 CARD11 708 0.48 0.25 YES
5 PSMB10 PSMB10 PSMB10 1411 0.3 0.24 YES
6 PRKCB PRKCB PRKCB 1499 0.29 0.26 YES
7 PSME2 PSME2 PSME2 1542 0.28 0.29 YES
8 CDKN1A CDKN1A CDKN1A 1797 0.24 0.3 YES
9 PSMA3 PSMA3 PSMA3 2092 0.21 0.31 YES
10 PSME1 PSME1 PSME1 2576 0.17 0.3 YES
11 BCL10 BCL10 BCL10 2671 0.17 0.31 YES
12 NFKBIA NFKBIA NFKBIA 2752 0.16 0.32 YES
13 MDM2 MDM2 MDM2 2865 0.15 0.33 YES
14 PSMA4 PSMA4 PSMA4 2986 0.15 0.34 YES
15 PSME4 PSME4 PSME4 3021 0.14 0.36 YES
16 PSMA6 PSMA6 PSMA6 3050 0.14 0.37 YES
17 PSMA5 PSMA5 PSMA5 3352 0.13 0.36 YES
18 PSMD14 PSMD14 PSMD14 3355 0.13 0.38 YES
19 PSMB3 PSMB3 PSMB3 3832 0.11 0.36 YES
20 PSMC1 PSMC1 PSMC1 3934 0.1 0.37 YES
21 NRAS NRAS NRAS 4011 0.1 0.37 YES
22 PSMB2 PSMB2 PSMB2 4038 0.1 0.38 YES
23 PSMC6 PSMC6 PSMC6 4144 0.098 0.39 YES
24 PSMA7 PSMA7 PSMA7 4221 0.095 0.39 YES
25 RICTOR RICTOR RICTOR 4249 0.094 0.4 YES
26 PSMD12 PSMD12 PSMD12 4348 0.091 0.4 YES
27 PSMC2 PSMC2 PSMC2 4564 0.086 0.4 YES
28 CREB1 CREB1 CREB1 4598 0.085 0.41 YES
29 PSMD11 PSMD11 PSMD11 4678 0.082 0.41 YES
30 PSMD7 PSMD7 PSMD7 4978 0.074 0.4 YES
31 PSMC4 PSMC4 PSMC4 5002 0.073 0.41 YES
32 CUL1 CUL1 CUL1 5121 0.07 0.41 YES
33 CHUK CHUK CHUK 5335 0.066 0.4 YES
34 PSMC3 PSMC3 PSMC3 5413 0.064 0.41 YES
35 MTOR MTOR MTOR 5420 0.064 0.41 YES
36 PSMC5 PSMC5 PSMC5 5505 0.062 0.42 YES
37 PSMB6 PSMB6 PSMB6 5587 0.06 0.42 YES
38 PSMA2 PSMA2 PSMA2 5653 0.059 0.42 YES
39 KRAS KRAS KRAS 6392 0.045 0.38 NO
40 PSMB1 PSMB1 PSMB1 6534 0.042 0.38 NO
41 NFKBIE NFKBIE NFKBIE 6591 0.041 0.38 NO
42 NFKBIB NFKBIB NFKBIB 6663 0.04 0.38 NO
43 PSMA1 PSMA1 PSMA1 6784 0.038 0.38 NO
44 PSMD8 PSMD8 PSMD8 6867 0.036 0.37 NO
45 PSMD5 PSMD5 PSMD5 6987 0.034 0.37 NO
46 PSMD13 PSMD13 PSMD13 7204 0.03 0.36 NO
47 PSMB5 PSMB5 PSMB5 7390 0.027 0.35 NO
48 PSMD3 PSMD3 PSMD3 7400 0.027 0.36 NO
49 HRAS HRAS HRAS 7479 0.026 0.35 NO
50 PTEN PTEN PTEN 7504 0.025 0.36 NO
51 CASP9 CASP9 CASP9 7861 0.02 0.34 NO
52 BAD BAD BAD 8127 0.016 0.32 NO
53 PSMB4 PSMB4 PSMB4 8551 0.0096 0.3 NO
54 RASGRP3 RASGRP3 RASGRP3 8704 0.0072 0.29 NO
55 PSMD4 PSMD4 PSMD4 8795 0.0059 0.29 NO
56 CDKN1B CDKN1B CDKN1B 8827 0.0055 0.29 NO
57 PSMB7 PSMB7 PSMB7 8860 0.0051 0.28 NO
58 SKP1 SKP1 SKP1 8868 0.005 0.28 NO
59 PSMF1 PSMF1 PSMF1 9188 0.000016 0.27 NO
60 MAP3K7 MAP3K7 MAP3K7 9223 -0.00039 0.26 NO
61 MLST8 MLST8 MLST8 9467 -0.0042 0.25 NO
62 FOXO4 FOXO4 FOXO4 9767 -0.0091 0.23 NO
63 PSMD1 PSMD1 PSMD1 9857 -0.01 0.23 NO
64 PSMD10 PSMD10 PSMD10 9992 -0.012 0.22 NO
65 AKT1S1 AKT1S1 AKT1S1 9995 -0.013 0.22 NO
66 GSK3A GSK3A GSK3A 10233 -0.017 0.21 NO
67 IKBKB IKBKB IKBKB 10411 -0.02 0.2 NO
68 IKBKG IKBKG IKBKG 10597 -0.023 0.2 NO
69 AKT1 AKT1 AKT1 10764 -0.025 0.19 NO
70 TRIB3 TRIB3 TRIB3 10856 -0.027 0.19 NO
71 FBXW11 FBXW11 FBXW11 10975 -0.029 0.18 NO
72 AKT3 AKT3 AKT3 10986 -0.029 0.19 NO
73 RPS6KB2 RPS6KB2 RPS6KB2 11013 -0.029 0.19 NO
74 MAPKAP1 MAPKAP1 MAPKAP1 11730 -0.042 0.15 NO
75 PHLPP1 PHLPP1 PHLPP1 11841 -0.044 0.15 NO
76 MALT1 MALT1 MALT1 12037 -0.048 0.14 NO
77 PSMD9 PSMD9 PSMD9 12065 -0.049 0.15 NO
78 PSMD6 PSMD6 PSMD6 12120 -0.05 0.15 NO
79 PSMD2 PSMD2 PSMD2 12180 -0.051 0.15 NO
80 BTRC BTRC BTRC 12316 -0.053 0.15 NO
81 AKT2 AKT2 AKT2 12618 -0.06 0.14 NO
82 TSC2 TSC2 TSC2 12803 -0.064 0.13 NO
83 PDPK1 PDPK1 PDPK1 13045 -0.07 0.13 NO
84 THEM4 THEM4 THEM4 13069 -0.071 0.13 NO
85 RELA RELA RELA 13088 -0.071 0.14 NO
86 UBA52 UBA52 UBA52 13271 -0.076 0.14 NO
87 RPS27A RPS27A RPS27A 14078 -0.1 0.1 NO
88 NR4A1 NR4A1 NR4A1 14139 -0.1 0.11 NO
89 FOXO1 FOXO1 FOXO1 15106 -0.15 0.067 NO
90 FOXO3 FOXO3 FOXO3 15484 -0.18 0.064 NO
91 REL REL REL 15764 -0.2 0.07 NO
92 PSMA8 PSMA8 PSMA8 15825 -0.21 0.088 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: KEGG CHEMOKINE SIGNALING PATHWAY.

Figure S74.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG CHEMOKINE 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 PHOSPHATIDYLINOSITOL SIGNALING SYSTEM

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 LCK LCK LCK 13 1.2 0.11 YES
2 IL2RG IL2RG IL2RG 42 1.1 0.21 YES
3 IL2RB IL2RB IL2RB 93 0.98 0.29 YES
4 IKZF3 IKZF3 IKZF3 160 0.86 0.36 YES
5 DOK2 DOK2 DOK2 180 0.84 0.44 YES
6 IFNG IFNG IFNG 216 0.8 0.51 YES
7 IL2RA IL2RA IL2RA 430 0.63 0.55 YES
8 STAT1 STAT1 STAT1 647 0.51 0.59 YES
9 JAK3 JAK3 JAK3 840 0.43 0.61 YES
10 SOCS2 SOCS2 SOCS2 992 0.38 0.64 YES
11 SYK SYK SYK 1272 0.32 0.65 YES
12 PRKCB PRKCB PRKCB 1499 0.29 0.66 YES
13 SOCS1 SOCS1 SOCS1 1957 0.23 0.66 YES
14 SOCS3 SOCS3 SOCS3 2083 0.21 0.67 YES
15 STAM2 STAM2 STAM2 2619 0.17 0.65 NO
16 STAT3 STAT3 STAT3 3622 0.12 0.61 NO
17 STAM STAM STAM 3643 0.12 0.62 NO
18 NRAS NRAS NRAS 4011 0.1 0.6 NO
19 PTK2B PTK2B PTK2B 4507 0.087 0.58 NO
20 SHC1 SHC1 SHC1 4802 0.079 0.57 NO
21 CISH CISH CISH 5004 0.073 0.57 NO
22 SOS1 SOS1 SOS1 5463 0.063 0.55 NO
23 JAK1 JAK1 JAK1 5700 0.058 0.54 NO
24 MAPK1 MAPK1 MAPK1 6004 0.052 0.52 NO
25 PIK3CA PIK3CA PIK3CA 6197 0.048 0.52 NO
26 KRAS KRAS KRAS 6392 0.045 0.51 NO
27 GRB2 GRB2 GRB2 7036 0.033 0.48 NO
28 PIK3R1 PIK3R1 PIK3R1 7416 0.027 0.46 NO
29 HRAS HRAS HRAS 7479 0.026 0.46 NO
30 RASA1 RASA1 RASA1 7778 0.021 0.44 NO
31 STAT5B STAT5B STAT5B 7974 0.018 0.43 NO
32 MAP2K1 MAP2K1 MAP2K1 8364 0.012 0.41 NO
33 MAPK14 MAPK14 MAPK14 8424 0.011 0.41 NO
34 MAPK9 MAPK9 MAPK9 8660 0.0079 0.39 NO
35 PTPN11 PTPN11 PTPN11 8822 0.0055 0.38 NO
36 MAPK3 MAPK3 MAPK3 8836 0.0053 0.38 NO
37 BCL2 BCL2 BCL2 9050 0.0022 0.37 NO
38 MAPK11 MAPK11 MAPK11 9144 0.00055 0.37 NO
39 PRKCE PRKCE PRKCE 9879 -0.011 0.33 NO
40 MAPKAPK2 MAPKAPK2 MAPKAPK2 10209 -0.016 0.31 NO
41 MAP2K2 MAP2K2 MAP2K2 11001 -0.029 0.26 NO
42 STAT5A STAT5A STAT5A 11033 -0.03 0.27 NO
43 GAB2 GAB2 GAB2 11073 -0.031 0.27 NO
44 RHOA RHOA RHOA 11289 -0.034 0.26 NO
45 FOS FOS FOS 11345 -0.035 0.26 NO
46 MAPK8 MAPK8 MAPK8 12380 -0.054 0.2 NO
47 PPP2R5D PPP2R5D PPP2R5D 12455 -0.056 0.2 NO
48 IRS2 IRS2 IRS2 13581 -0.085 0.14 NO
49 FYN FYN FYN 13586 -0.085 0.15 NO
50 JUN JUN JUN 13900 -0.095 0.14 NO
51 RAF1 RAF1 RAF1 14416 -0.12 0.12 NO
52 MYC MYC MYC 14680 -0.13 0.12 NO
53 CDK2 CDK2 CDK2 15380 -0.17 0.095 NO
54 IRS1 IRS1 IRS1 15864 -0.21 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: KEGG PHOSPHATIDYLINOSITOL SIGNALING SYSTEM.

Figure S76.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PHOSPHATIDYLINOSITOL SIGNALING SYSTEM, 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 LYSOSOME

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 CD3D CD3D CD3D 1 1.4 0.044 YES
2 CD8B CD8B CD8B 8 1.3 0.084 YES
3 CD8A CD8A CD8A 12 1.3 0.12 YES
4 LCK LCK LCK 13 1.2 0.16 YES
5 PDCD1 PDCD1 PDCD1 18 1.2 0.2 YES
6 CD3E CD3E CD3E 27 1.2 0.24 YES
7 GRAP2 GRAP2 GRAP2 28 1.2 0.27 YES
8 ZAP70 ZAP70 ZAP70 36 1.1 0.31 YES
9 CD247 CD247 CD247 40 1.1 0.34 YES
10 CD3G CD3G CD3G 77 1 0.37 YES
11 ITK ITK ITK 90 0.99 0.4 YES
12 ICOS ICOS ICOS 102 0.95 0.43 YES
13 CD40LG CD40LG CD40LG 113 0.92 0.46 YES
14 LCP2 LCP2 LCP2 146 0.88 0.48 YES
15 VAV1 VAV1 VAV1 151 0.87 0.51 YES
16 CTLA4 CTLA4 CTLA4 166 0.86 0.54 YES
17 PTPRC PTPRC PTPRC 208 0.82 0.56 YES
18 IFNG IFNG IFNG 216 0.8 0.58 YES
19 LAT LAT LAT 265 0.77 0.61 YES
20 IL10 IL10 IL10 307 0.73 0.63 YES
21 TNF TNF TNF 309 0.72 0.65 YES
22 RASGRP1 RASGRP1 RASGRP1 314 0.72 0.67 YES
23 PTPN6 PTPN6 PTPN6 318 0.72 0.69 YES
24 PIK3CG PIK3CG PIK3CG 367 0.68 0.71 YES
25 PIK3R5 PIK3R5 PIK3R5 453 0.61 0.73 YES
26 CD28 CD28 CD28 464 0.61 0.74 YES
27 NFATC2 NFATC2 NFATC2 573 0.55 0.76 YES
28 NFATC4 NFATC4 NFATC4 616 0.52 0.77 YES
29 CARD11 CARD11 CARD11 708 0.48 0.78 YES
30 MAP3K8 MAP3K8 MAP3K8 892 0.41 0.78 YES
31 CD4 CD4 CD4 1032 0.37 0.78 YES
32 PIK3R3 PIK3R3 PIK3R3 1372 0.3 0.78 NO
33 PRKCQ PRKCQ PRKCQ 1881 0.24 0.75 NO
34 PDK1 PDK1 PDK1 2199 0.2 0.74 NO
35 MAPK13 MAPK13 MAPK13 2203 0.2 0.75 NO
36 VAV3 VAV3 VAV3 2225 0.2 0.75 NO
37 MAPK12 MAPK12 MAPK12 2360 0.19 0.75 NO
38 BCL10 BCL10 BCL10 2671 0.17 0.74 NO
39 NFKBIA NFKBIA NFKBIA 2752 0.16 0.74 NO
40 PPP3CA PPP3CA PPP3CA 3259 0.13 0.71 NO
41 NRAS NRAS NRAS 4011 0.1 0.67 NO
42 VAV2 VAV2 VAV2 4053 0.1 0.67 NO
43 NFAT5 NFAT5 NFAT5 4122 0.099 0.67 NO
44 PPP3CC PPP3CC PPP3CC 4410 0.09 0.66 NO
45 CDC42 CDC42 CDC42 4438 0.089 0.66 NO
46 CHUK CHUK CHUK 5335 0.066 0.61 NO
47 SOS1 SOS1 SOS1 5463 0.063 0.6 NO
48 NFATC3 NFATC3 NFATC3 5647 0.059 0.6 NO
49 PPP3CB PPP3CB PPP3CB 5907 0.053 0.58 NO
50 MAPK1 MAPK1 MAPK1 6004 0.052 0.58 NO
51 PIK3CA PIK3CA PIK3CA 6197 0.048 0.57 NO
52 KRAS KRAS KRAS 6392 0.045 0.56 NO
53 NCK1 NCK1 NCK1 6495 0.043 0.55 NO
54 NFKBIE NFKBIE NFKBIE 6591 0.041 0.55 NO
55 NFKBIB NFKBIB NFKBIB 6663 0.04 0.55 NO
56 GRB2 GRB2 GRB2 7036 0.033 0.53 NO
57 NFKB1 NFKB1 NFKB1 7163 0.031 0.52 NO
58 MAP3K14 MAP3K14 MAP3K14 7292 0.029 0.51 NO
59 PIK3R1 PIK3R1 PIK3R1 7416 0.027 0.51 NO
60 HRAS HRAS HRAS 7479 0.026 0.5 NO
61 PIK3CD PIK3CD PIK3CD 7481 0.026 0.5 NO
62 PIK3CB PIK3CB PIK3CB 8010 0.018 0.48 NO
63 DLG1 DLG1 DLG1 8035 0.017 0.47 NO
64 PLCG1 PLCG1 PLCG1 8297 0.013 0.46 NO
65 MAP2K1 MAP2K1 MAP2K1 8364 0.012 0.46 NO
66 MAPK14 MAPK14 MAPK14 8424 0.011 0.45 NO
67 PPP3R1 PPP3R1 PPP3R1 8566 0.0094 0.44 NO
68 MAPK9 MAPK9 MAPK9 8660 0.0079 0.44 NO
69 MAPK3 MAPK3 MAPK3 8836 0.0053 0.43 NO
70 PAK1 PAK1 PAK1 9138 0.00064 0.41 NO
71 MAPK11 MAPK11 MAPK11 9144 0.00055 0.41 NO
72 MAP3K7 MAP3K7 MAP3K7 9223 -0.00039 0.41 NO
73 PAK6 PAK6 PAK6 9321 -0.0018 0.4 NO
74 TEC TEC TEC 9806 -0.0096 0.38 NO
75 MAP2K7 MAP2K7 MAP2K7 10278 -0.018 0.35 NO
76 IKBKB IKBKB IKBKB 10411 -0.02 0.34 NO
77 IKBKG IKBKG IKBKG 10597 -0.023 0.33 NO
78 AKT1 AKT1 AKT1 10764 -0.025 0.32 NO
79 PAK2 PAK2 PAK2 10946 -0.028 0.31 NO
80 AKT3 AKT3 AKT3 10986 -0.029 0.31 NO
81 MAP2K2 MAP2K2 MAP2K2 11001 -0.029 0.31 NO
82 RHOA RHOA RHOA 11289 -0.034 0.3 NO
83 FOS FOS FOS 11345 -0.035 0.29 NO
84 CBL CBL CBL 11664 -0.041 0.28 NO
85 CBLB CBLB CBLB 11709 -0.042 0.28 NO
86 MALT1 MALT1 MALT1 12037 -0.048 0.26 NO
87 SOS2 SOS2 SOS2 12060 -0.048 0.26 NO
88 PIK3R2 PIK3R2 PIK3R2 12192 -0.051 0.25 NO
89 GSK3B GSK3B GSK3B 12213 -0.051 0.25 NO
90 NCK2 NCK2 NCK2 12435 -0.056 0.24 NO
91 PAK4 PAK4 PAK4 12568 -0.059 0.24 NO
92 AKT2 AKT2 AKT2 12618 -0.06 0.23 NO
93 RELA RELA RELA 13088 -0.071 0.21 NO
94 CHP CHP CHP 13202 -0.075 0.2 NO
95 NFATC1 NFATC1 NFATC1 13223 -0.075 0.21 NO
96 FYN FYN FYN 13586 -0.085 0.19 NO
97 JUN JUN JUN 13900 -0.095 0.17 NO
98 CDK4 CDK4 CDK4 14010 -0.099 0.17 NO
99 RAF1 RAF1 RAF1 14416 -0.12 0.15 NO
100 PAK7 PAK7 PAK7 14771 -0.13 0.13 NO
101 CHP2 CHP2 CHP2 15788 -0.2 0.081 NO
102 PAK3 PAK3 PAK3 16500 -0.3 0.049 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: KEGG LYSOSOME.

Figure S78.  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 ENDOCYTOSIS

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 FCGR1A FCGR1A FCGR1A 128 0.9 0.048 YES
2 VAV1 VAV1 VAV1 151 0.87 0.099 YES
3 DOCK2 DOCK2 DOCK2 202 0.82 0.15 YES
4 PTPRC PTPRC PTPRC 208 0.82 0.2 YES
5 NCF1 NCF1 NCF1 210 0.82 0.24 YES
6 WAS WAS WAS 246 0.78 0.29 YES
7 LAT LAT LAT 265 0.77 0.34 YES
8 FCGR3A FCGR3A FCGR3A 319 0.72 0.38 YES
9 PIK3CG PIK3CG PIK3CG 367 0.68 0.42 YES
10 HCK HCK HCK 424 0.63 0.45 YES
11 INPP5D INPP5D INPP5D 438 0.62 0.49 YES
12 PIK3R5 PIK3R5 PIK3R5 453 0.61 0.52 YES
13 RAC2 RAC2 RAC2 462 0.61 0.56 YES
14 SYK SYK SYK 1272 0.32 0.53 YES
15 PIK3R3 PIK3R3 PIK3R3 1372 0.3 0.55 YES
16 PRKCB PRKCB PRKCB 1499 0.29 0.56 YES
17 SPHK1 SPHK1 SPHK1 1583 0.27 0.57 YES
18 ASAP3 ASAP3 ASAP3 1608 0.27 0.58 YES
19 PPAP2B PPAP2B PPAP2B 1727 0.25 0.59 YES
20 PLCG2 PLCG2 PLCG2 1739 0.25 0.61 YES
21 DNM3 DNM3 DNM3 1839 0.24 0.62 YES
22 FCGR2A FCGR2A FCGR2A 1841 0.24 0.63 YES
23 LYN LYN LYN 1922 0.23 0.64 YES
24 VAV3 VAV3 VAV3 2225 0.2 0.64 NO
25 FCGR2B FCGR2B FCGR2B 2599 0.17 0.62 NO
26 PRKCA PRKCA PRKCA 2621 0.17 0.63 NO
27 PLD1 PLD1 PLD1 2995 0.15 0.62 NO
28 PLA2G4A PLA2G4A PLA2G4A 3395 0.13 0.6 NO
29 PRKCG PRKCG PRKCG 3685 0.12 0.6 NO
30 VAV2 VAV2 VAV2 4053 0.1 0.58 NO
31 ASAP1 ASAP1 ASAP1 4257 0.094 0.57 NO
32 CDC42 CDC42 CDC42 4438 0.089 0.57 NO
33 ARF6 ARF6 ARF6 4962 0.074 0.54 NO
34 ARPC2 ARPC2 ARPC2 4995 0.073 0.55 NO
35 ARPC1B ARPC1B ARPC1B 5513 0.062 0.52 NO
36 VASP VASP VASP 5941 0.053 0.5 NO
37 MAPK1 MAPK1 MAPK1 6004 0.052 0.5 NO
38 PIK3CA PIK3CA PIK3CA 6197 0.048 0.49 NO
39 GSN GSN GSN 6288 0.046 0.49 NO
40 SPHK2 SPHK2 SPHK2 6299 0.046 0.49 NO
41 ASAP2 ASAP2 ASAP2 6340 0.046 0.49 NO
42 PPAP2C PPAP2C PPAP2C 6402 0.045 0.49 NO
43 RPS6KB1 RPS6KB1 RPS6KB1 6440 0.044 0.49 NO
44 PLA2G6 PLA2G6 PLA2G6 6554 0.041 0.48 NO
45 CRK CRK CRK 7210 0.03 0.45 NO
46 LIMK2 LIMK2 LIMK2 7216 0.03 0.45 NO
47 ARPC3 ARPC3 ARPC3 7264 0.029 0.45 NO
48 ARPC5 ARPC5 ARPC5 7369 0.028 0.45 NO
49 PIK3R1 PIK3R1 PIK3R1 7416 0.027 0.44 NO
50 PIK3CD PIK3CD PIK3CD 7481 0.026 0.44 NO
51 WASL WASL WASL 7789 0.021 0.43 NO
52 PIK3CB PIK3CB PIK3CB 8010 0.018 0.41 NO
53 DNM2 DNM2 DNM2 8060 0.017 0.41 NO
54 LIMK1 LIMK1 LIMK1 8091 0.016 0.41 NO
55 PLCG1 PLCG1 PLCG1 8297 0.013 0.4 NO
56 MAP2K1 MAP2K1 MAP2K1 8364 0.012 0.4 NO
57 PPAP2A PPAP2A PPAP2A 8498 0.01 0.39 NO
58 DNM1L DNM1L DNM1L 8711 0.0071 0.38 NO
59 CFL1 CFL1 CFL1 8834 0.0053 0.37 NO
60 MAPK3 MAPK3 MAPK3 8836 0.0053 0.37 NO
61 PAK1 PAK1 PAK1 9138 0.00064 0.36 NO
62 PIKFYVE PIKFYVE PIKFYVE 9470 -0.0043 0.34 NO
63 PLD2 PLD2 PLD2 9803 -0.0096 0.32 NO
64 PIP5K1C PIP5K1C PIP5K1C 9864 -0.011 0.31 NO
65 AMPH AMPH AMPH 9869 -0.011 0.32 NO
66 PRKCE PRKCE PRKCE 9879 -0.011 0.32 NO
67 RAC1 RAC1 RAC1 10537 -0.022 0.28 NO
68 MARCKSL1 MARCKSL1 MARCKSL1 10657 -0.024 0.27 NO
69 PIP5K1A PIP5K1A PIP5K1A 10689 -0.024 0.27 NO
70 AKT1 AKT1 AKT1 10764 -0.025 0.27 NO
71 WASF2 WASF2 WASF2 10826 -0.026 0.27 NO
72 ARPC1A ARPC1A ARPC1A 10883 -0.027 0.27 NO
73 AKT3 AKT3 AKT3 10986 -0.029 0.26 NO
74 RPS6KB2 RPS6KB2 RPS6KB2 11013 -0.029 0.26 NO
75 GAB2 GAB2 GAB2 11073 -0.031 0.26 NO
76 PIP4K2B PIP4K2B PIP4K2B 11448 -0.037 0.24 NO
77 ARPC5L ARPC5L ARPC5L 11557 -0.039 0.24 NO
78 CRKL CRKL CRKL 11586 -0.04 0.24 NO
79 FCGR2C FCGR2C FCGR2C 11675 -0.041 0.24 NO
80 MYO10 MYO10 MYO10 11775 -0.043 0.23 NO
81 CFL2 CFL2 CFL2 12105 -0.049 0.22 NO
82 PIK3R2 PIK3R2 PIK3R2 12192 -0.051 0.21 NO
83 AKT2 AKT2 AKT2 12618 -0.06 0.19 NO
84 ARPC4 ARPC4 ARPC4 12682 -0.061 0.19 NO
85 DNM1 DNM1 DNM1 13067 -0.071 0.18 NO
86 RAF1 RAF1 RAF1 14416 -0.12 0.1 NO
87 PRKCD PRKCD PRKCD 14486 -0.12 0.11 NO
88 WASF3 WASF3 WASF3 14693 -0.13 0.1 NO
89 MARCKS MARCKS MARCKS 14962 -0.14 0.096 NO
90 SCIN SCIN SCIN 15125 -0.15 0.096 NO
91 PIP5K1B PIP5K1B PIP5K1B 15411 -0.17 0.09 NO
92 WASF1 WASF1 WASF1 16778 -0.36 0.033 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: KEGG ENDOCYTOSIS.

Figure S80.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ENDOCYTOSIS, 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 = UVM-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt

  • Phenotype data file = UVM-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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