GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in BLCA-TP
Bladder Urothelial Carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1057F8D
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 BLCA-TP. Broad Institute of MIT and Harvard. doi:10.7908/C1057F8D
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 "BLCA-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: 713
Number of samples: 408
Original number of Gene Sets: 1320
Maximum gene set size: 933

Table 2.  Get Full Table pheno data info

phenotype info
pheno.type: 1 - 5 :[ clus1 ] 72
pheno.type: 2 - 5 :[ clus2 ] 137
pheno.type: 3 - 5 :[ clus3 ] 38
pheno.type: 4 - 5 :[ clus4 ] 104
pheno.type: 5 - 5 :[ clus5 ] 57

For the expression subtypes of 18215 genes in 409 samples, GSEA found enriched gene sets in each cluster using 408 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

  • clus1

    • Top enriched gene sets are KEGG PURINE METABOLISM, KEGG GLYCINE SERINE AND THREONINE METABOLISM, KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION, KEGG ARGININE AND PROLINE METABOLISM, KEGG HISTIDINE METABOLISM, KEGG TYROSINE METABOLISM, KEGG TRYPTOPHAN METABOLISM, KEGG O GLYCAN BIOSYNTHESIS, KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM, KEGG GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE

    • And common core enriched genes are AKT3, RPS6KA2, PIK3CD, PIK3CG, PIK3R5, ADCY2, ADCY4, ADCY5, ADCY9, ADCYAP1

  • clus2

    • Top enriched gene sets are KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS, KEGG FATTY ACID METABOLISM, KEGG STEROID HORMONE BIOSYNTHESIS, KEGG STARCH AND SUCROSE METABOLISM, KEGG GLYCOSYLPHOSPHATIDYLINOSITOL GPI ANCHOR BIOSYNTHESIS, KEGG LINOLEIC ACID METABOLISM, KEGG RETINOL METABOLISM, KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM, KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450, KEGG DRUG METABOLISM CYTOCHROME P450

    • And common core enriched genes are UGT1A1, UGT1A3, UGT1A4, UGT1A5, UGT1A6, UGT1A9, UGT2B10, UGT2B11, UGT2B28, UGT2B4

  • clus3

    • Top enriched gene sets are KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS, KEGG GLUTATHIONE METABOLISM, KEGG RETINOL METABOLISM, KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM, KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450, KEGG DRUG METABOLISM OTHER ENZYMES, KEGG BASAL TRANSCRIPTION FACTORS, BIOCARTA EGF PATHWAY, PID TRAIL PATHWAY, PID IGF1 PATHWAY

    • And common core enriched genes are ATF1, ATF2, CREB1, RPS6KA5, UGT1A1, UGT1A10, UGT1A3, UGT1A4, UGT1A5, UGT1A6

  • clus4

    • Top enriched gene sets are KEGG PYRIMIDINE METABOLISM, KEGG DNA REPLICATION, KEGG PROTEASOME, KEGG NUCLEOTIDE EXCISION REPAIR, KEGG CELL CYCLE, KEGG SNARE INTERACTIONS IN VESICULAR TRANSPORT, KEGG ANTIGEN PROCESSING AND PRESENTATION, KEGG TOLL LIKE RECEPTOR SIGNALING PATHWAY, KEGG NOD LIKE RECEPTOR SIGNALING PATHWAY, KEGG RIG I LIKE RECEPTOR SIGNALING PATHWAY

    • And common core enriched genes are PSMA1, PSMA2, PSMA3, PSMA5, PSMA6, PSMA7, PSMB2, PSMB5, PSMB7, PSMB8

  • clus5

    • Top enriched gene sets are KEGG LYSINE DEGRADATION, KEGG RNA DEGRADATION, KEGG DNA REPLICATION, KEGG SPLICEOSOME, KEGG NUCLEOTIDE EXCISION REPAIR, KEGG HOMOLOGOUS RECOMBINATION, KEGG CELL CYCLE, KEGG OOCYTE MEIOSIS, BIOCARTA CHREBP2 PATHWAY, PID FANCONI PATHWAY

    • And common core enriched genes are POLR2F, POLR2H, POLR2K, ERCC2, ERCC3, GTF2H2, GTF2H2B, GTF2H3, GTF2H4, MNAT1

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 PURINE METABOLISM 151 genes.ES.table 0.48 1.9 0 0.049 0.26 0.2 0.17 0.17 0 0.008
KEGG GLYCINE SERINE AND THREONINE METABOLISM 30 genes.ES.table 0.49 1.2 0.21 0.24 1 0.2 0.088 0.18 0.21 0
KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION 44 genes.ES.table 0.45 1.5 0.052 0.085 0.96 0.2 0.22 0.16 0.049 0
KEGG ARGININE AND PROLINE METABOLISM 52 genes.ES.table 0.42 1.3 0.1 0.18 1 0.31 0.23 0.24 0.14 0
KEGG HISTIDINE METABOLISM 29 genes.ES.table 0.45 1.3 0.17 0.23 1 0.24 0.19 0.2 0.2 0
KEGG TYROSINE METABOLISM 40 genes.ES.table 0.52 1.4 0.086 0.15 0.99 0.22 0.11 0.2 0.11 0
KEGG TRYPTOPHAN METABOLISM 38 genes.ES.table 0.58 1.6 0.0057 0.061 0.88 0.29 0.14 0.25 0.027 0
KEGG O GLYCAN BIOSYNTHESIS 29 genes.ES.table 0.57 1.5 0.02 0.09 0.96 0.31 0.18 0.26 0.055 0
KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM 44 genes.ES.table 0.4 1.5 0.086 0.097 0.97 0.39 0.34 0.26 0.061 0
KEGG GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE 26 genes.ES.table 0.56 1.6 0.018 0.063 0.89 0.19 0.11 0.17 0.029 0
genes ES table in pathway: KEGG PURINE METABOLISM

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 IGF1 IGF1 IGF1 4 1.1 0.18 YES
2 PIK3R5 PIK3R5 PIK3R5 731 0.57 0.23 YES
3 PIK3CG PIK3CG PIK3CG 1150 0.49 0.29 YES
4 AKT3 AKT3 AKT3 1222 0.48 0.37 YES
5 FIGF FIGF FIGF 1947 0.36 0.39 YES
6 PIK3CD PIK3CD PIK3CD 2055 0.35 0.44 YES
7 RPS6KA2 RPS6KA2 RPS6KA2 2398 0.3 0.47 YES
8 VEGFC VEGFC VEGFC 2591 0.28 0.51 YES
9 PRKAA2 PRKAA2 PRKAA2 2741 0.26 0.54 YES
10 VEGFB VEGFB VEGFB 3905 0.16 0.5 NO
11 ULK2 ULK2 ULK2 4630 0.12 0.48 NO
12 PIK3R1 PIK3R1 PIK3R1 5416 0.082 0.46 NO
13 PIK3R3 PIK3R3 PIK3R3 5581 0.076 0.46 NO
14 MAPK3 MAPK3 MAPK3 5941 0.065 0.45 NO
15 CAB39L CAB39L CAB39L 6102 0.06 0.45 NO
16 CAB39 CAB39 CAB39 7590 0.026 0.37 NO
17 HIF1A HIF1A HIF1A 7630 0.025 0.38 NO
18 EIF4E2 EIF4E2 EIF4E2 7853 0.021 0.37 NO
19 PIK3CA PIK3CA PIK3CA 7893 0.02 0.37 NO
20 DDIT4 DDIT4 DDIT4 8084 0.017 0.36 NO
21 RHEB RHEB RHEB 8117 0.017 0.36 NO
22 PGF PGF PGF 8132 0.016 0.36 NO
23 RPS6KA3 RPS6KA3 RPS6KA3 8594 0.0093 0.34 NO
24 RPTOR RPTOR RPTOR 8738 0.0072 0.33 NO
25 EIF4B EIF4B EIF4B 9182 0.0014 0.31 NO
26 STRADA STRADA STRADA 9241 0.00086 0.3 NO
27 MAPK1 MAPK1 MAPK1 9403 -0.0012 0.3 NO
28 AKT2 AKT2 AKT2 9424 -0.0015 0.3 NO
29 PIK3CB PIK3CB PIK3CB 9500 -0.0025 0.29 NO
30 TSC2 TSC2 TSC2 10144 -0.0097 0.26 NO
31 AKT1 AKT1 AKT1 10608 -0.015 0.24 NO
32 PRKAA1 PRKAA1 PRKAA1 10716 -0.017 0.23 NO
33 STK11 STK11 STK11 10862 -0.018 0.23 NO
34 ULK1 ULK1 ULK1 11091 -0.021 0.22 NO
35 PDPK1 PDPK1 PDPK1 11211 -0.022 0.22 NO
36 MLST8 MLST8 MLST8 11305 -0.023 0.21 NO
37 MTOR MTOR MTOR 11465 -0.025 0.21 NO
38 RICTOR RICTOR RICTOR 12089 -0.032 0.18 NO
39 RPS6KA6 RPS6KA6 RPS6KA6 12289 -0.034 0.18 NO
40 RPS6KB1 RPS6KB1 RPS6KB1 12925 -0.042 0.15 NO
41 RPS6KA1 RPS6KA1 RPS6KA1 13331 -0.047 0.13 NO
42 RPS6 RPS6 RPS6 13500 -0.05 0.13 NO
43 RPS6KB2 RPS6KB2 RPS6KB2 13557 -0.05 0.14 NO
44 TSC1 TSC1 TSC1 13570 -0.05 0.14 NO
45 PIK3R2 PIK3R2 PIK3R2 13683 -0.052 0.15 NO
46 ULK3 ULK3 ULK3 14060 -0.058 0.14 NO
47 EIF4E EIF4E EIF4E 14998 -0.075 0.097 NO
48 EIF4EBP1 EIF4EBP1 EIF4EBP1 15051 -0.076 0.11 NO
49 BRAF BRAF BRAF 17216 -0.16 0.015 NO
50 VEGFA VEGFA VEGFA 17895 -0.24 0.017 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 PURINE METABOLISM.

Figure S2.  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 GLYCINE SERINE AND THREONINE METABOLISM

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 PDE1A PDE1A PDE1A 23 0.96 0.062 YES
2 ADCY5 ADCY5 ADCY5 241 0.72 0.098 YES
3 ADCYAP1 ADCYAP1 ADCYAP1 343 0.67 0.14 YES
4 ADCY2 ADCY2 ADCY2 366 0.66 0.18 YES
5 PDE1B PDE1B PDE1B 879 0.54 0.19 YES
6 NTRK2 NTRK2 NTRK2 1005 0.52 0.21 YES
7 MEF2C MEF2C MEF2C 1132 0.49 0.24 YES
8 ADCY4 ADCY4 ADCY4 1152 0.49 0.27 YES
9 NTRK1 NTRK1 NTRK1 1182 0.48 0.3 YES
10 AKT3 AKT3 AKT3 1222 0.48 0.33 YES
11 NGF NGF NGF 1564 0.42 0.34 YES
12 ADORA2A ADORA2A ADORA2A 1654 0.41 0.36 YES
13 PRKAR2B PRKAR2B PRKAR2B 1713 0.4 0.38 YES
14 SHC2 SHC2 SHC2 2050 0.35 0.39 YES
15 IRS2 IRS2 IRS2 2259 0.32 0.4 YES
16 ADCYAP1R1 ADCYAP1R1 ADCYAP1R1 2294 0.32 0.42 YES
17 NR4A1 NR4A1 NR4A1 2322 0.31 0.44 YES
18 CAMK4 CAMK4 CAMK4 2394 0.3 0.45 YES
19 RPS6KA2 RPS6KA2 RPS6KA2 2398 0.3 0.47 YES
20 DNM1 DNM1 DNM1 2677 0.26 0.48 YES
21 MAPK11 MAPK11 MAPK11 2764 0.26 0.49 YES
22 ADCY9 ADCY9 ADCY9 2957 0.24 0.49 YES
23 PRKCG PRKCG PRKCG 3351 0.2 0.48 NO
24 MAPK12 MAPK12 MAPK12 3725 0.17 0.47 NO
25 ADCY7 ADCY7 ADCY7 3758 0.17 0.48 NO
26 ITPR2 ITPR2 ITPR2 4148 0.14 0.47 NO
27 FOXO1 FOXO1 FOXO1 4160 0.14 0.48 NO
28 DUSP3 DUSP3 DUSP3 4455 0.12 0.47 NO
29 RAPGEF1 RAPGEF1 RAPGEF1 4573 0.12 0.47 NO
30 SH3GL2 SH3GL2 SH3GL2 4627 0.12 0.48 NO
31 RAP1A RAP1A RAP1A 4954 0.1 0.47 NO
32 PRKAR2A PRKAR2A PRKAR2A 4975 0.099 0.47 NO
33 MEF2A MEF2A MEF2A 5150 0.092 0.47 NO
34 FOXO3 FOXO3 FOXO3 5321 0.085 0.47 NO
35 PIK3R1 PIK3R1 PIK3R1 5416 0.082 0.47 NO
36 AP2A2 AP2A2 AP2A2 5450 0.081 0.47 NO
37 PRKACB PRKACB PRKACB 5560 0.076 0.47 NO
38 STAT3 STAT3 STAT3 5586 0.076 0.47 NO
39 RHOA RHOA RHOA 5622 0.074 0.48 NO
40 FOXO4 FOXO4 FOXO4 5653 0.073 0.48 NO
41 CDKN1B CDKN1B CDKN1B 5709 0.071 0.48 NO
42 PRKCA PRKCA PRKCA 5733 0.07 0.48 NO
43 PTEN PTEN PTEN 5863 0.067 0.48 NO
44 MAPK3 MAPK3 MAPK3 5941 0.065 0.48 NO
45 RALB RALB RALB 6044 0.062 0.48 NO
46 MAP2K5 MAP2K5 MAP2K5 6110 0.06 0.48 NO
47 MAPKAPK2 MAPKAPK2 MAPKAPK2 6354 0.054 0.47 NO
48 CALM2 CALM2 CALM2 6510 0.05 0.46 NO
49 PRKCE PRKCE PRKCE 6534 0.049 0.47 NO
50 ADCY3 ADCY3 ADCY3 6589 0.047 0.47 NO
51 TRIB3 TRIB3 TRIB3 6628 0.046 0.47 NO
52 GRB2 GRB2 GRB2 6660 0.046 0.47 NO
53 MAPKAP1 MAPKAP1 MAPKAP1 6756 0.043 0.47 NO
54 MAPK7 MAPK7 MAPK7 6786 0.042 0.47 NO
55 MAPK14 MAPK14 MAPK14 6798 0.042 0.47 NO
56 CALM3 CALM3 CALM3 6871 0.04 0.47 NO
57 PPP2CB PPP2CB PPP2CB 6898 0.039 0.47 NO
58 CALM1 CALM1 CALM1 7048 0.036 0.46 NO
59 PRKAR1A PRKAR1A PRKAR1A 7276 0.032 0.45 NO
60 AP2B1 AP2B1 AP2B1 7491 0.028 0.44 NO
61 AP2A1 AP2A1 AP2A1 7626 0.025 0.44 NO
62 MAPKAPK3 MAPKAPK3 MAPKAPK3 7654 0.024 0.44 NO
63 PRKACA PRKACA PRKACA 7759 0.023 0.43 NO
64 PIK3CA PIK3CA PIK3CA 7893 0.02 0.43 NO
65 BAD BAD BAD 8050 0.018 0.42 NO
66 CDKN1A CDKN1A CDKN1A 8136 0.016 0.42 NO
67 CHUK CHUK CHUK 8322 0.014 0.41 NO
68 SHC1 SHC1 SHC1 8481 0.011 0.4 NO
69 CLTC CLTC CLTC 8561 0.0097 0.4 NO
70 PLCG1 PLCG1 PLCG1 8576 0.0096 0.4 NO
71 RPS6KA3 RPS6KA3 RPS6KA3 8594 0.0093 0.39 NO
72 AP2S1 AP2S1 AP2S1 8870 0.0055 0.38 NO
73 AP2M1 AP2M1 AP2M1 8953 0.0043 0.38 NO
74 CREB1 CREB1 CREB1 9002 0.0036 0.37 NO
75 SHC3 SHC3 SHC3 9114 0.0023 0.37 NO
76 MAP2K2 MAP2K2 MAP2K2 9219 0.0011 0.36 NO
77 KIDINS220 KIDINS220 KIDINS220 9223 0.0011 0.36 NO
78 IRS1 IRS1 IRS1 9384 -0.00091 0.35 NO
79 MAPK1 MAPK1 MAPK1 9403 -0.0012 0.35 NO
80 AKT2 AKT2 AKT2 9424 -0.0015 0.35 NO
81 CLTA CLTA CLTA 9450 -0.0018 0.35 NO
82 PIK3CB PIK3CB PIK3CB 9500 -0.0025 0.35 NO
83 ADCY6 ADCY6 ADCY6 9505 -0.0025 0.35 NO
84 RIT1 RIT1 RIT1 9520 -0.0026 0.35 NO
85 SOS1 SOS1 SOS1 9638 -0.004 0.34 NO
86 RALA RALA RALA 9688 -0.0047 0.34 NO
87 CRK CRK CRK 9730 -0.0051 0.34 NO
88 PPP2R1A PPP2R1A PPP2R1A 9760 -0.0054 0.33 NO
89 MAP2K1 MAP2K1 MAP2K1 10073 -0.0089 0.32 NO
90 TSC2 TSC2 TSC2 10144 -0.0097 0.31 NO
91 ELK1 ELK1 ELK1 10166 -0.0099 0.31 NO
92 ATF1 ATF1 ATF1 10248 -0.011 0.31 NO
93 PRKCD PRKCD PRKCD 10384 -0.013 0.3 NO
94 CASP9 CASP9 CASP9 10527 -0.014 0.3 NO
95 AKT1 AKT1 AKT1 10608 -0.015 0.29 NO
96 MDM2 MDM2 MDM2 10686 -0.016 0.29 NO
97 YWHAB YWHAB YWHAB 10763 -0.017 0.29 NO
98 THEM4 THEM4 THEM4 10836 -0.018 0.28 NO
99 AKT1S1 AKT1S1 AKT1S1 10984 -0.02 0.28 NO
100 FRS2 FRS2 FRS2 10990 -0.02 0.28 NO
101 PDPK1 PDPK1 PDPK1 11211 -0.022 0.27 NO
102 MLST8 MLST8 MLST8 11305 -0.023 0.26 NO
103 GSK3A GSK3A GSK3A 11372 -0.024 0.26 NO
104 RPS6KA5 RPS6KA5 RPS6KA5 11394 -0.024 0.26 NO
105 MTOR MTOR MTOR 11465 -0.025 0.26 NO
106 RAF1 RAF1 RAF1 11660 -0.027 0.25 NO
107 DUSP4 DUSP4 DUSP4 11678 -0.027 0.25 NO
108 PPP2R5D PPP2R5D PPP2R5D 11857 -0.029 0.24 NO
109 ADRBK1 ADRBK1 ADRBK1 11890 -0.03 0.24 NO
110 NRAS NRAS NRAS 11928 -0.03 0.24 NO
111 DNAL4 DNAL4 DNAL4 11941 -0.03 0.24 NO
112 RICTOR RICTOR RICTOR 12089 -0.032 0.24 NO
113 DNM2 DNM2 DNM2 12366 -0.035 0.23 NO
114 PPP2CA PPP2CA PPP2CA 12646 -0.038 0.21 NO
115 KRAS KRAS KRAS 12912 -0.042 0.2 NO
116 RALGDS RALGDS RALGDS 13295 -0.046 0.18 NO
117 RPS6KA1 RPS6KA1 RPS6KA1 13331 -0.047 0.18 NO
118 ADCY1 ADCY1 ADCY1 13422 -0.048 0.18 NO
119 PRKAR1B PRKAR1B PRKAR1B 13466 -0.049 0.18 NO
120 RPS6KB2 RPS6KB2 RPS6KB2 13557 -0.05 0.18 NO
121 PIK3R2 PIK3R2 PIK3R2 13683 -0.052 0.18 NO
122 PPP2R1B PPP2R1B PPP2R1B 14414 -0.064 0.14 NO
123 MAPK13 MAPK13 MAPK13 14419 -0.064 0.15 NO
124 ITPR3 ITPR3 ITPR3 14914 -0.073 0.12 NO
125 SRC SRC SRC 15238 -0.08 0.11 NO
126 DUSP7 DUSP7 DUSP7 16125 -0.11 0.069 NO
127 DUSP6 DUSP6 DUSP6 16495 -0.12 0.057 NO
128 HRAS HRAS HRAS 16604 -0.13 0.059 NO
129 PHLPP1 PHLPP1 PHLPP1 16773 -0.13 0.059 NO
130 CDK1 CDK1 CDK1 16896 -0.14 0.061 NO
131 BRAF BRAF BRAF 17216 -0.16 0.054 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 GLYCINE SERINE AND THREONINE METABOLISM.

Figure S4.  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 VALINE LEUCINE AND ISOLEUCINE DEGRADATION

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 CTSG CTSG CTSG 42 0.91 0.074 YES
2 CTSK CTSK CTSK 578 0.6 0.094 YES
3 AP1S2 AP1S2 AP1S2 1661 0.41 0.068 YES
4 SLC11A1 SLC11A1 SLC11A1 1797 0.39 0.093 YES
5 LAPTM5 LAPTM5 LAPTM5 1935 0.36 0.12 YES
6 ARSG ARSG ARSG 2238 0.32 0.13 YES
7 CTSW CTSW CTSW 2492 0.29 0.14 YES
8 HYAL1 HYAL1 HYAL1 2639 0.27 0.15 YES
9 ATP6V0D2 ATP6V0D2 ATP6V0D2 2747 0.26 0.17 YES
10 CTSO CTSO CTSO 2842 0.25 0.18 YES
11 ARSB ARSB ARSB 2845 0.25 0.2 YES
12 CTSF CTSF CTSF 3013 0.23 0.21 YES
13 ACP5 ACP5 ACP5 3104 0.22 0.23 YES
14 SMPD1 SMPD1 SMPD1 3133 0.22 0.24 YES
15 DNASE2B DNASE2B DNASE2B 3136 0.22 0.26 YES
16 CD68 CD68 CD68 3261 0.21 0.27 YES
17 CTSS CTSS CTSS 3521 0.19 0.27 YES
18 AP3B2 AP3B2 AP3B2 3733 0.17 0.28 YES
19 CTSL1 CTSL1 CTSL1 3830 0.17 0.28 YES
20 CTSZ CTSZ CTSZ 4024 0.15 0.29 YES
21 LIPA LIPA LIPA 4125 0.15 0.29 YES
22 LAMP3 LAMP3 LAMP3 4196 0.14 0.3 YES
23 CTSB CTSB CTSB 4253 0.14 0.31 YES
24 TPP1 TPP1 TPP1 4328 0.13 0.32 YES
25 ABCA2 ABCA2 ABCA2 4338 0.13 0.33 YES
26 PSAP PSAP PSAP 4707 0.11 0.32 YES
27 AP4S1 AP4S1 AP4S1 4711 0.11 0.32 YES
28 SLC17A5 SLC17A5 SLC17A5 4754 0.11 0.33 YES
29 PLA2G15 PLA2G15 PLA2G15 4757 0.11 0.34 YES
30 CLTCL1 CLTCL1 CLTCL1 4829 0.11 0.35 YES
31 MAN2B1 MAN2B1 MAN2B1 4836 0.1 0.35 YES
32 HEXB HEXB HEXB 4967 0.1 0.36 YES
33 SORT1 SORT1 SORT1 5002 0.098 0.36 YES
34 ASAH1 ASAH1 ASAH1 5119 0.093 0.36 YES
35 CTNS CTNS CTNS 5129 0.093 0.37 YES
36 NAGLU NAGLU NAGLU 5194 0.09 0.37 YES
37 ATP6V0D1 ATP6V0D1 ATP6V0D1 5207 0.09 0.38 YES
38 LGMN LGMN LGMN 5219 0.09 0.39 YES
39 FUCA1 FUCA1 FUCA1 5234 0.089 0.39 YES
40 GLB1 GLB1 GLB1 5249 0.088 0.4 YES
41 ACP2 ACP2 ACP2 5366 0.084 0.4 YES
42 CTSA CTSA CTSA 5410 0.082 0.41 YES
43 IDS IDS IDS 5428 0.082 0.41 YES
44 NAGA NAGA NAGA 5481 0.079 0.42 YES
45 CLN5 CLN5 CLN5 5512 0.078 0.42 YES
46 ATP6V0A4 ATP6V0A4 ATP6V0A4 5573 0.076 0.42 YES
47 NPC2 NPC2 NPC2 5644 0.074 0.43 YES
48 MANBA MANBA MANBA 5726 0.07 0.43 YES
49 NPC1 NPC1 NPC1 5727 0.07 0.43 YES
50 GAA GAA GAA 5734 0.07 0.44 YES
51 NEU1 NEU1 NEU1 5758 0.07 0.44 YES
52 GNS GNS GNS 5837 0.067 0.44 YES
53 GBA GBA GBA 5860 0.067 0.45 YES
54 ATP6V0A1 ATP6V0A1 ATP6V0A1 5893 0.066 0.45 YES
55 SCARB2 SCARB2 SCARB2 5907 0.066 0.46 YES
56 HEXA HEXA HEXA 5945 0.064 0.46 YES
57 GALC GALC GALC 5987 0.064 0.46 YES
58 NAGPA NAGPA NAGPA 6006 0.063 0.47 YES
59 IDUA IDUA IDUA 6024 0.062 0.47 YES
60 GGA2 GGA2 GGA2 6131 0.059 0.47 YES
61 LAMP2 LAMP2 LAMP2 6146 0.059 0.48 YES
62 PPT1 PPT1 PPT1 6153 0.059 0.48 YES
63 DNASE2 DNASE2 DNASE2 6217 0.057 0.48 YES
64 AP4B1 AP4B1 AP4B1 6266 0.056 0.48 YES
65 MCOLN1 MCOLN1 MCOLN1 6283 0.055 0.49 YES
66 CLTB CLTB CLTB 6294 0.055 0.49 YES
67 CD63 CD63 CD63 6428 0.052 0.49 YES
68 ARSA ARSA ARSA 6435 0.051 0.49 YES
69 SGSH SGSH SGSH 6463 0.051 0.5 YES
70 GUSB GUSB GUSB 6537 0.048 0.5 YES
71 LAMP1 LAMP1 LAMP1 6561 0.048 0.5 YES
72 CTSH CTSH CTSH 6714 0.044 0.49 NO
73 AP3S2 AP3S2 AP3S2 6816 0.042 0.49 NO
74 CTSD CTSD CTSD 6833 0.041 0.49 NO
75 ATP6V0A2 ATP6V0A2 ATP6V0A2 6861 0.04 0.5 NO
76 TCIRG1 TCIRG1 TCIRG1 7077 0.035 0.49 NO
77 GNPTG GNPTG GNPTG 7087 0.035 0.49 NO
78 LAPTM4A LAPTM4A LAPTM4A 7255 0.032 0.48 NO
79 CTSE CTSE CTSE 7277 0.032 0.48 NO
80 IGF2R IGF2R IGF2R 7291 0.032 0.48 NO
81 AP1M1 AP1M1 AP1M1 7468 0.028 0.48 NO
82 GALNS GALNS GALNS 7494 0.028 0.48 NO
83 GNPTAB GNPTAB GNPTAB 7558 0.026 0.48 NO
84 AP3S1 AP3S1 AP3S1 7976 0.019 0.46 NO
85 AP4E1 AP4E1 AP4E1 8370 0.013 0.44 NO
86 CLTC CLTC CLTC 8561 0.0097 0.43 NO
87 CLN3 CLN3 CLN3 8607 0.009 0.42 NO
88 ATP6V0C ATP6V0C ATP6V0C 8787 0.0066 0.42 NO
89 AP3M1 AP3M1 AP3M1 8894 0.0052 0.41 NO
90 SUMF1 SUMF1 SUMF1 8996 0.0036 0.4 NO
91 M6PR M6PR M6PR 9203 0.0013 0.39 NO
92 AP3D1 AP3D1 AP3D1 9300 0.00011 0.39 NO
93 ATP6V0B ATP6V0B ATP6V0B 9303 0.000072 0.39 NO
94 ATP6AP1 ATP6AP1 ATP6AP1 9395 -0.0011 0.38 NO
95 HGSNAT HGSNAT HGSNAT 9436 -0.0016 0.38 NO
96 CLTA CLTA CLTA 9450 -0.0018 0.38 NO
97 AP1B1 AP1B1 AP1B1 9861 -0.0064 0.36 NO
98 CD164 CD164 CD164 10056 -0.0087 0.35 NO
99 AP3B1 AP3B1 AP3B1 10438 -0.013 0.33 NO
100 AP4M1 AP4M1 AP4M1 10593 -0.015 0.32 NO
101 ENTPD4 ENTPD4 ENTPD4 10851 -0.018 0.31 NO
102 CTSC CTSC CTSC 10896 -0.019 0.31 NO
103 GM2A GM2A GM2A 10987 -0.02 0.3 NO
104 ATP6V1H ATP6V1H ATP6V1H 11006 -0.02 0.3 NO
105 GGA3 GGA3 GGA3 11157 -0.021 0.3 NO
106 AP1G1 AP1G1 AP1G1 11500 -0.025 0.28 NO
107 PPT2 PPT2 PPT2 11568 -0.026 0.28 NO
108 GLA GLA GLA 11584 -0.026 0.28 NO
109 NAPSA NAPSA NAPSA 13202 -0.045 0.2 NO
110 SLC11A2 SLC11A2 SLC11A2 13294 -0.046 0.19 NO
111 GGA1 GGA1 GGA1 13370 -0.048 0.19 NO
112 AGA AGA AGA 13373 -0.048 0.2 NO
113 LAPTM4B LAPTM4B LAPTM4B 13861 -0.055 0.18 NO
114 ABCB9 ABCB9 ABCB9 13998 -0.057 0.17 NO
115 MFSD8 MFSD8 MFSD8 14168 -0.06 0.17 NO
116 AP1S1 AP1S1 AP1S1 14968 -0.074 0.13 NO
117 AP3M2 AP3M2 AP3M2 15421 -0.084 0.11 NO
118 CTSL2 CTSL2 CTSL2 15570 -0.088 0.11 NO
119 AP1M2 AP1M2 AP1M2 16375 -0.12 0.076 NO
120 AP1S3 AP1S3 AP1S3 16616 -0.13 0.074 NO
121 PSAPL1 PSAPL1 PSAPL1 17272 -0.17 0.051 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 VALINE LEUCINE AND ISOLEUCINE DEGRADATION.

Figure S6.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG VALINE LEUCINE AND ISOLEUCINE DEGRADATION, 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 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 PDE1A PDE1A PDE1A 23 0.96 0.039 YES
2 ADCY5 ADCY5 ADCY5 241 0.72 0.058 YES
3 ADCYAP1 ADCYAP1 ADCYAP1 343 0.67 0.081 YES
4 ADCY2 ADCY2 ADCY2 366 0.66 0.11 YES
5 RASGRF2 RASGRF2 RASGRF2 571 0.6 0.12 YES
6 PCSK5 PCSK5 PCSK5 581 0.6 0.15 YES
7 NGFR NGFR NGFR 613 0.59 0.17 YES
8 PDE1B PDE1B PDE1B 879 0.54 0.18 YES
9 NTRK2 NTRK2 NTRK2 1005 0.52 0.19 YES
10 MEF2C MEF2C MEF2C 1132 0.49 0.21 YES
11 ADCY4 ADCY4 ADCY4 1152 0.49 0.23 YES
12 NTRK1 NTRK1 NTRK1 1182 0.48 0.25 YES
13 AKT3 AKT3 AKT3 1222 0.48 0.26 YES
14 VAV1 VAV1 VAV1 1231 0.48 0.28 YES
15 NGF NGF NGF 1564 0.42 0.28 YES
16 FGD2 FGD2 FGD2 1577 0.42 0.3 YES
17 TIAM2 TIAM2 TIAM2 1581 0.42 0.32 YES
18 ADORA2A ADORA2A ADORA2A 1654 0.41 0.33 YES
19 PRKAR2B PRKAR2B PRKAR2B 1713 0.4 0.34 YES
20 SHC2 SHC2 SHC2 2050 0.35 0.34 YES
21 RASGRF1 RASGRF1 RASGRF1 2243 0.32 0.34 YES
22 IRS2 IRS2 IRS2 2259 0.32 0.36 YES
23 ADCYAP1R1 ADCYAP1R1 ADCYAP1R1 2294 0.32 0.37 YES
24 NR4A1 NR4A1 NR4A1 2322 0.31 0.38 YES
25 CAMK4 CAMK4 CAMK4 2394 0.3 0.39 YES
26 RPS6KA2 RPS6KA2 RPS6KA2 2398 0.3 0.4 YES
27 KALRN KALRN KALRN 2541 0.28 0.41 YES
28 DNM1 DNM1 DNM1 2677 0.26 0.41 YES
29 ARHGAP4 ARHGAP4 ARHGAP4 2687 0.26 0.42 YES
30 ARHGEF6 ARHGEF6 ARHGEF6 2742 0.26 0.43 YES
31 MAPK11 MAPK11 MAPK11 2764 0.26 0.44 YES
32 PREX1 PREX1 PREX1 2911 0.24 0.44 YES
33 ARHGEF17 ARHGEF17 ARHGEF17 2952 0.24 0.45 YES
34 ADCY9 ADCY9 ADCY9 2957 0.24 0.46 YES
35 MAG MAG MAG 3071 0.23 0.46 YES
36 PRKCG PRKCG PRKCG 3351 0.2 0.45 YES
37 MAPK12 MAPK12 MAPK12 3725 0.17 0.44 YES
38 ADCY7 ADCY7 ADCY7 3758 0.17 0.45 YES
39 FGD3 FGD3 FGD3 3814 0.17 0.45 YES
40 AKAP13 AKAP13 AKAP13 3975 0.16 0.45 YES
41 ARHGEF3 ARHGEF3 ARHGEF3 3995 0.16 0.45 YES
42 ITPR2 ITPR2 ITPR2 4148 0.14 0.45 YES
43 FOXO1 FOXO1 FOXO1 4160 0.14 0.46 YES
44 DUSP3 DUSP3 DUSP3 4455 0.12 0.45 YES
45 PCSK6 PCSK6 PCSK6 4460 0.12 0.45 YES
46 RAPGEF1 RAPGEF1 RAPGEF1 4573 0.12 0.45 YES
47 SH3GL2 SH3GL2 SH3GL2 4627 0.12 0.45 YES
48 APH1B APH1B APH1B 4725 0.11 0.45 YES
49 ARHGEF9 ARHGEF9 ARHGEF9 4812 0.11 0.45 YES
50 ITSN1 ITSN1 ITSN1 4868 0.1 0.45 YES
51 RAP1A RAP1A RAP1A 4954 0.1 0.45 YES
52 PRKAR2A PRKAR2A PRKAR2A 4975 0.099 0.46 YES
53 MEF2A MEF2A MEF2A 5150 0.092 0.45 YES
54 PLEKHG2 PLEKHG2 PLEKHG2 5310 0.086 0.44 YES
55 FOXO3 FOXO3 FOXO3 5321 0.085 0.45 YES
56 FGD4 FGD4 FGD4 5346 0.085 0.45 YES
57 PIK3R1 PIK3R1 PIK3R1 5416 0.082 0.45 YES
58 AP2A2 AP2A2 AP2A2 5450 0.081 0.45 YES
59 OMG OMG OMG 5535 0.077 0.45 YES
60 PRKACB PRKACB PRKACB 5560 0.076 0.45 YES
61 STAT3 STAT3 STAT3 5586 0.076 0.45 YES
62 LINGO1 LINGO1 LINGO1 5604 0.075 0.46 YES
63 RHOA RHOA RHOA 5622 0.074 0.46 YES
64 FOXO4 FOXO4 FOXO4 5653 0.073 0.46 YES
65 ARHGEF2 ARHGEF2 ARHGEF2 5654 0.073 0.46 YES
66 CDKN1B CDKN1B CDKN1B 5709 0.071 0.46 YES
67 PRKCA PRKCA PRKCA 5733 0.07 0.46 YES
68 PTEN PTEN PTEN 5863 0.067 0.46 NO
69 ARHGEF1 ARHGEF1 ARHGEF1 5884 0.066 0.46 NO
70 MAPK3 MAPK3 MAPK3 5941 0.065 0.46 NO
71 RALB RALB RALB 6044 0.062 0.46 NO
72 MAP2K5 MAP2K5 MAP2K5 6110 0.06 0.46 NO
73 PSEN2 PSEN2 PSEN2 6196 0.058 0.45 NO
74 MAPKAPK2 MAPKAPK2 MAPKAPK2 6354 0.054 0.45 NO
75 TRIO TRIO TRIO 6445 0.051 0.44 NO
76 MAGED1 MAGED1 MAGED1 6487 0.05 0.44 NO
77 CALM2 CALM2 CALM2 6510 0.05 0.44 NO
78 PRKCE PRKCE PRKCE 6534 0.049 0.45 NO
79 ADCY3 ADCY3 ADCY3 6589 0.047 0.44 NO
80 TRIB3 TRIB3 TRIB3 6628 0.046 0.44 NO
81 SQSTM1 SQSTM1 SQSTM1 6655 0.046 0.45 NO
82 GRB2 GRB2 GRB2 6660 0.046 0.45 NO
83 MAPKAP1 MAPKAP1 MAPKAP1 6756 0.043 0.44 NO
84 MAPK7 MAPK7 MAPK7 6786 0.042 0.44 NO
85 MAPK14 MAPK14 MAPK14 6798 0.042 0.44 NO
86 CALM3 CALM3 CALM3 6871 0.04 0.44 NO
87 PPP2CB PPP2CB PPP2CB 6898 0.039 0.44 NO
88 ABR ABR ABR 6910 0.039 0.44 NO
89 CALM1 CALM1 CALM1 7048 0.036 0.44 NO
90 PRKAR1A PRKAR1A PRKAR1A 7276 0.032 0.43 NO
91 FGD1 FGD1 FGD1 7406 0.029 0.42 NO
92 BCL2L11 BCL2L11 BCL2L11 7454 0.028 0.42 NO
93 AP2B1 AP2B1 AP2B1 7491 0.028 0.42 NO
94 AP2A1 AP2A1 AP2A1 7626 0.025 0.41 NO
95 MAPKAPK3 MAPKAPK3 MAPKAPK3 7654 0.024 0.41 NO
96 NFKBIA NFKBIA NFKBIA 7714 0.023 0.41 NO
97 PRKACA PRKACA PRKACA 7759 0.023 0.41 NO
98 MYD88 MYD88 MYD88 7860 0.021 0.4 NO
99 RTN4 RTN4 RTN4 7875 0.02 0.4 NO
100 PIK3CA PIK3CA PIK3CA 7893 0.02 0.4 NO
101 MCF2 MCF2 MCF2 8016 0.018 0.4 NO
102 BAD BAD BAD 8050 0.018 0.4 NO
103 CDKN1A CDKN1A CDKN1A 8136 0.016 0.39 NO
104 CHUK CHUK CHUK 8322 0.014 0.38 NO
105 SHC1 SHC1 SHC1 8481 0.011 0.37 NO
106 ARHGEF18 ARHGEF18 ARHGEF18 8540 0.0099 0.37 NO
107 CLTC CLTC CLTC 8561 0.0097 0.37 NO
108 PLCG1 PLCG1 PLCG1 8576 0.0096 0.37 NO
109 RPS6KA3 RPS6KA3 RPS6KA3 8594 0.0093 0.37 NO
110 RELA RELA RELA 8722 0.0074 0.36 NO
111 SOS2 SOS2 SOS2 8864 0.0056 0.36 NO
112 AP2S1 AP2S1 AP2S1 8870 0.0055 0.36 NO
113 AP2M1 AP2M1 AP2M1 8953 0.0043 0.35 NO
114 RIPK2 RIPK2 RIPK2 8974 0.004 0.35 NO
115 IRAK1 IRAK1 IRAK1 8992 0.0037 0.35 NO
116 CREB1 CREB1 CREB1 9002 0.0036 0.35 NO
117 ARHGDIA ARHGDIA ARHGDIA 9046 0.003 0.35 NO
118 SHC3 SHC3 SHC3 9114 0.0023 0.34 NO
119 MAP2K2 MAP2K2 MAP2K2 9219 0.0011 0.34 NO
120 KIDINS220 KIDINS220 KIDINS220 9223 0.0011 0.34 NO
121 FURIN FURIN FURIN 9289 0.00033 0.33 NO
122 APH1A APH1A APH1A 9382 -0.00083 0.33 NO
123 IRS1 IRS1 IRS1 9384 -0.00091 0.33 NO
124 MAPK1 MAPK1 MAPK1 9403 -0.0012 0.33 NO
125 AKT2 AKT2 AKT2 9424 -0.0015 0.33 NO
126 NGEF NGEF NGEF 9428 -0.0016 0.33 NO
127 CLTA CLTA CLTA 9450 -0.0018 0.32 NO
128 PIK3CB PIK3CB PIK3CB 9500 -0.0025 0.32 NO
129 ADCY6 ADCY6 ADCY6 9505 -0.0025 0.32 NO
130 RIT1 RIT1 RIT1 9520 -0.0026 0.32 NO
131 SOS1 SOS1 SOS1 9638 -0.004 0.32 NO
132 RALA RALA RALA 9688 -0.0047 0.31 NO
133 RPS27A RPS27A RPS27A 9725 -0.0051 0.31 NO
134 CRK CRK CRK 9730 -0.0051 0.31 NO
135 PPP2R1A PPP2R1A PPP2R1A 9760 -0.0054 0.31 NO
136 UBA52 UBA52 UBA52 9804 -0.0058 0.31 NO
137 TRAF6 TRAF6 TRAF6 10003 -0.0082 0.3 NO
138 MAP2K1 MAP2K1 MAP2K1 10073 -0.0089 0.29 NO
139 PRKCI PRKCI PRKCI 10129 -0.0094 0.29 NO
140 TSC2 TSC2 TSC2 10144 -0.0097 0.29 NO
141 ELK1 ELK1 ELK1 10166 -0.0099 0.29 NO
142 ATF1 ATF1 ATF1 10248 -0.011 0.29 NO
143 PSEN1 PSEN1 PSEN1 10264 -0.011 0.29 NO
144 PRKCD PRKCD PRKCD 10384 -0.013 0.28 NO
145 CASP3 CASP3 CASP3 10392 -0.013 0.28 NO
146 CASP9 CASP9 CASP9 10527 -0.014 0.27 NO
147 AKT1 AKT1 AKT1 10608 -0.015 0.27 NO
148 ARHGEF4 ARHGEF4 ARHGEF4 10618 -0.015 0.27 NO
149 MDM2 MDM2 MDM2 10686 -0.016 0.27 NO
150 AATF AATF AATF 10690 -0.016 0.27 NO
151 YWHAB YWHAB YWHAB 10763 -0.017 0.26 NO
152 THEM4 THEM4 THEM4 10836 -0.018 0.26 NO
153 PSENEN PSENEN PSENEN 10866 -0.018 0.26 NO
154 AKT1S1 AKT1S1 AKT1S1 10984 -0.02 0.25 NO
155 FRS2 FRS2 FRS2 10990 -0.02 0.25 NO
156 PDPK1 PDPK1 PDPK1 11211 -0.022 0.24 NO
157 ARHGEF12 ARHGEF12 ARHGEF12 11266 -0.023 0.24 NO
158 MLST8 MLST8 MLST8 11305 -0.023 0.24 NO
159 IKBKB IKBKB IKBKB 11369 -0.024 0.24 NO
160 GSK3A GSK3A GSK3A 11372 -0.024 0.24 NO
161 RPS6KA5 RPS6KA5 RPS6KA5 11394 -0.024 0.24 NO
162 RAC1 RAC1 RAC1 11415 -0.024 0.24 NO
163 MTOR MTOR MTOR 11465 -0.025 0.24 NO
164 HDAC3 HDAC3 HDAC3 11475 -0.025 0.24 NO
165 RAF1 RAF1 RAF1 11660 -0.027 0.23 NO
166 DUSP4 DUSP4 DUSP4 11678 -0.027 0.23 NO
167 PPP2R5D PPP2R5D PPP2R5D 11857 -0.029 0.22 NO
168 ADRBK1 ADRBK1 ADRBK1 11890 -0.03 0.22 NO
169 NRAS NRAS NRAS 11928 -0.03 0.22 NO
170 DNAL4 DNAL4 DNAL4 11941 -0.03 0.22 NO
171 NCSTN NCSTN NCSTN 11956 -0.03 0.22 NO
172 NET1 NET1 NET1 11988 -0.031 0.22 NO
173 CASP2 CASP2 CASP2 12010 -0.031 0.22 NO
174 RICTOR RICTOR RICTOR 12089 -0.032 0.22 NO
175 ARHGEF11 ARHGEF11 ARHGEF11 12156 -0.033 0.21 NO
176 PRDM4 PRDM4 PRDM4 12166 -0.033 0.21 NO
177 DNM2 DNM2 DNM2 12366 -0.035 0.2 NO
178 PPP2CA PPP2CA PPP2CA 12646 -0.038 0.19 NO
179 NGFRAP1 NGFRAP1 NGFRAP1 12821 -0.041 0.18 NO
180 KRAS KRAS KRAS 12912 -0.042 0.18 NO
181 TIAM1 TIAM1 TIAM1 12939 -0.042 0.18 NO
182 RALGDS RALGDS RALGDS 13295 -0.046 0.16 NO
183 RPS6KA1 RPS6KA1 RPS6KA1 13331 -0.047 0.16 NO
184 ADAM17 ADAM17 ADAM17 13389 -0.048 0.16 NO
185 ADCY1 ADCY1 ADCY1 13422 -0.048 0.16 NO
186 PRKAR1B PRKAR1B PRKAR1B 13466 -0.049 0.16 NO
187 RPS6KB2 RPS6KB2 RPS6KB2 13557 -0.05 0.16 NO
188 PIK3R2 PIK3R2 PIK3R2 13683 -0.052 0.15 NO
189 YWHAE YWHAE YWHAE 14171 -0.06 0.13 NO
190 PPP2R1B PPP2R1B PPP2R1B 14414 -0.064 0.12 NO
191 MAPK13 MAPK13 MAPK13 14419 -0.064 0.12 NO
192 HDAC1 HDAC1 HDAC1 14649 -0.068 0.11 NO
193 ITPR3 ITPR3 ITPR3 14914 -0.073 0.1 NO
194 SMPD2 SMPD2 SMPD2 14990 -0.075 0.098 NO
195 HDAC2 HDAC2 HDAC2 15076 -0.077 0.097 NO
196 MAPK8 MAPK8 MAPK8 15084 -0.077 0.1 NO
197 SRC SRC SRC 15238 -0.08 0.095 NO
198 ECT2 ECT2 ECT2 15975 -0.1 0.058 NO
199 DUSP7 DUSP7 DUSP7 16125 -0.11 0.054 NO
200 ITGB3BP ITGB3BP ITGB3BP 16142 -0.11 0.058 NO
201 DUSP6 DUSP6 DUSP6 16495 -0.12 0.044 NO
202 HRAS HRAS HRAS 16604 -0.13 0.043 NO
203 PHLPP1 PHLPP1 PHLPP1 16773 -0.13 0.039 NO
204 CDK1 CDK1 CDK1 16896 -0.14 0.039 NO
205 BRAF BRAF BRAF 17216 -0.16 0.028 NO
206 ARHGEF16 ARHGEF16 ARHGEF16 17245 -0.16 0.033 NO
207 OBSCN OBSCN OBSCN 17666 -0.2 0.018 NO
208 VAV3 VAV3 VAV3 18008 -0.26 0.01 NO

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

Figure S8.  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 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 RUNX1T1 RUNX1T1 RUNX1T1 62 0.88 0.1 YES
2 ZBTB16 ZBTB16 ZBTB16 166 0.77 0.19 YES
3 FLT3 FLT3 FLT3 603 0.59 0.24 YES
4 PIK3R5 PIK3R5 PIK3R5 731 0.57 0.3 YES
5 SPI1 SPI1 SPI1 991 0.52 0.34 YES
6 PIK3CG PIK3CG PIK3CG 1150 0.49 0.4 YES
7 AKT3 AKT3 AKT3 1222 0.48 0.45 YES
8 LEF1 LEF1 LEF1 1666 0.4 0.47 YES
9 PIK3CD PIK3CD PIK3CD 2055 0.35 0.49 YES
10 TCF7L1 TCF7L1 TCF7L1 2392 0.3 0.51 YES
11 PIM2 PIM2 PIM2 2552 0.28 0.54 YES
12 KIT KIT KIT 2762 0.26 0.56 YES
13 TCF7 TCF7 TCF7 2836 0.25 0.58 YES
14 STAT5A STAT5A STAT5A 3291 0.21 0.58 NO
15 STAT5B STAT5B STAT5B 5040 0.096 0.5 NO
16 RARA RARA RARA 5086 0.094 0.5 NO
17 PIK3R1 PIK3R1 PIK3R1 5416 0.082 0.5 NO
18 RUNX1 RUNX1 RUNX1 5523 0.078 0.5 NO
19 PIK3R3 PIK3R3 PIK3R3 5581 0.076 0.51 NO
20 STAT3 STAT3 STAT3 5586 0.076 0.52 NO
21 MAPK3 MAPK3 MAPK3 5941 0.065 0.5 NO
22 NFKB1 NFKB1 NFKB1 6345 0.054 0.49 NO
23 GRB2 GRB2 GRB2 6660 0.046 0.48 NO
24 ARAF ARAF ARAF 6679 0.045 0.48 NO
25 CCNA1 CCNA1 CCNA1 7037 0.036 0.46 NO
26 PIM1 PIM1 PIM1 7637 0.025 0.43 NO
27 PML PML PML 7644 0.025 0.44 NO
28 IKBKG IKBKG IKBKG 7740 0.023 0.43 NO
29 PIK3CA PIK3CA PIK3CA 7893 0.02 0.43 NO
30 BAD BAD BAD 8050 0.018 0.42 NO
31 CHUK CHUK CHUK 8322 0.014 0.41 NO
32 RELA RELA RELA 8722 0.0074 0.39 NO
33 SOS2 SOS2 SOS2 8864 0.0056 0.38 NO
34 MYC MYC MYC 9157 0.0017 0.36 NO
35 MAP2K2 MAP2K2 MAP2K2 9219 0.0011 0.36 NO
36 MAPK1 MAPK1 MAPK1 9403 -0.0012 0.35 NO
37 AKT2 AKT2 AKT2 9424 -0.0015 0.35 NO
38 PIK3CB PIK3CB PIK3CB 9500 -0.0025 0.35 NO
39 SOS1 SOS1 SOS1 9638 -0.004 0.34 NO
40 MAP2K1 MAP2K1 MAP2K1 10073 -0.0089 0.32 NO
41 AKT1 AKT1 AKT1 10608 -0.015 0.29 NO
42 IKBKB IKBKB IKBKB 11369 -0.024 0.25 NO
43 MTOR MTOR MTOR 11465 -0.025 0.25 NO
44 RAF1 RAF1 RAF1 11660 -0.027 0.24 NO
45 NRAS NRAS NRAS 11928 -0.03 0.23 NO
46 TCF7L2 TCF7L2 TCF7L2 11930 -0.03 0.23 NO
47 KRAS KRAS KRAS 12912 -0.042 0.18 NO
48 RPS6KB1 RPS6KB1 RPS6KB1 12925 -0.042 0.19 NO
49 PPARD PPARD PPARD 13438 -0.049 0.17 NO
50 RPS6KB2 RPS6KB2 RPS6KB2 13557 -0.05 0.16 NO
51 PIK3R2 PIK3R2 PIK3R2 13683 -0.052 0.16 NO
52 CCND1 CCND1 CCND1 14702 -0.069 0.12 NO
53 EIF4EBP1 EIF4EBP1 EIF4EBP1 15051 -0.076 0.11 NO
54 CEBPA CEBPA CEBPA 16364 -0.12 0.048 NO
55 HRAS HRAS HRAS 16604 -0.13 0.05 NO
56 JUP JUP JUP 17040 -0.15 0.044 NO
57 BRAF BRAF BRAF 17216 -0.16 0.054 NO

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

Figure S10.  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 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 MYOCD MYOCD MYOCD 298 0.69 0.029 YES
2 BLK BLK BLK 397 0.66 0.067 YES
3 PIK3R6 PIK3R6 PIK3R6 525 0.61 0.1 YES
4 ITGB3 ITGB3 ITGB3 728 0.57 0.13 YES
5 PIK3R5 PIK3R5 PIK3R5 731 0.57 0.16 YES
6 SLA SLA SLA 746 0.56 0.2 YES
7 TAGLN TAGLN TAGLN 753 0.56 0.24 YES
8 ACTA2 ACTA2 ACTA2 854 0.54 0.27 YES
9 PIK3CG PIK3CG PIK3CG 1150 0.49 0.28 YES
10 HCK HCK HCK 1225 0.48 0.31 YES
11 S1PR1 S1PR1 S1PR1 1290 0.47 0.34 YES
12 LCK LCK LCK 1406 0.45 0.36 YES
13 PDGFRB PDGFRB PDGFRB 1512 0.43 0.38 YES
14 SPHK1 SPHK1 SPHK1 1873 0.37 0.39 YES
15 PIK3CD PIK3CD PIK3CD 2055 0.35 0.4 YES
16 FYN FYN FYN 2169 0.33 0.42 YES
17 FGR FGR FGR 2438 0.3 0.42 YES
18 PTPRJ PTPRJ PTPRJ 2465 0.29 0.44 YES
19 LRP1 LRP1 LRP1 2772 0.26 0.44 YES
20 PDGFB PDGFB PDGFB 2959 0.24 0.44 YES
21 DOCK4 DOCK4 DOCK4 3053 0.23 0.45 YES
22 STAT5A STAT5A STAT5A 3291 0.21 0.46 YES
23 JAK2 JAK2 JAK2 3658 0.18 0.45 YES
24 CYFIP2 CYFIP2 CYFIP2 3701 0.18 0.46 YES
25 DOK1 DOK1 DOK1 3709 0.18 0.47 YES
26 LYN LYN LYN 3836 0.16 0.47 YES
27 SLC9A3R2 SLC9A3R2 SLC9A3R2 4183 0.14 0.46 YES
28 PPP2R2B PPP2R2B PPP2R2B 4186 0.14 0.47 YES
29 ITGAV ITGAV ITGAV 4218 0.14 0.48 YES
30 GAB1 GAB1 GAB1 4454 0.12 0.47 YES
31 ABL1 ABL1 ABL1 4485 0.12 0.48 YES
32 RAPGEF1 RAPGEF1 RAPGEF1 4573 0.12 0.48 YES
33 SIPA1 SIPA1 SIPA1 4625 0.12 0.49 YES
34 JUN JUN JUN 4720 0.11 0.49 YES
35 FOS FOS FOS 4761 0.11 0.49 YES
36 PLA2G4A PLA2G4A PLA2G4A 4814 0.11 0.5 YES
37 EPS8 EPS8 EPS8 4940 0.1 0.5 YES
38 RAP1A RAP1A RAP1A 4954 0.1 0.5 YES
39 JUND JUND JUND 5001 0.098 0.51 YES
40 SRF SRF SRF 5008 0.098 0.51 YES
41 STAT5B STAT5B STAT5B 5040 0.096 0.52 YES
42 ARPC1B ARPC1B ARPC1B 5075 0.095 0.52 YES
43 PIK3R1 PIK3R1 PIK3R1 5416 0.082 0.51 YES
44 STAT1 STAT1 STAT1 5421 0.082 0.52 YES
45 PIK3R3 PIK3R3 PIK3R3 5581 0.076 0.51 YES
46 STAT3 STAT3 STAT3 5586 0.076 0.52 YES
47 RHOA RHOA RHOA 5622 0.074 0.52 YES
48 PRKCA PRKCA PRKCA 5733 0.07 0.52 YES
49 YWHAH YWHAH YWHAH 5762 0.07 0.52 YES
50 KSR1 KSR1 KSR1 5844 0.067 0.52 YES
51 PTEN PTEN PTEN 5863 0.067 0.52 YES
52 MAPK3 MAPK3 MAPK3 5941 0.065 0.52 YES
53 BAIAP2 BAIAP2 BAIAP2 5985 0.064 0.52 YES
54 IQGAP1 IQGAP1 IQGAP1 6444 0.051 0.5 NO
55 PRKCE PRKCE PRKCE 6534 0.049 0.5 NO
56 GRB2 GRB2 GRB2 6660 0.046 0.5 NO
57 PIN1 PIN1 PIN1 6777 0.043 0.49 NO
58 USP6NL USP6NL USP6NL 7138 0.034 0.48 NO
59 PTPN1 PTPN1 PTPN1 7159 0.034 0.48 NO
60 BCAR1 BCAR1 BCAR1 7197 0.033 0.48 NO
61 ARPC4 ARPC4 ARPC4 7209 0.033 0.48 NO
62 RAP1B RAP1B RAP1B 7223 0.033 0.48 NO
63 ACTN4 ACTN4 ACTN4 7399 0.03 0.47 NO
64 ARPC5 ARPC5 ARPC5 7569 0.026 0.46 NO
65 CBL CBL CBL 7640 0.025 0.46 NO
66 CSK CSK CSK 7766 0.022 0.46 NO
67 PIK3CA PIK3CA PIK3CA 7893 0.02 0.45 NO
68 ARAP1 ARAP1 ARAP1 7944 0.02 0.45 NO
69 RASA1 RASA1 RASA1 8103 0.017 0.44 NO
70 MAPK9 MAPK9 MAPK9 8111 0.017 0.44 NO
71 GRB10 GRB10 GRB10 8188 0.015 0.44 NO
72 NCK1 NCK1 NCK1 8328 0.013 0.43 NO
73 MAPK10 MAPK10 MAPK10 8384 0.012 0.43 NO
74 ACTR2 ACTR2 ACTR2 8439 0.012 0.43 NO
75 SHC1 SHC1 SHC1 8481 0.011 0.43 NO
76 WASF2 WASF2 WASF2 8560 0.0097 0.42 NO
77 PLCG1 PLCG1 PLCG1 8576 0.0096 0.42 NO
78 RPS6KA3 RPS6KA3 RPS6KA3 8594 0.0093 0.42 NO
79 ACTR3 ACTR3 ACTR3 8781 0.0067 0.41 NO
80 PAG1 PAG1 PAG1 8825 0.0062 0.41 NO
81 ARPC2 ARPC2 ARPC2 8847 0.0058 0.41 NO
82 ARHGDIA ARHGDIA ARHGDIA 9046 0.003 0.4 NO
83 MYC MYC MYC 9157 0.0017 0.39 NO
84 PTPN11 PTPN11 PTPN11 9216 0.0011 0.39 NO
85 MAP2K2 MAP2K2 MAP2K2 9219 0.0011 0.39 NO
86 MAPK1 MAPK1 MAPK1 9403 -0.0012 0.38 NO
87 NCK2 NCK2 NCK2 9474 -0.0022 0.38 NO
88 RAB5A RAB5A RAB5A 9478 -0.0022 0.38 NO
89 PTPN2 PTPN2 PTPN2 9499 -0.0024 0.38 NO
90 PIK3CB PIK3CB PIK3CB 9500 -0.0025 0.38 NO
91 SOS1 SOS1 SOS1 9638 -0.004 0.37 NO
92 CRK CRK CRK 9730 -0.0051 0.36 NO
93 PPP2R1A PPP2R1A PPP2R1A 9760 -0.0054 0.36 NO
94 RAB4A RAB4A RAB4A 9917 -0.0071 0.36 NO
95 MAP2K1 MAP2K1 MAP2K1 10073 -0.0089 0.35 NO
96 ELK1 ELK1 ELK1 10166 -0.0099 0.34 NO
97 PRKCD PRKCD PRKCD 10384 -0.013 0.33 NO
98 ABI1 ABI1 ABI1 10526 -0.014 0.32 NO
99 YWHAB YWHAB YWHAB 10763 -0.017 0.31 NO
100 EIF2AK2 EIF2AK2 EIF2AK2 10854 -0.018 0.31 NO
101 MAP2K7 MAP2K7 MAP2K7 10948 -0.019 0.3 NO
102 NCKAP1 NCKAP1 NCKAP1 11184 -0.022 0.29 NO
103 SLC9A3R1 SLC9A3R1 SLC9A3R1 11232 -0.022 0.29 NO
104 RAC1 RAC1 RAC1 11415 -0.024 0.28 NO
105 RAF1 RAF1 RAF1 11660 -0.027 0.27 NO
106 MLLT4 MLLT4 MLLT4 11837 -0.029 0.26 NO
107 NRAS NRAS NRAS 11928 -0.03 0.26 NO
108 ARPC3 ARPC3 ARPC3 12158 -0.033 0.25 NO
109 YWHAQ YWHAQ YWHAQ 12189 -0.033 0.25 NO
110 DNM2 DNM2 DNM2 12366 -0.035 0.24 NO
111 YWHAG YWHAG YWHAG 12403 -0.036 0.24 NO
112 MAP2K4 MAP2K4 MAP2K4 12539 -0.037 0.24 NO
113 PPP2CA PPP2CA PPP2CA 12646 -0.038 0.24 NO
114 KRAS KRAS KRAS 12912 -0.042 0.22 NO
115 WASL WASL WASL 13194 -0.045 0.21 NO
116 VAV2 VAV2 VAV2 13368 -0.047 0.2 NO
117 CTTN CTTN CTTN 13540 -0.05 0.2 NO
118 PIK3R2 PIK3R2 PIK3R2 13683 -0.052 0.19 NO
119 YES1 YES1 YES1 14047 -0.058 0.18 NO
120 YWHAE YWHAE YWHAE 14171 -0.06 0.18 NO
121 PAK1 PAK1 PAK1 14247 -0.061 0.18 NO
122 YWHAZ YWHAZ YWHAZ 14605 -0.067 0.16 NO
123 MAPK8 MAPK8 MAPK8 15084 -0.077 0.14 NO
124 SRC SRC SRC 15238 -0.08 0.14 NO
125 HRAS HRAS HRAS 16604 -0.13 0.068 NO
126 SFN SFN SFN 16969 -0.14 0.057 NO
127 BRAF BRAF BRAF 17216 -0.16 0.054 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: KEGG TYROSINE METABOLISM.

Figure S12.  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 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 PDE1A PDE1A PDE1A 23 0.96 0.092 YES
2 ADCY5 ADCY5 ADCY5 241 0.72 0.15 YES
3 ADCY2 ADCY2 ADCY2 366 0.66 0.21 YES
4 PDE1B PDE1B PDE1B 879 0.54 0.23 YES
5 PDGFRA PDGFRA PDGFRA 896 0.54 0.28 YES
6 ADCY4 ADCY4 ADCY4 1152 0.49 0.32 YES
7 AKT3 AKT3 AKT3 1222 0.48 0.36 YES
8 PDGFRB PDGFRB PDGFRB 1512 0.43 0.39 YES
9 PRKAR2B PRKAR2B PRKAR2B 1713 0.4 0.41 YES
10 NR4A1 NR4A1 NR4A1 2322 0.31 0.41 YES
11 CAMK4 CAMK4 CAMK4 2394 0.3 0.44 YES
12 ADCY9 ADCY9 ADCY9 2957 0.24 0.43 YES
13 PDGFB PDGFB PDGFB 2959 0.24 0.45 YES
14 STAT5A STAT5A STAT5A 3291 0.21 0.45 YES
15 PRKCG PRKCG PRKCG 3351 0.2 0.47 YES
16 ADCY7 ADCY7 ADCY7 3758 0.17 0.46 YES
17 ITPR2 ITPR2 ITPR2 4148 0.14 0.46 YES
18 FOXO1 FOXO1 FOXO1 4160 0.14 0.47 YES
19 RAPGEF1 RAPGEF1 RAPGEF1 4573 0.12 0.46 YES
20 PDGFA PDGFA PDGFA 4877 0.1 0.45 YES
21 PRKAR2A PRKAR2A PRKAR2A 4975 0.099 0.46 YES
22 STAT5B STAT5B STAT5B 5040 0.096 0.46 YES
23 FOXO3 FOXO3 FOXO3 5321 0.085 0.45 YES
24 PIK3R1 PIK3R1 PIK3R1 5416 0.082 0.46 YES
25 STAT1 STAT1 STAT1 5421 0.082 0.46 YES
26 PRKACB PRKACB PRKACB 5560 0.076 0.46 YES
27 STAT3 STAT3 STAT3 5586 0.076 0.47 YES
28 FOXO4 FOXO4 FOXO4 5653 0.073 0.47 YES
29 CDKN1B CDKN1B CDKN1B 5709 0.071 0.48 YES
30 PRKCA PRKCA PRKCA 5733 0.07 0.48 YES
31 PTEN PTEN PTEN 5863 0.067 0.48 YES
32 MAPK3 MAPK3 MAPK3 5941 0.065 0.48 YES
33 CALM2 CALM2 CALM2 6510 0.05 0.46 NO
34 PRKCE PRKCE PRKCE 6534 0.049 0.46 NO
35 ADCY3 ADCY3 ADCY3 6589 0.047 0.46 NO
36 TRIB3 TRIB3 TRIB3 6628 0.046 0.47 NO
37 GRB2 GRB2 GRB2 6660 0.046 0.47 NO
38 MAPKAP1 MAPKAP1 MAPKAP1 6756 0.043 0.47 NO
39 CALM3 CALM3 CALM3 6871 0.04 0.46 NO
40 CALM1 CALM1 CALM1 7048 0.036 0.46 NO
41 BCAR1 BCAR1 BCAR1 7197 0.033 0.45 NO
42 PRKAR1A PRKAR1A PRKAR1A 7276 0.032 0.45 NO
43 PRKACA PRKACA PRKACA 7759 0.023 0.43 NO
44 PIK3CA PIK3CA PIK3CA 7893 0.02 0.42 NO
45 BAD BAD BAD 8050 0.018 0.42 NO
46 RASA1 RASA1 RASA1 8103 0.017 0.42 NO
47 CDKN1A CDKN1A CDKN1A 8136 0.016 0.41 NO
48 CHUK CHUK CHUK 8322 0.014 0.41 NO
49 NCK1 NCK1 NCK1 8328 0.013 0.41 NO
50 PLCG1 PLCG1 PLCG1 8576 0.0096 0.39 NO
51 CREB1 CREB1 CREB1 9002 0.0036 0.37 NO
52 MAP2K2 MAP2K2 MAP2K2 9219 0.0011 0.36 NO
53 MAPK1 MAPK1 MAPK1 9403 -0.0012 0.35 NO
54 AKT2 AKT2 AKT2 9424 -0.0015 0.35 NO
55 NCK2 NCK2 NCK2 9474 -0.0022 0.35 NO
56 PIK3CB PIK3CB PIK3CB 9500 -0.0025 0.34 NO
57 ADCY6 ADCY6 ADCY6 9505 -0.0025 0.34 NO
58 SOS1 SOS1 SOS1 9638 -0.004 0.34 NO
59 CRK CRK CRK 9730 -0.0051 0.33 NO
60 STAT6 STAT6 STAT6 9968 -0.0078 0.32 NO
61 MAP2K1 MAP2K1 MAP2K1 10073 -0.0089 0.32 NO
62 TSC2 TSC2 TSC2 10144 -0.0097 0.31 NO
63 PRKCD PRKCD PRKCD 10384 -0.013 0.3 NO
64 CASP9 CASP9 CASP9 10527 -0.014 0.29 NO
65 AKT1 AKT1 AKT1 10608 -0.015 0.29 NO
66 MDM2 MDM2 MDM2 10686 -0.016 0.29 NO
67 YWHAB YWHAB YWHAB 10763 -0.017 0.29 NO
68 THEM4 THEM4 THEM4 10836 -0.018 0.28 NO
69 AKT1S1 AKT1S1 AKT1S1 10984 -0.02 0.28 NO
70 PDPK1 PDPK1 PDPK1 11211 -0.022 0.27 NO
71 MLST8 MLST8 MLST8 11305 -0.023 0.26 NO
72 GSK3A GSK3A GSK3A 11372 -0.024 0.26 NO
73 MTOR MTOR MTOR 11465 -0.025 0.26 NO
74 RAF1 RAF1 RAF1 11660 -0.027 0.25 NO
75 ADRBK1 ADRBK1 ADRBK1 11890 -0.03 0.24 NO
76 NRAS NRAS NRAS 11928 -0.03 0.24 NO
77 RICTOR RICTOR RICTOR 12089 -0.032 0.24 NO
78 KRAS KRAS KRAS 12912 -0.042 0.2 NO
79 ADCY1 ADCY1 ADCY1 13422 -0.048 0.17 NO
80 PRKAR1B PRKAR1B PRKAR1B 13466 -0.049 0.18 NO
81 RPS6KB2 RPS6KB2 RPS6KB2 13557 -0.05 0.18 NO
82 PIK3R2 PIK3R2 PIK3R2 13683 -0.052 0.17 NO
83 ITPR3 ITPR3 ITPR3 14914 -0.073 0.11 NO
84 CRKL CRKL CRKL 15222 -0.08 0.1 NO
85 SRC SRC SRC 15238 -0.08 0.11 NO
86 HRAS HRAS HRAS 16604 -0.13 0.048 NO
87 PHLPP1 PHLPP1 PHLPP1 16773 -0.13 0.052 NO
88 GRB7 GRB7 GRB7 16818 -0.14 0.062 NO
89 CDK1 CDK1 CDK1 16896 -0.14 0.072 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: KEGG TRYPTOPHAN METABOLISM.

Figure S14.  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 O GLYCAN BIOSYNTHESIS

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 AGTR1 AGTR1 AGTR1 50 0.9 0.084 YES
2 SLC2A4 SLC2A4 SLC2A4 209 0.74 0.15 YES
3 ITGA7 ITGA7 ITGA7 283 0.7 0.21 YES
4 ITGA11 ITGA11 ITGA11 424 0.64 0.27 YES
5 AVPR2 AVPR2 AVPR2 670 0.57 0.31 YES
6 ACAP1 ACAP1 ACAP1 806 0.55 0.35 YES
7 IL2RA IL2RA IL2RA 856 0.54 0.4 YES
8 ITGA10 ITGA10 ITGA10 1082 0.5 0.44 YES
9 BIN1 BIN1 BIN1 1141 0.49 0.48 YES
10 ITGA9 ITGA9 ITGA9 1149 0.49 0.53 YES
11 TSHR TSHR TSHR 1210 0.48 0.57 YES
12 ITGA8 ITGA8 ITGA8 1445 0.44 0.6 YES
13 ITGA4 ITGA4 ITGA4 1519 0.43 0.64 YES
14 EDNRB EDNRB EDNRB 1674 0.4 0.67 YES
15 ITGA5 ITGA5 ITGA5 1942 0.36 0.69 YES
16 ITGA1 ITGA1 ITGA1 2379 0.3 0.7 YES
17 CPE CPE CPE 2610 0.27 0.71 YES
18 ITGAV ITGAV ITGAV 4218 0.14 0.64 NO
19 PIP5K1C PIP5K1C PIP5K1C 5195 0.09 0.59 NO
20 ITGB1 ITGB1 ITGB1 5528 0.078 0.58 NO
21 EXOC6 EXOC6 EXOC6 5776 0.069 0.57 NO
22 ADRB2 ADRB2 ADRB2 7029 0.036 0.51 NO
23 KLC1 KLC1 KLC1 7332 0.031 0.5 NO
24 EXOC3 EXOC3 EXOC3 7696 0.024 0.48 NO
25 SPAG9 SPAG9 SPAG9 7747 0.023 0.48 NO
26 SCAMP2 SCAMP2 SCAMP2 7755 0.023 0.48 NO
27 VAMP3 VAMP3 VAMP3 7826 0.021 0.48 NO
28 CTNNB1 CTNNB1 CTNNB1 8364 0.013 0.45 NO
29 EXOC4 EXOC4 EXOC4 8514 0.01 0.44 NO
30 CLTC CLTC CLTC 8561 0.0097 0.44 NO
31 EXOC2 EXOC2 EXOC2 8791 0.0066 0.43 NO
32 PLD1 PLD1 PLD1 9490 -0.0024 0.39 NO
33 RALA RALA RALA 9688 -0.0047 0.38 NO
34 ARF6 ARF6 ARF6 9901 -0.007 0.37 NO
35 ITGA2 ITGA2 ITGA2 10002 -0.0081 0.36 NO
36 CTNNA1 CTNNA1 CTNNA1 10224 -0.011 0.35 NO
37 EXOC5 EXOC5 EXOC5 10293 -0.012 0.35 NO
38 PLD2 PLD2 PLD2 11010 -0.02 0.31 NO
39 DNM2 DNM2 DNM2 12366 -0.035 0.24 NO
40 ASAP2 ASAP2 ASAP2 13011 -0.043 0.21 NO
41 EXOC7 EXOC7 EXOC7 13377 -0.048 0.19 NO
42 EXOC1 EXOC1 EXOC1 15542 -0.088 0.083 NO
43 CTNND1 CTNND1 CTNND1 15593 -0.089 0.089 NO
44 MAPK8IP3 MAPK8IP3 MAPK8IP3 15694 -0.092 0.092 NO
45 ITGA3 ITGA3 ITGA3 15840 -0.096 0.094 NO
46 NME1 NME1 NME1 15967 -0.1 0.096 NO
47 ITGA6 ITGA6 ITGA6 16753 -0.13 0.066 NO
48 CDH1 CDH1 CDH1 16846 -0.14 0.074 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: KEGG O GLYCAN BIOSYNTHESIS.

Figure S16.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG O GLYCAN 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 AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM

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 PDE1A PDE1A PDE1A 23 0.96 0.09 YES
2 ADCY5 ADCY5 ADCY5 241 0.72 0.15 YES
3 ADCY2 ADCY2 ADCY2 366 0.66 0.2 YES
4 ADAM12 ADAM12 ADAM12 679 0.57 0.24 YES
5 PDE1B PDE1B PDE1B 879 0.54 0.28 YES
6 ADCY4 ADCY4 ADCY4 1152 0.49 0.31 YES
7 LRIG1 LRIG1 LRIG1 1178 0.48 0.36 YES
8 AKT3 AKT3 AKT3 1222 0.48 0.4 YES
9 PRKAR2B PRKAR2B PRKAR2B 1713 0.4 0.41 YES
10 NR4A1 NR4A1 NR4A1 2322 0.31 0.4 YES
11 CAMK4 CAMK4 CAMK4 2394 0.3 0.43 YES
12 SPRY1 SPRY1 SPRY1 2628 0.27 0.44 YES
13 SH3KBP1 SH3KBP1 SH3KBP1 2941 0.24 0.45 YES
14 ADCY9 ADCY9 ADCY9 2957 0.24 0.47 YES
15 PRKCG PRKCG PRKCG 3351 0.2 0.47 YES
16 ADCY7 ADCY7 ADCY7 3758 0.17 0.46 YES
17 ITPR2 ITPR2 ITPR2 4148 0.14 0.45 YES
18 FOXO1 FOXO1 FOXO1 4160 0.14 0.46 YES
19 GAB1 GAB1 GAB1 4454 0.12 0.46 YES
20 SH3GL2 SH3GL2 SH3GL2 4627 0.12 0.46 YES
21 PRKAR2A PRKAR2A PRKAR2A 4975 0.099 0.45 YES
22 FOXO3 FOXO3 FOXO3 5321 0.085 0.44 YES
23 PIK3R1 PIK3R1 PIK3R1 5416 0.082 0.44 YES
24 AP2A2 AP2A2 AP2A2 5450 0.081 0.45 YES
25 PRKACB PRKACB PRKACB 5560 0.076 0.45 YES
26 FOXO4 FOXO4 FOXO4 5653 0.073 0.45 YES
27 CDKN1B CDKN1B CDKN1B 5709 0.071 0.46 YES
28 PRKCA PRKCA PRKCA 5733 0.07 0.46 YES
29 PTEN PTEN PTEN 5863 0.067 0.46 YES
30 SPRY2 SPRY2 SPRY2 5903 0.066 0.47 YES
31 MAPK3 MAPK3 MAPK3 5941 0.065 0.47 YES
32 EPS15 EPS15 EPS15 5958 0.064 0.48 YES
33 CALM2 CALM2 CALM2 6510 0.05 0.45 NO
34 PRKCE PRKCE PRKCE 6534 0.049 0.45 NO
35 ADCY3 ADCY3 ADCY3 6589 0.047 0.45 NO
36 TRIB3 TRIB3 TRIB3 6628 0.046 0.46 NO
37 GRB2 GRB2 GRB2 6660 0.046 0.46 NO
38 MAPKAP1 MAPKAP1 MAPKAP1 6756 0.043 0.46 NO
39 CALM3 CALM3 CALM3 6871 0.04 0.46 NO
40 CALM1 CALM1 CALM1 7048 0.036 0.45 NO
41 PRKAR1A PRKAR1A PRKAR1A 7276 0.032 0.44 NO
42 AP2B1 AP2B1 AP2B1 7491 0.028 0.43 NO
43 AP2A1 AP2A1 AP2A1 7626 0.025 0.42 NO
44 CBL CBL CBL 7640 0.025 0.43 NO
45 PRKACA PRKACA PRKACA 7759 0.023 0.42 NO
46 CSK CSK CSK 7766 0.022 0.42 NO
47 PIK3CA PIK3CA PIK3CA 7893 0.02 0.42 NO
48 BAD BAD BAD 8050 0.018 0.41 NO
49 CDKN1A CDKN1A CDKN1A 8136 0.016 0.41 NO
50 CHUK CHUK CHUK 8322 0.014 0.4 NO
51 SHC1 SHC1 SHC1 8481 0.011 0.39 NO
52 CLTC CLTC CLTC 8561 0.0097 0.39 NO
53 PLCG1 PLCG1 PLCG1 8576 0.0096 0.39 NO
54 EPN1 EPN1 EPN1 8770 0.0068 0.38 NO
55 PAG1 PAG1 PAG1 8825 0.0062 0.38 NO
56 AP2S1 AP2S1 AP2S1 8870 0.0055 0.38 NO
57 AP2M1 AP2M1 AP2M1 8953 0.0043 0.37 NO
58 CREB1 CREB1 CREB1 9002 0.0036 0.37 NO
59 MAP2K2 MAP2K2 MAP2K2 9219 0.0011 0.36 NO
60 MAPK1 MAPK1 MAPK1 9403 -0.0012 0.35 NO
61 AKT2 AKT2 AKT2 9424 -0.0015 0.35 NO
62 CLTA CLTA CLTA 9450 -0.0018 0.34 NO
63 ADCY6 ADCY6 ADCY6 9505 -0.0025 0.34 NO
64 SOS1 SOS1 SOS1 9638 -0.004 0.34 NO
65 CDC42 CDC42 CDC42 9702 -0.0049 0.33 NO
66 RPS27A RPS27A RPS27A 9725 -0.0051 0.33 NO
67 STAM2 STAM2 STAM2 9772 -0.0056 0.33 NO
68 UBA52 UBA52 UBA52 9804 -0.0058 0.33 NO
69 MAP2K1 MAP2K1 MAP2K1 10073 -0.0089 0.31 NO
70 TSC2 TSC2 TSC2 10144 -0.0097 0.31 NO
71 PRKCD PRKCD PRKCD 10384 -0.013 0.3 NO
72 EGF EGF EGF 10425 -0.013 0.3 NO
73 CASP9 CASP9 CASP9 10527 -0.014 0.29 NO
74 AKT1 AKT1 AKT1 10608 -0.015 0.29 NO
75 MDM2 MDM2 MDM2 10686 -0.016 0.29 NO
76 YWHAB YWHAB YWHAB 10763 -0.017 0.28 NO
77 THEM4 THEM4 THEM4 10836 -0.018 0.28 NO
78 AKT1S1 AKT1S1 AKT1S1 10984 -0.02 0.28 NO
79 EPS15L1 EPS15L1 EPS15L1 11024 -0.02 0.28 NO
80 PDPK1 PDPK1 PDPK1 11211 -0.022 0.27 NO
81 MLST8 MLST8 MLST8 11305 -0.023 0.26 NO
82 GSK3A GSK3A GSK3A 11372 -0.024 0.26 NO
83 MTOR MTOR MTOR 11465 -0.025 0.26 NO
84 CDC37 CDC37 CDC37 11510 -0.025 0.26 NO
85 STAM STAM STAM 11606 -0.026 0.26 NO
86 RAF1 RAF1 RAF1 11660 -0.027 0.26 NO
87 ADRBK1 ADRBK1 ADRBK1 11890 -0.03 0.25 NO
88 NRAS NRAS NRAS 11928 -0.03 0.25 NO
89 RICTOR RICTOR RICTOR 12089 -0.032 0.24 NO
90 HSP90AA1 HSP90AA1 HSP90AA1 12529 -0.037 0.22 NO
91 KRAS KRAS KRAS 12912 -0.042 0.2 NO
92 ADAM10 ADAM10 ADAM10 13179 -0.045 0.2 NO
93 ADAM17 ADAM17 ADAM17 13389 -0.048 0.19 NO
94 ADCY1 ADCY1 ADCY1 13422 -0.048 0.19 NO
95 PRKAR1B PRKAR1B PRKAR1B 13466 -0.049 0.19 NO
96 RPS6KB2 RPS6KB2 RPS6KB2 13557 -0.05 0.19 NO
97 HGS HGS HGS 13627 -0.051 0.19 NO
98 EGFR EGFR EGFR 14159 -0.06 0.17 NO
99 ITPR3 ITPR3 ITPR3 14914 -0.073 0.14 NO
100 SRC SRC SRC 15238 -0.08 0.12 NO
101 HRAS HRAS HRAS 16604 -0.13 0.062 NO
102 PHLPP1 PHLPP1 PHLPP1 16773 -0.13 0.065 NO
103 CDK1 CDK1 CDK1 16896 -0.14 0.072 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: KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM.

Figure S18.  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 GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE

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 BTK BTK BTK 229 0.73 0.047 YES
2 CD79B CD79B CD79B 285 0.7 0.1 YES
3 CD79A CD79A CD79A 293 0.69 0.16 YES
4 BLK BLK BLK 397 0.66 0.21 YES
5 CD19 CD19 CD19 511 0.62 0.25 YES
6 PRKCB PRKCB PRKCB 795 0.56 0.28 YES
7 PIK3AP1 PIK3AP1 PIK3AP1 930 0.53 0.32 YES
8 AKT3 AKT3 AKT3 1222 0.48 0.34 YES
9 VAV1 VAV1 VAV1 1231 0.48 0.38 YES
10 RASGRP1 RASGRP1 RASGRP1 2037 0.35 0.36 YES
11 PIK3CD PIK3CD PIK3CD 2055 0.35 0.39 YES
12 FYN FYN FYN 2169 0.33 0.41 YES
13 NR4A1 NR4A1 NR4A1 2322 0.31 0.43 YES
14 RASGRP3 RASGRP3 RASGRP3 2326 0.31 0.45 YES
15 PSMA8 PSMA8 PSMA8 2380 0.3 0.48 YES
16 SH3KBP1 SH3KBP1 SH3KBP1 2941 0.24 0.46 YES
17 PLCG2 PLCG2 PLCG2 3257 0.21 0.46 YES
18 PSMB9 PSMB9 PSMB9 3348 0.2 0.48 YES
19 BLNK BLNK BLNK 3645 0.18 0.47 YES
20 LYN LYN LYN 3836 0.16 0.48 YES
21 ITPR2 ITPR2 ITPR2 4148 0.14 0.47 YES
22 FOXO1 FOXO1 FOXO1 4160 0.14 0.48 YES
23 ORAI1 ORAI1 ORAI1 4710 0.11 0.46 NO
24 NFKBIE NFKBIE NFKBIE 5057 0.095 0.45 NO
25 SYK SYK SYK 5275 0.087 0.44 NO
26 FOXO3 FOXO3 FOXO3 5321 0.085 0.45 NO
27 PIK3R1 PIK3R1 PIK3R1 5416 0.082 0.45 NO
28 FOXO4 FOXO4 FOXO4 5653 0.073 0.44 NO
29 CDKN1B CDKN1B CDKN1B 5709 0.071 0.45 NO
30 PTEN PTEN PTEN 5863 0.067 0.44 NO
31 STIM1 STIM1 STIM1 5882 0.066 0.45 NO
32 CBLB CBLB CBLB 5919 0.065 0.45 NO
33 MALT1 MALT1 MALT1 6136 0.059 0.44 NO
34 PSMB10 PSMB10 PSMB10 6240 0.057 0.44 NO
35 PSMB8 PSMB8 PSMB8 6507 0.05 0.43 NO
36 CALM2 CALM2 CALM2 6510 0.05 0.44 NO
37 TRIB3 TRIB3 TRIB3 6628 0.046 0.43 NO
38 GRB2 GRB2 GRB2 6660 0.046 0.44 NO
39 MAPKAP1 MAPKAP1 MAPKAP1 6756 0.043 0.43 NO
40 CALM3 CALM3 CALM3 6871 0.04 0.43 NO
41 NFKBIB NFKBIB NFKBIB 6928 0.039 0.43 NO
42 CALM1 CALM1 CALM1 7048 0.036 0.43 NO
43 FBXW11 FBXW11 FBXW11 7579 0.026 0.4 NO
44 PSMD8 PSMD8 PSMD8 7608 0.026 0.4 NO
45 CBL CBL CBL 7640 0.025 0.4 NO
46 NFKBIA NFKBIA NFKBIA 7714 0.023 0.4 NO
47 IKBKG IKBKG IKBKG 7740 0.023 0.4 NO
48 BAD BAD BAD 8050 0.018 0.38 NO
49 CDKN1A CDKN1A CDKN1A 8136 0.016 0.38 NO
50 CHUK CHUK CHUK 8322 0.014 0.37 NO
51 NCK1 NCK1 NCK1 8328 0.013 0.37 NO
52 SHC1 SHC1 SHC1 8481 0.011 0.36 NO
53 PLCG1 PLCG1 PLCG1 8576 0.0096 0.36 NO
54 CUL1 CUL1 CUL1 8679 0.0081 0.36 NO
55 RELA RELA RELA 8722 0.0074 0.35 NO
56 SKP1 SKP1 SKP1 8885 0.0054 0.34 NO
57 CREB1 CREB1 CREB1 9002 0.0036 0.34 NO
58 PSMC3 PSMC3 PSMC3 9078 0.0026 0.34 NO
59 PSMD1 PSMD1 PSMD1 9243 0.00084 0.33 NO
60 PSMD9 PSMD9 PSMD9 9290 0.00028 0.32 NO
61 PSME1 PSME1 PSME1 9420 -0.0015 0.32 NO
62 AKT2 AKT2 AKT2 9424 -0.0015 0.32 NO
63 SOS1 SOS1 SOS1 9638 -0.004 0.3 NO
64 PSMD7 PSMD7 PSMD7 9722 -0.0051 0.3 NO
65 RPS27A RPS27A RPS27A 9725 -0.0051 0.3 NO
66 UBA52 UBA52 UBA52 9804 -0.0058 0.3 NO
67 PSMA7 PSMA7 PSMA7 9985 -0.0079 0.29 NO
68 PSMD13 PSMD13 PSMD13 10029 -0.0084 0.29 NO
69 PSMC5 PSMC5 PSMC5 10108 -0.0092 0.28 NO
70 TSC2 TSC2 TSC2 10144 -0.0097 0.28 NO
71 PSMD2 PSMD2 PSMD2 10235 -0.011 0.28 NO
72 PSMF1 PSMF1 PSMF1 10309 -0.012 0.27 NO
73 CARD11 CARD11 CARD11 10395 -0.013 0.27 NO
74 CASP9 CASP9 CASP9 10527 -0.014 0.26 NO
75 PSME2 PSME2 PSME2 10563 -0.015 0.26 NO
76 AKT1 AKT1 AKT1 10608 -0.015 0.26 NO
77 MDM2 MDM2 MDM2 10686 -0.016 0.26 NO
78 PSMC1 PSMC1 PSMC1 10830 -0.018 0.25 NO
79 THEM4 THEM4 THEM4 10836 -0.018 0.25 NO
80 PSMC4 PSMC4 PSMC4 10875 -0.019 0.25 NO
81 PSMC2 PSMC2 PSMC2 10973 -0.02 0.25 NO
82 AKT1S1 AKT1S1 AKT1S1 10984 -0.02 0.25 NO
83 PSMB6 PSMB6 PSMB6 11011 -0.02 0.25 NO
84 PSMD4 PSMD4 PSMD4 11042 -0.02 0.25 NO
85 PSMB2 PSMB2 PSMB2 11127 -0.021 0.25 NO
86 PDPK1 PDPK1 PDPK1 11211 -0.022 0.25 NO
87 MLST8 MLST8 MLST8 11305 -0.023 0.24 NO
88 PSMB5 PSMB5 PSMB5 11351 -0.024 0.24 NO
89 IKBKB IKBKB IKBKB 11369 -0.024 0.24 NO
90 GSK3A GSK3A GSK3A 11372 -0.024 0.24 NO
91 MAP3K7 MAP3K7 MAP3K7 11464 -0.025 0.24 NO
92 MTOR MTOR MTOR 11465 -0.025 0.24 NO
93 PSMA2 PSMA2 PSMA2 11527 -0.026 0.24 NO
94 PSMB3 PSMB3 PSMB3 11534 -0.026 0.24 NO
95 NRAS NRAS NRAS 11928 -0.03 0.22 NO
96 RICTOR RICTOR RICTOR 12089 -0.032 0.22 NO
97 BTRC BTRC BTRC 12115 -0.032 0.22 NO
98 PSMB4 PSMB4 PSMB4 12210 -0.033 0.22 NO
99 PSMD6 PSMD6 PSMD6 12402 -0.036 0.21 NO
100 PSMA1 PSMA1 PSMA1 12536 -0.037 0.2 NO
101 PSMB1 PSMB1 PSMB1 12852 -0.041 0.19 NO
102 KRAS KRAS KRAS 12912 -0.042 0.19 NO
103 PSMA5 PSMA5 PSMA5 12934 -0.042 0.19 NO
104 PSMB7 PSMB7 PSMB7 13276 -0.046 0.18 NO
105 PSMA6 PSMA6 PSMA6 13318 -0.047 0.18 NO
106 PSME4 PSME4 PSME4 13356 -0.047 0.18 NO
107 PSMA4 PSMA4 PSMA4 13363 -0.047 0.19 NO
108 REL REL REL 13388 -0.048 0.19 NO
109 RPS6KB2 RPS6KB2 RPS6KB2 13557 -0.05 0.18 NO
110 PSMD3 PSMD3 PSMD3 13588 -0.051 0.18 NO
111 PSMD5 PSMD5 PSMD5 13676 -0.052 0.18 NO
112 PSMD10 PSMD10 PSMD10 13978 -0.057 0.17 NO
113 PSMC6 PSMC6 PSMC6 14116 -0.059 0.17 NO
114 PSMD11 PSMD11 PSMD11 14225 -0.061 0.17 NO
115 PSMD12 PSMD12 PSMD12 14653 -0.068 0.15 NO
116 PSMD14 PSMD14 PSMD14 14663 -0.068 0.16 NO
117 PSMA3 PSMA3 PSMA3 14720 -0.07 0.16 NO
118 BCL10 BCL10 BCL10 14824 -0.072 0.16 NO
119 ITPR3 ITPR3 ITPR3 14914 -0.073 0.16 NO
120 HRAS HRAS HRAS 16604 -0.13 0.077 NO
121 PHLPP1 PHLPP1 PHLPP1 16773 -0.13 0.079 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: KEGG GLYCOSAMINOGLYCAN BIOSYNTHESIS HEPARAN SULFATE.

Figure S20.  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 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 PENTOSE AND GLUCURONATE INTERCONVERSIONS 27 genes.ES.table 0.75 1.6 0.019 0.54 0.9 0.67 0.17 0.55 0.28 0.14
KEGG FATTY ACID METABOLISM 40 genes.ES.table 0.5 1.5 0.072 0.6 0.99 0.45 0.21 0.36 0.43 0.17
KEGG STEROID HORMONE BIOSYNTHESIS 52 genes.ES.table 0.64 1.6 0.012 0.58 0.95 0.54 0.12 0.48 0.35 0.16
KEGG STARCH AND SUCROSE METABOLISM 47 genes.ES.table 0.54 1.5 0.055 0.54 0.99 0.34 0.074 0.32 0.39 0.14
KEGG GLYCOSYLPHOSPHATIDYLINOSITOL GPI ANCHOR BIOSYNTHESIS 25 genes.ES.table 0.53 1.8 0.02 1 0.65 0.52 0.27 0.38 0.38 0.24
KEGG LINOLEIC ACID METABOLISM 25 genes.ES.table 0.68 1.5 0.027 0.54 0.96 0.52 0.088 0.48 0.36 0.15
KEGG RETINOL METABOLISM 61 genes.ES.table 0.66 1.6 0.032 0.52 0.91 0.46 0.088 0.42 0.29 0.14
KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM 39 genes.ES.table 0.66 1.7 0.012 0.56 0.76 0.36 0.09 0.33 0.22 0.14
KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450 67 genes.ES.table 0.73 1.7 0.011 0.83 0.76 0.57 0.13 0.49 0.32 0.2
KEGG DRUG METABOLISM CYTOCHROME P450 67 genes.ES.table 0.64 1.6 0.043 0.54 0.96 0.54 0.13 0.47 0.35 0.15
genes ES table in pathway: KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS

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 PIGZ PIGZ PIGZ 223 0.47 0.17 YES
2 GPLD1 GPLD1 GPLD1 393 0.4 0.31 YES
3 PIGL PIGL PIGL 1496 0.22 0.34 YES
4 PGAP1 PGAP1 PGAP1 1576 0.21 0.41 YES
5 PIGF PIGF PIGF 2652 0.14 0.41 YES
6 PIGU PIGU PIGU 3407 0.1 0.41 YES
7 PIGP PIGP PIGP 3802 0.091 0.42 YES
8 PIGA PIGA PIGA 4182 0.08 0.43 YES
9 PIGH PIGH PIGH 4205 0.08 0.46 YES
10 PIGB PIGB PIGB 4376 0.075 0.48 YES
11 PIGQ PIGQ PIGQ 4574 0.07 0.5 YES
12 PIGN PIGN PIGN 4593 0.07 0.52 YES
13 PIGM PIGM PIGM 4940 0.061 0.52 YES
14 PIGV PIGV PIGV 6286 0.033 0.46 NO
15 PIGG PIGG PIGG 7394 0.014 0.41 NO
16 PIGY PIGY PIGY 7447 0.013 0.41 NO
17 PIGC PIGC PIGC 8860 -0.011 0.34 NO
18 DPM2 DPM2 DPM2 9624 -0.023 0.3 NO
19 GPAA1 GPAA1 GPAA1 9896 -0.027 0.3 NO
20 PIGW PIGW PIGW 9918 -0.028 0.31 NO
21 PIGO PIGO PIGO 10282 -0.034 0.3 NO
22 PIGT PIGT PIGT 10414 -0.036 0.31 NO
23 PIGX PIGX PIGX 12569 -0.085 0.22 NO
24 PIGS PIGS PIGS 13353 -0.11 0.22 NO
25 PIGK PIGK PIGK 13474 -0.11 0.26 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 PENTOSE AND GLUCURONATE INTERCONVERSIONS.

Figure S22.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS, 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 FATTY ACID METABOLISM

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 UGT1A1 UGT1A1 UGT1A1 102 0.58 0.036 YES
2 CYP3A5 CYP3A5 CYP3A5 169 0.51 0.069 YES
3 CYP2C8 CYP2C8 CYP2C8 204 0.48 0.1 YES
4 UGT1A9 UGT1A9 UGT1A9 206 0.48 0.14 YES
5 UGT1A6 UGT1A6 UGT1A6 248 0.46 0.17 YES
6 ADH6 ADH6 ADH6 256 0.46 0.2 YES
7 UGT2B28 UGT2B28 UGT2B28 296 0.44 0.23 YES
8 AKR1C2 AKR1C2 AKR1C2 310 0.43 0.26 YES
9 UGT1A3 UGT1A3 UGT1A3 387 0.4 0.28 YES
10 CYP2C9 CYP2C9 CYP2C9 388 0.4 0.31 YES
11 AKR1C3 AKR1C3 AKR1C3 413 0.39 0.34 YES
12 CYP3A7 CYP3A7 CYP3A7 427 0.39 0.37 YES
13 GSTM4 GSTM4 GSTM4 447 0.38 0.39 YES
14 UGT2B7 UGT2B7 UGT2B7 499 0.37 0.42 YES
15 CYP1A1 CYP1A1 CYP1A1 630 0.34 0.44 YES
16 UGT2B15 UGT2B15 UGT2B15 634 0.34 0.46 YES
17 GSTM2 GSTM2 GSTM2 643 0.34 0.48 YES
18 UGT2B4 UGT2B4 UGT2B4 867 0.3 0.49 YES
19 AKR1C1 AKR1C1 AKR1C1 917 0.29 0.51 YES
20 UGT2A3 UGT2A3 UGT2A3 969 0.28 0.53 YES
21 CYP1A2 CYP1A2 CYP1A2 983 0.28 0.55 YES
22 UGT1A5 UGT1A5 UGT1A5 991 0.28 0.57 YES
23 UGT1A4 UGT1A4 UGT1A4 1026 0.28 0.59 YES
24 UGT2B11 UGT2B11 UGT2B11 1033 0.27 0.6 YES
25 CYP2C19 CYP2C19 CYP2C19 1039 0.27 0.62 YES
26 GSTM3 GSTM3 GSTM3 1205 0.25 0.63 YES
27 UGT2B10 UGT2B10 UGT2B10 1338 0.23 0.64 YES
28 MGST2 MGST2 MGST2 1391 0.23 0.66 YES
29 AKR1C4 AKR1C4 AKR1C4 1453 0.22 0.67 YES
30 CYP2C18 CYP2C18 CYP2C18 1599 0.21 0.68 YES
31 ADH1C ADH1C ADH1C 1601 0.21 0.69 YES
32 ALDH3B2 ALDH3B2 ALDH3B2 1657 0.2 0.7 YES
33 CYP3A43 CYP3A43 CYP3A43 2087 0.17 0.69 YES
34 ADH4 ADH4 ADH4 2277 0.16 0.69 YES
35 GSTA1 GSTA1 GSTA1 2294 0.16 0.7 YES
36 GSTM1 GSTM1 GSTM1 2346 0.16 0.71 YES
37 UGT1A8 UGT1A8 UGT1A8 2404 0.15 0.72 YES
38 MGST1 MGST1 MGST1 2408 0.15 0.73 YES
39 GSTA2 GSTA2 GSTA2 2887 0.13 0.71 NO
40 GSTO2 GSTO2 GSTO2 2960 0.12 0.72 NO
41 UGT1A10 UGT1A10 UGT1A10 3000 0.12 0.73 NO
42 ADH1A ADH1A ADH1A 3471 0.1 0.71 NO
43 GSTK1 GSTK1 GSTK1 4008 0.085 0.68 NO
44 GSTZ1 GSTZ1 GSTZ1 4235 0.079 0.68 NO
45 ADH1B ADH1B ADH1B 4495 0.072 0.67 NO
46 GSTT1 GSTT1 GSTT1 4628 0.069 0.67 NO
47 CYP3A4 CYP3A4 CYP3A4 6226 0.034 0.58 NO
48 ALDH3B1 ALDH3B1 ALDH3B1 6352 0.031 0.57 NO
49 CYP2E1 CYP2E1 CYP2E1 6450 0.03 0.57 NO
50 MGST3 MGST3 MGST3 6675 0.026 0.56 NO
51 ADH5 ADH5 ADH5 7421 0.014 0.52 NO
52 GSTT2 GSTT2 GSTT2 7703 0.0087 0.51 NO
53 ALDH3A1 ALDH3A1 ALDH3A1 8321 -0.0025 0.47 NO
54 ADH7 ADH7 ADH7 8670 -0.0083 0.45 NO
55 UGT2A1 UGT2A1 UGT2A1 8752 -0.0094 0.45 NO
56 DHDH DHDH DHDH 8895 -0.012 0.44 NO
57 GSTP1 GSTP1 GSTP1 9007 -0.014 0.44 NO
58 GSTO1 GSTO1 GSTO1 9054 -0.014 0.44 NO
59 UGT1A7 UGT1A7 UGT1A7 9148 -0.016 0.43 NO
60 EPHX1 EPHX1 EPHX1 9840 -0.026 0.4 NO
61 CYP2F1 CYP2F1 CYP2F1 10039 -0.03 0.39 NO
62 CYP2B6 CYP2B6 CYP2B6 11486 -0.058 0.31 NO
63 GSTM5 GSTM5 GSTM5 12002 -0.071 0.29 NO
64 ALDH1A3 ALDH1A3 ALDH1A3 13876 -0.13 0.2 NO
65 CYP1B1 CYP1B1 CYP1B1 14152 -0.14 0.19 NO
66 CYP2S1 CYP2S1 CYP2S1 14914 -0.18 0.16 NO
67 GSTA4 GSTA4 GSTA4 16416 -0.28 0.098 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 FATTY ACID METABOLISM.

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

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 UGT1A1 UGT1A1 UGT1A1 102 0.58 0.083 YES
2 UGT1A9 UGT1A9 UGT1A9 206 0.48 0.15 YES
3 UGT1A6 UGT1A6 UGT1A6 248 0.46 0.22 YES
4 UGT2B28 UGT2B28 UGT2B28 296 0.44 0.28 YES
5 UGT1A3 UGT1A3 UGT1A3 387 0.4 0.34 YES
6 UGT2B7 UGT2B7 UGT2B7 499 0.37 0.39 YES
7 UGT2B15 UGT2B15 UGT2B15 634 0.34 0.44 YES
8 UGT2B4 UGT2B4 UGT2B4 867 0.3 0.47 YES
9 UGT2A3 UGT2A3 UGT2A3 969 0.28 0.51 YES
10 UGT1A5 UGT1A5 UGT1A5 991 0.28 0.55 YES
11 UGT1A4 UGT1A4 UGT1A4 1026 0.28 0.59 YES
12 UGT2B11 UGT2B11 UGT2B11 1033 0.27 0.63 YES
13 UGT2B10 UGT2B10 UGT2B10 1338 0.23 0.65 YES
14 ALAS1 ALAS1 ALAS1 1642 0.21 0.66 YES
15 UGT1A8 UGT1A8 UGT1A8 2404 0.15 0.64 NO
16 PPOX PPOX PPOX 2501 0.15 0.66 NO
17 UGT1A10 UGT1A10 UGT1A10 3000 0.12 0.65 NO
18 MMAB MMAB MMAB 5320 0.051 0.53 NO
19 ALAD ALAD ALAD 6214 0.034 0.49 NO
20 EARS2 EARS2 EARS2 7224 0.017 0.44 NO
21 HMOX2 HMOX2 HMOX2 7250 0.017 0.44 NO
22 COX15 COX15 COX15 7403 0.014 0.43 NO
23 GUSB GUSB GUSB 8182 -0.00011 0.39 NO
24 UGT2A1 UGT2A1 UGT2A1 8752 -0.0094 0.36 NO
25 ALAS2 ALAS2 ALAS2 9040 -0.014 0.34 NO
26 UGT1A7 UGT1A7 UGT1A7 9148 -0.016 0.34 NO
27 COX10 COX10 COX10 9339 -0.019 0.33 NO
28 FTH1 FTH1 FTH1 9766 -0.025 0.31 NO
29 UROD UROD UROD 10047 -0.03 0.3 NO
30 HCCS HCCS HCCS 10438 -0.037 0.29 NO
31 HMBS HMBS HMBS 10812 -0.044 0.27 NO
32 HMOX1 HMOX1 HMOX1 10993 -0.048 0.27 NO
33 BLVRB BLVRB BLVRB 11477 -0.058 0.25 NO
34 CPOX CPOX CPOX 11881 -0.068 0.24 NO
35 EPRS EPRS EPRS 12456 -0.082 0.22 NO
36 UROS UROS UROS 12682 -0.088 0.22 NO
37 FECH FECH FECH 13309 -0.11 0.21 NO
38 CP CP CP 14809 -0.17 0.15 NO
39 BLVRA BLVRA BLVRA 15858 -0.24 0.13 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 STEROID HORMONE BIOSYNTHESIS.

Figure S26.  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 STARCH AND SUCROSE 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 SULT2A1 SULT2A1 SULT2A1 45 0.67 0.054 YES
2 UGT1A1 UGT1A1 UGT1A1 102 0.58 0.1 YES
3 SULT1A2 SULT1A2 SULT1A2 140 0.53 0.14 YES
4 UGT1A9 UGT1A9 UGT1A9 206 0.48 0.18 YES
5 UGT1A6 UGT1A6 UGT1A6 248 0.46 0.22 YES
6 UGT2B28 UGT2B28 UGT2B28 296 0.44 0.25 YES
7 UGT1A3 UGT1A3 UGT1A3 387 0.4 0.28 YES
8 GSTM4 GSTM4 GSTM4 447 0.38 0.31 YES
9 UGT2B7 UGT2B7 UGT2B7 499 0.37 0.34 YES
10 SULT1A1 SULT1A1 SULT1A1 701 0.33 0.36 YES
11 UGT2B4 UGT2B4 UGT2B4 867 0.3 0.37 YES
12 ACSM1 ACSM1 ACSM1 941 0.29 0.39 YES
13 SULT1C2 SULT1C2 SULT1C2 960 0.29 0.42 YES
14 CYP1A2 CYP1A2 CYP1A2 983 0.28 0.44 YES
15 UGT1A5 UGT1A5 UGT1A5 991 0.28 0.46 YES
16 UGT1A4 UGT1A4 UGT1A4 1026 0.28 0.48 YES
17 UGT2B11 UGT2B11 UGT2B11 1033 0.27 0.51 YES
18 SULT1E1 SULT1E1 SULT1E1 1142 0.26 0.52 YES
19 UGT2B10 UGT2B10 UGT2B10 1338 0.23 0.53 YES
20 MGST2 MGST2 MGST2 1391 0.23 0.55 YES
21 COMT COMT COMT 1640 0.21 0.55 YES
22 SULT1A3 SULT1A3 SULT1A3 1951 0.18 0.55 YES
23 GCLC GCLC GCLC 2077 0.17 0.56 YES
24 GSTA1 GSTA1 GSTA1 2294 0.16 0.56 YES
25 GSTM1 GSTM1 GSTM1 2346 0.16 0.57 YES
26 NAT1 NAT1 NAT1 2371 0.15 0.58 YES
27 MAT1A MAT1A MAT1A 2373 0.15 0.6 YES
28 UGT1A8 UGT1A8 UGT1A8 2404 0.15 0.61 YES
29 MGST1 MGST1 MGST1 2408 0.15 0.62 YES
30 GGT7 GGT7 GGT7 2535 0.14 0.62 YES
31 GSTA2 GSTA2 GSTA2 2887 0.13 0.62 NO
32 GSTO2 GSTO2 GSTO2 2960 0.12 0.62 NO
33 OPLAH OPLAH OPLAH 3414 0.1 0.61 NO
34 GSS GSS GSS 5160 0.055 0.52 NO
35 CNDP2 CNDP2 CNDP2 5423 0.049 0.5 NO
36 NAT2 NAT2 NAT2 5562 0.046 0.5 NO
37 MAT2A MAT2A MAT2A 6198 0.034 0.47 NO
38 GGCT GGCT GGCT 6241 0.034 0.47 NO
39 MGST3 MGST3 MGST3 6675 0.026 0.45 NO
40 SULT1B1 SULT1B1 SULT1B1 6731 0.025 0.45 NO
41 BPNT1 BPNT1 BPNT1 7949 0.0041 0.38 NO
42 MTR MTR MTR 8160 0.00029 0.37 NO
43 AHCY AHCY AHCY 8356 -0.0031 0.36 NO
44 UGDH UGDH UGDH 8398 -0.0038 0.36 NO
45 SULT1C4 SULT1C4 SULT1C4 8535 -0.0061 0.35 NO
46 UGT2A1 UGT2A1 UGT2A1 8752 -0.0094 0.34 NO
47 MAT2B MAT2B MAT2B 8972 -0.013 0.33 NO
48 GSTP1 GSTP1 GSTP1 9007 -0.014 0.33 NO
49 PAPSS1 PAPSS1 PAPSS1 9019 -0.014 0.33 NO
50 GSTO1 GSTO1 GSTO1 9054 -0.014 0.33 NO
51 SULT4A1 SULT4A1 SULT4A1 9128 -0.016 0.32 NO
52 UGT1A7 UGT1A7 UGT1A7 9148 -0.016 0.32 NO
53 TPMT TPMT TPMT 10261 -0.034 0.26 NO
54 UGP2 UGP2 UGP2 11413 -0.056 0.21 NO
55 SLC35D1 SLC35D1 SLC35D1 11498 -0.058 0.21 NO
56 GSTM5 GSTM5 GSTM5 12002 -0.071 0.18 NO
57 GCLM GCLM GCLM 12766 -0.091 0.15 NO
58 GGT5 GGT5 GGT5 14921 -0.18 0.048 NO
59 SULT2B1 SULT2B1 SULT2B1 16004 -0.25 0.0088 NO
60 GGT1 GGT1 GGT1 16069 -0.25 0.027 NO
61 GSTA4 GSTA4 GSTA4 16416 -0.28 0.031 NO
62 PAPSS2 PAPSS2 PAPSS2 17479 -0.39 0.006 NO
63 NNMT NNMT NNMT 17496 -0.4 0.039 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 STARCH AND SUCROSE METABOLISM.

Figure S28.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG STARCH AND SUCROSE 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 GLYCOSYLPHOSPHATIDYLINOSITOL GPI ANCHOR BIOSYNTHESIS

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 UCP3 UCP3 UCP3 507 0.37 0.052 YES
2 UCP2 UCP2 UCP2 1122 0.26 0.075 YES
3 NDUFA7 NDUFA7 NDUFA7 2547 0.14 0.027 YES
4 UQCRQ UQCRQ UQCRQ 2751 0.14 0.045 YES
5 ATP5I ATP5I ATP5I 3218 0.11 0.044 YES
6 NDUFA3 NDUFA3 NDUFA3 3260 0.11 0.066 YES
7 COX6C COX6C COX6C 3280 0.11 0.089 YES
8 COX6B1 COX6B1 COX6B1 3455 0.1 0.1 YES
9 NDUFA2 NDUFA2 NDUFA2 3483 0.1 0.12 YES
10 NDUFA1 NDUFA1 NDUFA1 3595 0.098 0.14 YES
11 COX6A1 COX6A1 COX6A1 3691 0.095 0.15 YES
12 COX7C COX7C COX7C 3721 0.094 0.17 YES
13 ATP5D ATP5D ATP5D 3781 0.092 0.19 YES
14 COX5B COX5B COX5B 3971 0.086 0.2 YES
15 NDUFV3 NDUFV3 NDUFV3 3991 0.085 0.21 YES
16 NDUFS7 NDUFS7 NDUFS7 4015 0.085 0.23 YES
17 COX4I1 COX4I1 COX4I1 4021 0.085 0.25 YES
18 UQCR11 UQCR11 UQCR11 4051 0.084 0.27 YES
19 NDUFB7 NDUFB7 NDUFB7 4061 0.084 0.28 YES
20 NDUFA13 NDUFA13 NDUFA13 4074 0.083 0.3 YES
21 COX5A COX5A COX5A 4133 0.082 0.32 YES
22 NDUFC1 NDUFC1 NDUFC1 4149 0.081 0.33 YES
23 NDUFA5 NDUFA5 NDUFA5 4318 0.077 0.34 YES
24 NDUFV2 NDUFV2 NDUFV2 4398 0.075 0.35 YES
25 COX7B COX7B COX7B 4565 0.07 0.36 YES
26 NDUFB10 NDUFB10 NDUFB10 4702 0.067 0.36 YES
27 NDUFA6 NDUFA6 NDUFA6 4711 0.067 0.38 YES
28 UQCRHL UQCRHL UQCRHL 4828 0.064 0.38 YES
29 NDUFS5 NDUFS5 NDUFS5 4869 0.062 0.4 YES
30 NDUFS8 NDUFS8 NDUFS8 4926 0.061 0.41 YES
31 UQCRH UQCRH UQCRH 4942 0.061 0.42 YES
32 CYC1 CYC1 CYC1 5027 0.058 0.43 YES
33 NDUFB1 NDUFB1 NDUFB1 5036 0.058 0.44 YES
34 UQCRB UQCRB UQCRB 5061 0.057 0.45 YES
35 ATP5J2 ATP5J2 ATP5J2 5126 0.056 0.46 YES
36 NDUFB8 NDUFB8 NDUFB8 5220 0.054 0.46 YES
37 ATP5C1 ATP5C1 ATP5C1 5360 0.05 0.47 YES
38 ATP5H ATP5H ATP5H 5520 0.047 0.47 YES
39 ATP5L ATP5L ATP5L 5569 0.046 0.48 YES
40 ETFA ETFA ETFA 5623 0.045 0.48 YES
41 NDUFA11 NDUFA11 NDUFA11 5651 0.044 0.49 YES
42 NDUFA10 NDUFA10 NDUFA10 5673 0.044 0.5 YES
43 ETFDH ETFDH ETFDH 5766 0.042 0.5 YES
44 ATP5O ATP5O ATP5O 5777 0.042 0.51 YES
45 NDUFB4 NDUFB4 NDUFB4 5930 0.039 0.51 YES
46 NDUFC2 NDUFC2 NDUFC2 6251 0.034 0.5 YES
47 NDUFA4 NDUFA4 NDUFA4 6316 0.032 0.51 YES
48 UCP1 UCP1 UCP1 6323 0.032 0.51 YES
49 NDUFB2 NDUFB2 NDUFB2 6397 0.031 0.52 YES
50 ATP5G1 ATP5G1 ATP5G1 6565 0.028 0.51 YES
51 ETFB ETFB ETFB 6644 0.027 0.51 YES
52 ATP5E ATP5E ATP5E 6647 0.026 0.52 YES
53 UQCRC1 UQCRC1 UQCRC1 6658 0.026 0.52 YES
54 NDUFA8 NDUFA8 NDUFA8 6717 0.026 0.53 YES
55 ATP5A1 ATP5A1 ATP5A1 6758 0.025 0.53 YES
56 COX8A COX8A COX8A 6786 0.024 0.53 YES
57 ATP5J ATP5J ATP5J 6824 0.024 0.54 YES
58 CYCS CYCS CYCS 6957 0.021 0.54 NO
59 NDUFB9 NDUFB9 NDUFB9 7027 0.02 0.54 NO
60 ATP5F1 ATP5F1 ATP5F1 7088 0.019 0.54 NO
61 SDHD SDHD SDHD 7316 0.015 0.53 NO
62 UQCRC2 UQCRC2 UQCRC2 7578 0.011 0.52 NO
63 NDUFS2 NDUFS2 NDUFS2 7674 0.0092 0.51 NO
64 NDUFA12 NDUFA12 NDUFA12 7721 0.0083 0.51 NO
65 NDUFV1 NDUFV1 NDUFV1 7754 0.0075 0.51 NO
66 NDUFB5 NDUFB5 NDUFB5 7783 0.0071 0.51 NO
67 NDUFS3 NDUFS3 NDUFS3 7853 0.0057 0.51 NO
68 SDHC SDHC SDHC 8276 -0.0016 0.48 NO
69 ATP5B ATP5B ATP5B 8589 -0.007 0.47 NO
70 NDUFA9 NDUFA9 NDUFA9 8629 -0.0078 0.47 NO
71 NDUFAB1 NDUFAB1 NDUFAB1 8654 -0.0081 0.47 NO
72 SDHB SDHB SDHB 8784 -0.0099 0.46 NO
73 NDUFB3 NDUFB3 NDUFB3 9089 -0.015 0.45 NO
74 NDUFS6 NDUFS6 NDUFS6 9538 -0.022 0.43 NO
75 COX7A2L COX7A2L COX7A2L 9705 -0.024 0.43 NO
76 UQCRFS1 UQCRFS1 UQCRFS1 9726 -0.024 0.43 NO
77 NDUFB6 NDUFB6 NDUFB6 9784 -0.025 0.43 NO
78 NDUFS4 NDUFS4 NDUFS4 10296 -0.034 0.41 NO
79 NDUFS1 NDUFS1 NDUFS1 11022 -0.048 0.38 NO
80 SDHA SDHA SDHA 11553 -0.06 0.37 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 GLYCOSYLPHOSPHATIDYLINOSITOL GPI ANCHOR BIOSYNTHESIS.

Figure S30.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GLYCOSYLPHOSPHATIDYLINOSITOL GPI ANCHOR 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 LINOLEIC ACID 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 UGT1A1 UGT1A1 UGT1A1 102 0.58 0.094 YES
2 UGT1A9 UGT1A9 UGT1A9 206 0.48 0.17 YES
3 UGT1A6 UGT1A6 UGT1A6 248 0.46 0.25 YES
4 UGT2B28 UGT2B28 UGT2B28 296 0.44 0.32 YES
5 UGT1A3 UGT1A3 UGT1A3 387 0.4 0.38 YES
6 UGT2B7 UGT2B7 UGT2B7 499 0.37 0.44 YES
7 UGT2B15 UGT2B15 UGT2B15 634 0.34 0.49 YES
8 UGT2B4 UGT2B4 UGT2B4 867 0.3 0.53 YES
9 UGT2A3 UGT2A3 UGT2A3 969 0.28 0.57 YES
10 UGT1A5 UGT1A5 UGT1A5 991 0.28 0.62 YES
11 UGT1A4 UGT1A4 UGT1A4 1026 0.28 0.67 YES
12 UGT2B11 UGT2B11 UGT2B11 1033 0.27 0.71 YES
13 UGT2B10 UGT2B10 UGT2B10 1338 0.23 0.74 YES
14 UGT1A8 UGT1A8 UGT1A8 2404 0.15 0.7 YES
15 CRYL1 CRYL1 CRYL1 2763 0.13 0.71 YES
16 UGT1A10 UGT1A10 UGT1A10 3000 0.12 0.72 YES
17 XYLB XYLB XYLB 3019 0.12 0.74 YES
18 DCXR DCXR DCXR 3136 0.12 0.75 YES
19 AKR1B1 AKR1B1 AKR1B1 6263 0.033 0.58 NO
20 GUSB GUSB GUSB 8182 -0.00011 0.48 NO
21 UGDH UGDH UGDH 8398 -0.0038 0.47 NO
22 UGT2A1 UGT2A1 UGT2A1 8752 -0.0094 0.45 NO
23 DHDH DHDH DHDH 8895 -0.012 0.44 NO
24 UGT1A7 UGT1A7 UGT1A7 9148 -0.016 0.43 NO
25 UGP2 UGP2 UGP2 11413 -0.056 0.32 NO
26 RPE RPE RPE 12158 -0.075 0.29 NO
27 LOC729020 LOC729020 LOC729020 16092 -0.25 0.12 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 LINOLEIC ACID METABOLISM.

Figure S32.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG LINOLEIC ACID 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 RETINOL 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 UGT1A1 UGT1A1 UGT1A1 102 0.58 0.038 YES
2 CYP3A5 CYP3A5 CYP3A5 169 0.51 0.073 YES
3 CYP2C8 CYP2C8 CYP2C8 204 0.48 0.11 YES
4 UGT1A9 UGT1A9 UGT1A9 206 0.48 0.14 YES
5 UGT1A6 UGT1A6 UGT1A6 248 0.46 0.18 YES
6 ADH6 ADH6 ADH6 256 0.46 0.21 YES
7 UGT2B28 UGT2B28 UGT2B28 296 0.44 0.24 YES
8 DGAT2 DGAT2 DGAT2 336 0.42 0.27 YES
9 UGT1A3 UGT1A3 UGT1A3 387 0.4 0.3 YES
10 CYP2C9 CYP2C9 CYP2C9 388 0.4 0.33 YES
11 CYP3A7 CYP3A7 CYP3A7 427 0.39 0.36 YES
12 CYP4A11 CYP4A11 CYP4A11 489 0.37 0.38 YES
13 UGT2B7 UGT2B7 UGT2B7 499 0.37 0.41 YES
14 CYP1A1 CYP1A1 CYP1A1 630 0.34 0.43 YES
15 UGT2B15 UGT2B15 UGT2B15 634 0.34 0.45 YES
16 UGT2B4 UGT2B4 UGT2B4 867 0.3 0.46 YES
17 BCMO1 BCMO1 BCMO1 922 0.29 0.48 YES
18 UGT2A3 UGT2A3 UGT2A3 969 0.28 0.5 YES
19 CYP1A2 CYP1A2 CYP1A2 983 0.28 0.52 YES
20 UGT1A5 UGT1A5 UGT1A5 991 0.28 0.54 YES
21 UGT1A4 UGT1A4 UGT1A4 1026 0.28 0.56 YES
22 UGT2B11 UGT2B11 UGT2B11 1033 0.27 0.58 YES
23 CYP2C19 CYP2C19 CYP2C19 1039 0.27 0.6 YES
24 CYP4A22 CYP4A22 CYP4A22 1230 0.25 0.61 YES
25 UGT2B10 UGT2B10 UGT2B10 1338 0.23 0.62 YES
26 ALDH1A2 ALDH1A2 ALDH1A2 1564 0.21 0.63 YES
27 CYP2C18 CYP2C18 CYP2C18 1599 0.21 0.64 YES
28 ADH1C ADH1C ADH1C 1601 0.21 0.66 YES
29 CYP3A43 CYP3A43 CYP3A43 2087 0.17 0.64 NO
30 ADH4 ADH4 ADH4 2277 0.16 0.64 NO
31 UGT1A8 UGT1A8 UGT1A8 2404 0.15 0.65 NO
32 UGT1A10 UGT1A10 UGT1A10 3000 0.12 0.63 NO
33 DGAT1 DGAT1 DGAT1 3157 0.12 0.63 NO
34 DHRS3 DHRS3 DHRS3 3416 0.1 0.62 NO
35 ADH1A ADH1A ADH1A 3471 0.1 0.62 NO
36 RDH12 RDH12 RDH12 4240 0.079 0.59 NO
37 RDH16 RDH16 RDH16 4322 0.077 0.59 NO
38 RDH10 RDH10 RDH10 4381 0.075 0.59 NO
39 ADH1B ADH1B ADH1B 4495 0.072 0.59 NO
40 RDH5 RDH5 RDH5 6166 0.035 0.5 NO
41 CYP3A4 CYP3A4 CYP3A4 6226 0.034 0.5 NO
42 CYP26A1 CYP26A1 CYP26A1 6243 0.034 0.5 NO
43 CYP2A6 CYP2A6 CYP2A6 6908 0.022 0.47 NO
44 RDH11 RDH11 RDH11 6950 0.021 0.47 NO
45 PNPLA4 PNPLA4 PNPLA4 7371 0.014 0.45 NO
46 ADH5 ADH5 ADH5 7421 0.014 0.44 NO
47 DHRS4L2 DHRS4L2 DHRS4L2 8199 -0.00039 0.4 NO
48 ADH7 ADH7 ADH7 8670 -0.0083 0.38 NO
49 UGT2A1 UGT2A1 UGT2A1 8752 -0.0094 0.37 NO
50 DHRS4 DHRS4 DHRS4 8924 -0.012 0.36 NO
51 RETSAT RETSAT RETSAT 9072 -0.015 0.36 NO
52 UGT1A7 UGT1A7 UGT1A7 9148 -0.016 0.35 NO
53 CYP2B6 CYP2B6 CYP2B6 11486 -0.058 0.23 NO
54 LRAT LRAT LRAT 12709 -0.089 0.17 NO
55 AWAT2 AWAT2 AWAT2 13286 -0.11 0.14 NO
56 CYP26C1 CYP26C1 CYP26C1 13438 -0.11 0.15 NO
57 RPE65 RPE65 RPE65 14245 -0.15 0.11 NO
58 RDH8 RDH8 RDH8 15136 -0.19 0.078 NO
59 ALDH1A1 ALDH1A1 ALDH1A1 16658 -0.3 0.017 NO
60 DHRS9 DHRS9 DHRS9 17542 -0.4 -0.0016 NO
61 CYP26B1 CYP26B1 CYP26B1 17994 -0.5 0.011 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 RETINOL METABOLISM.

Figure S34.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG RETINOL 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 PORPHYRIN AND CHLOROPHYLL 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 HSD17B2 HSD17B2 HSD17B2 65 0.64 0.048 YES
2 UGT1A1 UGT1A1 UGT1A1 102 0.58 0.093 YES
3 CYP3A5 CYP3A5 CYP3A5 169 0.51 0.13 YES
4 UGT1A9 UGT1A9 UGT1A9 206 0.48 0.17 YES
5 UGT1A6 UGT1A6 UGT1A6 248 0.46 0.2 YES
6 UGT2B28 UGT2B28 UGT2B28 296 0.44 0.23 YES
7 AKR1C2 AKR1C2 AKR1C2 310 0.43 0.27 YES
8 UGT1A3 UGT1A3 UGT1A3 387 0.4 0.3 YES
9 AKR1C3 AKR1C3 AKR1C3 413 0.39 0.33 YES
10 CYP3A7 CYP3A7 CYP3A7 427 0.39 0.36 YES
11 UGT2B7 UGT2B7 UGT2B7 499 0.37 0.38 YES
12 CYP1A1 CYP1A1 CYP1A1 630 0.34 0.4 YES
13 UGT2B15 UGT2B15 UGT2B15 634 0.34 0.43 YES
14 UGT2B4 UGT2B4 UGT2B4 867 0.3 0.44 YES
15 AKR1C1 AKR1C1 AKR1C1 917 0.29 0.46 YES
16 UGT2A3 UGT2A3 UGT2A3 969 0.28 0.48 YES
17 UGT1A5 UGT1A5 UGT1A5 991 0.28 0.5 YES
18 UGT1A4 UGT1A4 UGT1A4 1026 0.28 0.53 YES
19 UGT2B11 UGT2B11 UGT2B11 1033 0.27 0.55 YES
20 SULT1E1 SULT1E1 SULT1E1 1142 0.26 0.56 YES
21 UGT2B10 UGT2B10 UGT2B10 1338 0.23 0.57 YES
22 AKR1C4 AKR1C4 AKR1C4 1453 0.22 0.58 YES
23 COMT COMT COMT 1640 0.21 0.59 YES
24 HSD3B1 HSD3B1 HSD3B1 1659 0.2 0.6 YES
25 STS STS STS 1776 0.19 0.61 YES
26 HSD11B2 HSD11B2 HSD11B2 1876 0.19 0.62 YES
27 AKR1D1 AKR1D1 AKR1D1 1931 0.18 0.64 YES
28 CYP3A43 CYP3A43 CYP3A43 2087 0.17 0.64 YES
29 UGT1A8 UGT1A8 UGT1A8 2404 0.15 0.64 NO
30 HSD17B7 HSD17B7 HSD17B7 2543 0.14 0.64 NO
31 UGT1A10 UGT1A10 UGT1A10 3000 0.12 0.62 NO
32 SRD5A2 SRD5A2 SRD5A2 3085 0.12 0.63 NO
33 HSD3B2 HSD3B2 HSD3B2 4010 0.085 0.58 NO
34 CYP11A1 CYP11A1 CYP11A1 4109 0.082 0.59 NO
35 HSD17B8 HSD17B8 HSD17B8 5436 0.049 0.52 NO
36 HSD17B1 HSD17B1 HSD17B1 5807 0.042 0.5 NO
37 CYP3A4 CYP3A4 CYP3A4 6226 0.034 0.48 NO
38 CYP7A1 CYP7A1 CYP7A1 6997 0.021 0.44 NO
39 SRD5A3 SRD5A3 SRD5A3 7021 0.02 0.44 NO
40 UGT2A1 UGT2A1 UGT2A1 8752 -0.0094 0.34 NO
41 UGT1A7 UGT1A7 UGT1A7 9148 -0.016 0.32 NO
42 CYP17A1 CYP17A1 CYP17A1 11209 -0.052 0.22 NO
43 HSD17B12 HSD17B12 HSD17B12 12732 -0.09 0.14 NO
44 CYP1B1 CYP1B1 CYP1B1 14152 -0.14 0.072 NO
45 HSD17B3 HSD17B3 HSD17B3 14253 -0.15 0.078 NO
46 CYP21A2 CYP21A2 CYP21A2 14610 -0.16 0.071 NO
47 HSD11B1 HSD11B1 HSD11B1 15230 -0.2 0.053 NO
48 HSD17B6 HSD17B6 HSD17B6 15990 -0.25 0.031 NO
49 SULT2B1 SULT2B1 SULT2B1 16004 -0.25 0.05 NO
50 SRD5A1 SRD5A1 SRD5A1 16051 -0.25 0.068 NO
51 CYP19A1 CYP19A1 CYP19A1 16603 -0.29 0.062 NO
52 CYP7B1 CYP7B1 CYP7B1 16903 -0.32 0.071 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 PORPHYRIN AND CHLOROPHYLL METABOLISM.

Figure S36.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PORPHYRIN AND CHLOROPHYLL 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 METABOLISM OF XENOBIOTICS BY CYTOCHROME P450

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 UGT1A1 UGT1A1 UGT1A1 102 0.58 0.034 YES
2 CYP3A5 CYP3A5 CYP3A5 169 0.51 0.064 YES
3 CYP2C8 CYP2C8 CYP2C8 204 0.48 0.095 YES
4 UGT1A9 UGT1A9 UGT1A9 206 0.48 0.13 YES
5 UGT1A6 UGT1A6 UGT1A6 248 0.46 0.16 YES
6 FMO5 FMO5 FMO5 250 0.46 0.19 YES
7 ADH6 ADH6 ADH6 256 0.46 0.22 YES
8 UGT2B28 UGT2B28 UGT2B28 296 0.44 0.24 YES
9 MAOA MAOA MAOA 331 0.42 0.27 YES
10 UGT1A3 UGT1A3 UGT1A3 387 0.4 0.3 YES
11 CYP2C9 CYP2C9 CYP2C9 388 0.4 0.32 YES
12 CYP3A7 CYP3A7 CYP3A7 427 0.39 0.35 YES
13 GSTM4 GSTM4 GSTM4 447 0.38 0.37 YES
14 UGT2B7 UGT2B7 UGT2B7 499 0.37 0.4 YES
15 UGT2B15 UGT2B15 UGT2B15 634 0.34 0.41 YES
16 GSTM2 GSTM2 GSTM2 643 0.34 0.43 YES
17 UGT2B4 UGT2B4 UGT2B4 867 0.3 0.44 YES
18 UGT2A3 UGT2A3 UGT2A3 969 0.28 0.46 YES
19 CYP1A2 CYP1A2 CYP1A2 983 0.28 0.47 YES
20 UGT1A5 UGT1A5 UGT1A5 991 0.28 0.49 YES
21 UGT1A4 UGT1A4 UGT1A4 1026 0.28 0.51 YES
22 UGT2B11 UGT2B11 UGT2B11 1033 0.27 0.53 YES
23 CYP2C19 CYP2C19 CYP2C19 1039 0.27 0.55 YES
24 CYP2D6 CYP2D6 CYP2D6 1110 0.26 0.56 YES
25 GSTM3 GSTM3 GSTM3 1205 0.25 0.57 YES
26 UGT2B10 UGT2B10 UGT2B10 1338 0.23 0.58 YES
27 MGST2 MGST2 MGST2 1391 0.23 0.59 YES
28 CYP2C18 CYP2C18 CYP2C18 1599 0.21 0.6 YES
29 ADH1C ADH1C ADH1C 1601 0.21 0.61 YES
30 ALDH3B2 ALDH3B2 ALDH3B2 1657 0.2 0.62 YES
31 CYP3A43 CYP3A43 CYP3A43 2087 0.17 0.61 YES
32 ADH4 ADH4 ADH4 2277 0.16 0.61 YES
33 GSTA1 GSTA1 GSTA1 2294 0.16 0.62 YES
34 GSTM1 GSTM1 GSTM1 2346 0.16 0.63 YES
35 UGT1A8 UGT1A8 UGT1A8 2404 0.15 0.63 YES
36 MGST1 MGST1 MGST1 2408 0.15 0.64 YES
37 GSTA2 GSTA2 GSTA2 2887 0.13 0.63 NO
38 GSTO2 GSTO2 GSTO2 2960 0.12 0.63 NO
39 UGT1A10 UGT1A10 UGT1A10 3000 0.12 0.64 NO
40 ADH1A ADH1A ADH1A 3471 0.1 0.62 NO
41 GSTK1 GSTK1 GSTK1 4008 0.085 0.59 NO
42 GSTZ1 GSTZ1 GSTZ1 4235 0.079 0.59 NO
43 ADH1B ADH1B ADH1B 4495 0.072 0.58 NO
44 GSTT1 GSTT1 GSTT1 4628 0.069 0.57 NO
45 CYP3A4 CYP3A4 CYP3A4 6226 0.034 0.49 NO
46 ALDH3B1 ALDH3B1 ALDH3B1 6352 0.031 0.48 NO
47 CYP2E1 CYP2E1 CYP2E1 6450 0.03 0.48 NO
48 MGST3 MGST3 MGST3 6675 0.026 0.47 NO
49 CYP2A6 CYP2A6 CYP2A6 6908 0.022 0.46 NO
50 ADH5 ADH5 ADH5 7421 0.014 0.43 NO
51 GSTT2 GSTT2 GSTT2 7703 0.0087 0.42 NO
52 ALDH3A1 ALDH3A1 ALDH3A1 8321 -0.0025 0.38 NO
53 ADH7 ADH7 ADH7 8670 -0.0083 0.36 NO
54 UGT2A1 UGT2A1 UGT2A1 8752 -0.0094 0.36 NO
55 GSTP1 GSTP1 GSTP1 9007 -0.014 0.35 NO
56 GSTO1 GSTO1 GSTO1 9054 -0.014 0.34 NO
57 UGT1A7 UGT1A7 UGT1A7 9148 -0.016 0.34 NO
58 CYP2B6 CYP2B6 CYP2B6 11486 -0.058 0.22 NO
59 FMO4 FMO4 FMO4 11984 -0.07 0.19 NO
60 GSTM5 GSTM5 GSTM5 12002 -0.071 0.2 NO
61 FMO3 FMO3 FMO3 12473 -0.082 0.18 NO
62 ALDH1A3 ALDH1A3 ALDH1A3 13876 -0.13 0.11 NO
63 GSTA4 GSTA4 GSTA4 16416 -0.28 -0.012 NO
64 AOX1 AOX1 AOX1 17110 -0.34 -0.027 NO
65 FMO2 FMO2 FMO2 17398 -0.38 -0.017 NO
66 MAOB MAOB MAOB 17548 -0.4 0.0017 NO
67 FMO1 FMO1 FMO1 18008 -0.5 0.01 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 METABOLISM OF XENOBIOTICS BY CYTOCHROME P450.

Figure S38.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450, 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 CYTOCHROME P450

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 PLA2G2F PLA2G2F PLA2G2F 23 0.74 0.11 YES
2 CYP2J2 CYP2J2 CYP2J2 130 0.54 0.19 YES
3 CYP3A5 CYP3A5 CYP3A5 169 0.51 0.26 YES
4 CYP2C8 CYP2C8 CYP2C8 204 0.48 0.34 YES
5 CYP2C9 CYP2C9 CYP2C9 388 0.4 0.39 YES
6 CYP3A7 CYP3A7 CYP3A7 427 0.39 0.44 YES
7 PLA2G10 PLA2G10 PLA2G10 747 0.32 0.48 YES
8 PLA2G6 PLA2G6 PLA2G6 791 0.31 0.52 YES
9 ALOX15 ALOX15 ALOX15 833 0.31 0.57 YES
10 CYP1A2 CYP1A2 CYP1A2 983 0.28 0.6 YES
11 CYP2C19 CYP2C19 CYP2C19 1039 0.27 0.64 YES
12 JMJD7-PLA2G4B JMJD7-PLA2G4B JMJD7-PLA2G4B 1100 0.26 0.68 YES
13 CYP2C18 CYP2C18 CYP2C18 1599 0.21 0.68 YES
14 CYP3A43 CYP3A43 CYP3A43 2087 0.17 0.68 NO
15 PLA2G1B PLA2G1B PLA2G1B 2679 0.14 0.67 NO
16 PLA2G12A PLA2G12A PLA2G12A 3060 0.12 0.67 NO
17 PLA2G2A PLA2G2A PLA2G2A 3545 0.1 0.66 NO
18 CYP3A4 CYP3A4 CYP3A4 6226 0.034 0.52 NO
19 CYP2E1 CYP2E1 CYP2E1 6450 0.03 0.51 NO
20 PLA2G4A PLA2G4A PLA2G4A 11974 -0.07 0.22 NO
21 PLA2G3 PLA2G3 PLA2G3 13164 -0.1 0.17 NO
22 AKR1B10 AKR1B10 AKR1B10 13537 -0.12 0.16 NO
23 PLA2G2D PLA2G2D PLA2G2D 13813 -0.13 0.17 NO
24 PLA2G4E PLA2G4E PLA2G4E 15363 -0.2 0.11 NO
25 PLA2G5 PLA2G5 PLA2G5 16337 -0.27 0.1 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 DRUG METABOLISM CYTOCHROME P450.

Figure S40.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG DRUG METABOLISM CYTOCHROME P450, 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 PENTOSE AND GLUCURONATE INTERCONVERSIONS 27 genes.ES.table 0.68 1.5 0.073 1 0.98 0.52 0.12 0.46 1 0.72
KEGG GLUTATHIONE METABOLISM 46 genes.ES.table 0.45 1.4 0.12 1 0.99 0.41 0.13 0.36 1 0.59
KEGG RETINOL METABOLISM 61 genes.ES.table 0.55 1.4 0.11 1 0.99 0.39 0.098 0.36 1 0.62
KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM 39 genes.ES.table 0.61 1.6 0.056 1 0.95 0.36 0.097 0.32 1 0.61
KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450 67 genes.ES.table 0.6 1.4 0.11 1 0.99 0.52 0.13 0.46 1 0.62
KEGG DRUG METABOLISM OTHER ENZYMES 47 genes.ES.table 0.59 1.6 0.022 1 0.94 0.4 0.096 0.37 1 0.63
KEGG BASAL TRANSCRIPTION FACTORS 34 genes.ES.table 0.44 1.4 0.12 1 0.99 0.24 0.16 0.2 1 0.63
BIOCARTA EGF PATHWAY 31 genes.ES.table 0.43 1.4 0.14 1 0.99 0.42 0.28 0.3 1 0.67
PID TRAIL PATHWAY 28 genes.ES.table 0.44 1.4 0.16 1 0.99 0.43 0.25 0.32 1 0.63
PID IGF1 PATHWAY 30 genes.ES.table 0.36 1.4 0.11 1 0.99 0.53 0.32 0.36 1 0.67
genes ES table in pathway: KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS

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 PLA2G4A PLA2G4A PLA2G4A 239 0.37 0.12 YES
2 MITF MITF MITF 510 0.28 0.2 YES
3 PPARGC1A PPARGC1A PPARGC1A 739 0.23 0.27 YES
4 NOS2 NOS2 NOS2 1199 0.18 0.31 YES
5 KRT19 KRT19 KRT19 1310 0.17 0.36 YES
6 ATF2 ATF2 ATF2 1529 0.15 0.4 YES
7 PTGS2 PTGS2 PTGS2 2206 0.11 0.41 YES
8 HSPB1 HSPB1 HSPB1 2321 0.11 0.44 YES
9 RPS6KA5 RPS6KA5 RPS6KA5 2624 0.097 0.46 YES
10 ELK4 ELK4 ELK4 3017 0.084 0.46 YES
11 CEBPB CEBPB CEBPB 3726 0.067 0.45 YES
12 CREB1 CREB1 CREB1 3783 0.066 0.47 YES
13 ATF1 ATF1 ATF1 3788 0.065 0.49 YES
14 ESR1 ESR1 ESR1 4068 0.06 0.5 YES
15 KRT8 KRT8 KRT8 4289 0.055 0.5 YES
16 DDIT3 DDIT3 DDIT3 4294 0.055 0.52 YES
17 MEF2A MEF2A MEF2A 4856 0.045 0.51 NO
18 HBP1 HBP1 HBP1 5068 0.041 0.51 NO
19 JUN JUN JUN 5136 0.04 0.52 NO
20 EIF4E EIF4E EIF4E 5480 0.035 0.52 NO
21 MKNK1 MKNK1 MKNK1 6008 0.027 0.5 NO
22 SLC9A1 SLC9A1 SLC9A1 6252 0.024 0.49 NO
23 ATF6 ATF6 ATF6 7028 0.014 0.45 NO
24 RPS6KA4 RPS6KA4 RPS6KA4 7168 0.012 0.45 NO
25 CSNK2A1 CSNK2A1 CSNK2A1 7336 0.0099 0.44 NO
26 MAPKAPK5 MAPKAPK5 MAPKAPK5 7766 0.0047 0.42 NO
27 CSNK2A2 CSNK2A2 CSNK2A2 7993 0.0017 0.41 NO
28 MAPKAPK2 MAPKAPK2 MAPKAPK2 8105 0.00048 0.4 NO
29 MAPK14 MAPK14 MAPK14 8184 -0.00051 0.4 NO
30 TP53 TP53 TP53 8744 -0.0074 0.37 NO
31 RAB5A RAB5A RAB5A 9012 -0.011 0.36 NO
32 CSNK2B CSNK2B CSNK2B 10188 -0.027 0.31 NO
33 USF1 USF1 USF1 10674 -0.035 0.29 NO
34 MAPKAPK3 MAPKAPK3 MAPKAPK3 11078 -0.041 0.28 NO
35 GDI1 GDI1 GDI1 11285 -0.045 0.29 NO
36 EIF4EBP1 EIF4EBP1 EIF4EBP1 12937 -0.08 0.23 NO
37 MAPK11 MAPK11 MAPK11 13230 -0.088 0.24 NO
38 MEF2C MEF2C MEF2C 13323 -0.091 0.27 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 PENTOSE AND GLUCURONATE INTERCONVERSIONS.

Figure S42.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PENTOSE AND GLUCURONATE INTERCONVERSIONS, 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 GLUTATHIONE METABOLISM

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 ADHFE1 ADHFE1 ADHFE1 499 0.28 0.1 YES
2 D2HGDH D2HGDH D2HGDH 2110 0.12 0.072 YES
3 IDH1 IDH1 IDH1 2114 0.12 0.13 YES
4 SLC16A8 SLC16A8 SLC16A8 2350 0.11 0.17 YES
5 LDHB LDHB LDHB 2461 0.1 0.21 YES
6 NNT NNT NNT 3107 0.082 0.21 YES
7 SUCLG2 SUCLG2 SUCLG2 3193 0.079 0.24 YES
8 PDP2 PDP2 PDP2 3362 0.075 0.27 YES
9 SLC16A3 SLC16A3 SLC16A3 3480 0.072 0.3 YES
10 ACO2 ACO2 ACO2 3707 0.067 0.32 YES
11 PDPR PDPR PDPR 3800 0.065 0.34 YES
12 DLD DLD DLD 4043 0.06 0.36 YES
13 SUCLA2 SUCLA2 SUCLA2 4182 0.058 0.38 YES
14 SDHD SDHD SDHD 4271 0.056 0.4 YES
15 PDK1 PDK1 PDK1 4844 0.045 0.39 YES
16 PDP1 PDP1 PDP1 4850 0.045 0.41 YES
17 DLST DLST DLST 5002 0.042 0.42 YES
18 IDH3A IDH3A IDH3A 5620 0.033 0.4 NO
19 CS CS CS 6027 0.027 0.39 NO
20 SDHB SDHB SDHB 6258 0.024 0.39 NO
21 LDHA LDHA LDHA 6553 0.02 0.39 NO
22 SDHA SDHA SDHA 6586 0.02 0.39 NO
23 PDK3 PDK3 PDK3 6635 0.019 0.4 NO
24 DLAT DLAT DLAT 6638 0.019 0.41 NO
25 IDH3G IDH3G IDH3G 7242 0.011 0.38 NO
26 PDHB PDHB PDHB 7358 0.0097 0.38 NO
27 SDHC SDHC SDHC 7476 0.0084 0.38 NO
28 MDH2 MDH2 MDH2 7547 0.0075 0.38 NO
29 PDK2 PDK2 PDK2 8323 -0.0024 0.34 NO
30 SUCLG1 SUCLG1 SUCLG1 8492 -0.0045 0.33 NO
31 OGDH OGDH OGDH 8778 -0.0078 0.32 NO
32 FH FH FH 9049 -0.011 0.31 NO
33 PDHX PDHX PDHX 9105 -0.012 0.31 NO
34 L2HGDH L2HGDH L2HGDH 9314 -0.015 0.3 NO
35 IDH2 IDH2 IDH2 9381 -0.016 0.31 NO
36 PDHA1 PDHA1 PDHA1 10119 -0.026 0.28 NO
37 BSG BSG BSG 10270 -0.028 0.28 NO
38 IDH3B IDH3B IDH3B 10290 -0.028 0.3 NO
39 PDK4 PDK4 PDK4 13263 -0.089 0.18 NO
40 SLC16A1 SLC16A1 SLC16A1 15851 -0.2 0.13 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 GLUTATHIONE METABOLISM.

Figure S44.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG GLUTATHIONE 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 RETINOL METABOLISM

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 MAPK10 MAPK10 MAPK10 138 0.44 0.18 YES
2 DUSP7 DUSP7 DUSP7 945 0.21 0.23 YES
3 DUSP6 DUSP6 DUSP6 1403 0.16 0.28 YES
4 ATF2 ATF2 ATF2 1529 0.15 0.34 YES
5 RPS6KA1 RPS6KA1 RPS6KA1 1627 0.14 0.39 YES
6 RPS6KA5 RPS6KA5 RPS6KA5 2624 0.097 0.38 YES
7 PPP2CB PPP2CB PPP2CB 2724 0.094 0.42 YES
8 FOS FOS FOS 2763 0.093 0.45 YES
9 MAPK8 MAPK8 MAPK8 3712 0.067 0.43 YES
10 CREB1 CREB1 CREB1 3783 0.066 0.46 YES
11 ATF1 ATF1 ATF1 3788 0.065 0.48 YES
12 MEF2A MEF2A MEF2A 4856 0.045 0.44 NO
13 JUN JUN JUN 5136 0.04 0.45 NO
14 PPP2CA PPP2CA PPP2CA 6247 0.024 0.4 NO
15 MAPK1 MAPK1 MAPK1 6298 0.023 0.4 NO
16 RPS6KA3 RPS6KA3 RPS6KA3 7038 0.014 0.37 NO
17 DUSP4 DUSP4 DUSP4 7298 0.01 0.36 NO
18 MAPKAPK2 MAPKAPK2 MAPKAPK2 8105 0.00048 0.32 NO
19 MAPK14 MAPK14 MAPK14 8184 -0.00051 0.31 NO
20 PPP2R1A PPP2R1A PPP2R1A 8509 -0.0047 0.3 NO
21 MAPK9 MAPK9 MAPK9 9994 -0.024 0.22 NO
22 ELK1 ELK1 ELK1 10344 -0.029 0.22 NO
23 DUSP3 DUSP3 DUSP3 10536 -0.032 0.22 NO
24 MAPK7 MAPK7 MAPK7 11229 -0.044 0.2 NO
25 PPP2R5D PPP2R5D PPP2R5D 11268 -0.045 0.22 NO
26 PPP2R1B PPP2R1B PPP2R1B 11482 -0.048 0.23 NO
27 MAPK3 MAPK3 MAPK3 12494 -0.069 0.2 NO
28 RPS6KA2 RPS6KA2 RPS6KA2 12530 -0.07 0.23 NO
29 MAPK11 MAPK11 MAPK11 13230 -0.088 0.23 NO
30 MEF2C MEF2C MEF2C 13323 -0.091 0.27 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 RETINOL METABOLISM.

Figure S46.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG RETINOL 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 PORPHYRIN AND CHLOROPHYLL METABOLISM

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 UGT1A10 UGT1A10 UGT1A10 19 0.63 0.074 YES
2 UGT2B28 UGT2B28 UGT2B28 116 0.45 0.12 YES
3 UGT1A8 UGT1A8 UGT1A8 117 0.45 0.18 YES
4 UGT1A9 UGT1A9 UGT1A9 131 0.44 0.23 YES
5 DPYD DPYD DPYD 230 0.37 0.27 YES
6 CYP3A5 CYP3A5 CYP3A5 261 0.36 0.31 YES
7 UGT1A7 UGT1A7 UGT1A7 349 0.33 0.34 YES
8 XDH XDH XDH 381 0.32 0.38 YES
9 UGT1A6 UGT1A6 UGT1A6 393 0.31 0.42 YES
10 UGT1A1 UGT1A1 UGT1A1 503 0.28 0.44 YES
11 UGT1A4 UGT1A4 UGT1A4 539 0.27 0.48 YES
12 UGT1A3 UGT1A3 UGT1A3 686 0.24 0.5 YES
13 UGT2A1 UGT2A1 UGT2A1 707 0.24 0.52 YES
14 CYP3A4 CYP3A4 CYP3A4 966 0.2 0.53 YES
15 CYP2A6 CYP2A6 CYP2A6 1036 0.2 0.55 YES
16 UGT2B11 UGT2B11 UGT2B11 1158 0.18 0.57 YES
17 UPP2 UPP2 UPP2 1647 0.14 0.56 YES
18 UGT1A5 UGT1A5 UGT1A5 1739 0.14 0.57 YES
19 CES1 CES1 CES1 1740 0.14 0.59 YES
20 CES2 CES2 CES2 3087 0.082 0.52 NO
21 CYP3A7 CYP3A7 CYP3A7 4375 0.053 0.46 NO
22 TK2 TK2 TK2 4838 0.045 0.44 NO
23 NAT1 NAT1 NAT1 5505 0.035 0.4 NO
24 CYP3A43 CYP3A43 CYP3A43 5575 0.034 0.4 NO
25 HPRT1 HPRT1 HPRT1 6325 0.023 0.37 NO
26 IMPDH2 IMPDH2 IMPDH2 6364 0.022 0.37 NO
27 UMPS UMPS UMPS 7853 0.0036 0.29 NO
28 GMPS GMPS GMPS 9006 -0.01 0.22 NO
29 UCKL1 UCKL1 UCKL1 9437 -0.016 0.2 NO
30 TPMT TPMT TPMT 9812 -0.021 0.18 NO
31 UGT2B4 UGT2B4 UGT2B4 9939 -0.023 0.18 NO
32 ITPA ITPA ITPA 11509 -0.049 0.099 NO
33 TK1 TK1 TK1 12294 -0.065 0.064 NO
34 UGT2B15 UGT2B15 UGT2B15 12774 -0.076 0.046 NO
35 UCK2 UCK2 UCK2 12793 -0.076 0.054 NO
36 TYMP TYMP TYMP 12815 -0.077 0.063 NO
37 GUSB GUSB GUSB 12847 -0.078 0.07 NO
38 IMPDH1 IMPDH1 IMPDH1 13844 -0.11 0.028 NO
39 UCK1 UCK1 UCK1 13906 -0.11 0.038 NO
40 UGT2B10 UGT2B10 UGT2B10 13984 -0.11 0.047 NO
41 UPP1 UPP1 UPP1 14345 -0.13 0.043 NO
42 NAT2 NAT2 NAT2 14966 -0.16 0.027 NO
43 UGT2B7 UGT2B7 UGT2B7 15138 -0.16 0.037 NO
44 DPYS DPYS DPYS 15857 -0.2 0.022 NO
45 UPB1 UPB1 UPB1 15956 -0.21 0.042 NO
46 UGT2A3 UGT2A3 UGT2A3 17017 -0.28 0.017 NO
47 CDA CDA CDA 17965 -0.4 0.013 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: KEGG PORPHYRIN AND CHLOROPHYLL METABOLISM.

Figure S48.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG PORPHYRIN AND CHLOROPHYLL 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 METABOLISM OF XENOBIOTICS BY CYTOCHROME P450

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 CP CP CP 2 0.85 0.12 YES
2 UGT1A10 UGT1A10 UGT1A10 19 0.63 0.21 YES
3 UGT2B28 UGT2B28 UGT2B28 116 0.45 0.27 YES
4 UGT1A8 UGT1A8 UGT1A8 117 0.45 0.33 YES
5 UGT1A9 UGT1A9 UGT1A9 131 0.44 0.4 YES
6 UGT1A7 UGT1A7 UGT1A7 349 0.33 0.43 YES
7 UGT1A6 UGT1A6 UGT1A6 393 0.31 0.47 YES
8 UGT1A1 UGT1A1 UGT1A1 503 0.28 0.5 YES
9 UGT1A4 UGT1A4 UGT1A4 539 0.27 0.54 YES
10 UGT1A3 UGT1A3 UGT1A3 686 0.24 0.57 YES
11 UGT2A1 UGT2A1 UGT2A1 707 0.24 0.6 YES
12 UGT2B11 UGT2B11 UGT2B11 1158 0.18 0.6 YES
13 UGT1A5 UGT1A5 UGT1A5 1739 0.14 0.59 YES
14 ALAS2 ALAS2 ALAS2 1760 0.14 0.61 YES
15 BLVRB BLVRB BLVRB 2909 0.087 0.56 NO
16 FECH FECH FECH 3014 0.085 0.56 NO
17 CPOX CPOX CPOX 3407 0.074 0.55 NO
18 COX15 COX15 COX15 4423 0.052 0.5 NO
19 EARS2 EARS2 EARS2 4620 0.049 0.5 NO
20 MMAB MMAB MMAB 5251 0.038 0.47 NO
21 HCCS HCCS HCCS 6030 0.027 0.43 NO
22 FTH1 FTH1 FTH1 7595 0.0069 0.35 NO
23 BLVRA BLVRA BLVRA 7987 0.0018 0.33 NO
24 EPRS EPRS EPRS 8473 -0.0043 0.3 NO
25 UROD UROD UROD 8791 -0.008 0.28 NO
26 COX10 COX10 COX10 9004 -0.01 0.27 NO
27 UGT2B4 UGT2B4 UGT2B4 9939 -0.023 0.22 NO
28 HMOX2 HMOX2 HMOX2 10464 -0.031 0.2 NO
29 HMBS HMBS HMBS 11841 -0.055 0.13 NO
30 ALAS1 ALAS1 ALAS1 12537 -0.07 0.1 NO
31 UGT2B15 UGT2B15 UGT2B15 12774 -0.076 0.1 NO
32 GUSB GUSB GUSB 12847 -0.078 0.11 NO
33 ALAD ALAD ALAD 12956 -0.081 0.12 NO
34 PPOX PPOX PPOX 13069 -0.084 0.12 NO
35 UROS UROS UROS 13964 -0.11 0.087 NO
36 UGT2B10 UGT2B10 UGT2B10 13984 -0.11 0.1 NO
37 UGT2B7 UGT2B7 UGT2B7 15138 -0.16 0.062 NO
38 UGT2A3 UGT2A3 UGT2A3 17017 -0.28 -0.001 NO
39 HMOX1 HMOX1 HMOX1 18111 -0.46 0.0047 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: KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450.

Figure S50.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG METABOLISM OF XENOBIOTICS BY CYTOCHROME P450, 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 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 CCND1 CCND1 CCND1 761 0.23 0.056 YES
2 PIK3R1 PIK3R1 PIK3R1 834 0.22 0.15 YES
3 CTNND1 CTNND1 CTNND1 2335 0.11 0.11 YES
4 CDH1 CDH1 CDH1 2501 0.1 0.14 YES
5 KLHL20 KLHL20 KLHL20 2726 0.094 0.17 YES
6 NCKAP1 NCKAP1 NCKAP1 2738 0.093 0.21 YES
7 WASF2 WASF2 WASF2 2996 0.085 0.23 YES
8 JUP JUP JUP 3006 0.085 0.27 YES
9 CTNNA1 CTNNA1 CTNNA1 3722 0.067 0.26 YES
10 SRC SRC SRC 3959 0.062 0.27 YES
11 TJP1 TJP1 TJP1 4163 0.058 0.28 YES
12 PIK3CA PIK3CA PIK3CA 4329 0.055 0.3 YES
13 RAC1 RAC1 RAC1 4733 0.047 0.3 YES
14 IQGAP1 IQGAP1 IQGAP1 4855 0.045 0.31 YES
15 AKT1 AKT1 AKT1 5122 0.04 0.31 YES
16 ABI1 ABI1 ABI1 5268 0.038 0.32 YES
17 CRK CRK CRK 5294 0.038 0.33 YES
18 CDC42 CDC42 CDC42 5405 0.036 0.34 YES
19 CTTN CTTN CTTN 6038 0.027 0.32 NO
20 CSNK2A1 CSNK2A1 CSNK2A1 7336 0.0099 0.25 NO
21 DLG1 DLG1 DLG1 7704 0.0055 0.24 NO
22 ARF6 ARF6 ARF6 7789 0.0044 0.23 NO
23 CSNK2A2 CSNK2A2 CSNK2A2 7993 0.0017 0.22 NO
24 CTNNB1 CTNNB1 CTNNB1 8665 -0.0064 0.19 NO
25 ITGB7 ITGB7 ITGB7 9464 -0.017 0.15 NO
26 MLLT4 MLLT4 MLLT4 9691 -0.02 0.15 NO
27 RAP1B RAP1B RAP1B 10115 -0.026 0.13 NO
28 PIP5K1C PIP5K1C PIP5K1C 10162 -0.026 0.14 NO
29 RHOA RHOA RHOA 10177 -0.027 0.15 NO
30 CSNK2B CSNK2B CSNK2B 10188 -0.027 0.16 NO
31 TIAM1 TIAM1 TIAM1 10204 -0.027 0.18 NO
32 AP1M1 AP1M1 AP1M1 10284 -0.028 0.18 NO
33 RAP1A RAP1A RAP1A 10586 -0.033 0.18 NO
34 ITGAE ITGAE ITGAE 11179 -0.043 0.17 NO
35 NME1 NME1 NME1 11290 -0.045 0.18 NO
36 ENAH ENAH ENAH 12149 -0.062 0.16 NO
37 VAV2 VAV2 VAV2 13937 -0.11 0.11 NO
38 RAPGEF1 RAPGEF1 RAPGEF1 14458 -0.13 0.14 NO
39 CYFIP2 CYFIP2 CYFIP2 15208 -0.17 0.16 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: KEGG DRUG METABOLISM OTHER ENZYMES.

Figure S52.  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 BASAL TRANSCRIPTION FACTORS

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 UGT1A10 UGT1A10 UGT1A10 19 0.63 0.12 YES
2 UGT2B28 UGT2B28 UGT2B28 116 0.45 0.2 YES
3 UGT1A8 UGT1A8 UGT1A8 117 0.45 0.28 YES
4 UGT1A9 UGT1A9 UGT1A9 131 0.44 0.37 YES
5 UGT1A7 UGT1A7 UGT1A7 349 0.33 0.42 YES
6 UGT1A6 UGT1A6 UGT1A6 393 0.31 0.48 YES
7 UGT1A1 UGT1A1 UGT1A1 503 0.28 0.52 YES
8 UGT1A4 UGT1A4 UGT1A4 539 0.27 0.57 YES
9 UGT1A3 UGT1A3 UGT1A3 686 0.24 0.61 YES
10 UGT2A1 UGT2A1 UGT2A1 707 0.24 0.65 YES
11 UGT2B11 UGT2B11 UGT2B11 1158 0.18 0.66 YES
12 UGT1A5 UGT1A5 UGT1A5 1739 0.14 0.66 YES
13 LOC729020 LOC729020 LOC729020 1987 0.12 0.67 YES
14 UGDH UGDH UGDH 2128 0.12 0.68 YES
15 RPE RPE RPE 3665 0.068 0.61 NO
16 UGP2 UGP2 UGP2 7373 0.0095 0.41 NO
17 CRYL1 CRYL1 CRYL1 7580 0.007 0.4 NO
18 DCXR DCXR DCXR 8906 -0.0093 0.33 NO
19 XYLB XYLB XYLB 9674 -0.02 0.29 NO
20 UGT2B4 UGT2B4 UGT2B4 9939 -0.023 0.28 NO
21 UGT2B15 UGT2B15 UGT2B15 12774 -0.076 0.14 NO
22 GUSB GUSB GUSB 12847 -0.078 0.15 NO
23 DHDH DHDH DHDH 13584 -0.099 0.13 NO
24 AKR1B1 AKR1B1 AKR1B1 13706 -0.1 0.14 NO
25 UGT2B10 UGT2B10 UGT2B10 13984 -0.11 0.15 NO
26 UGT2B7 UGT2B7 UGT2B7 15138 -0.16 0.12 NO
27 UGT2A3 UGT2A3 UGT2A3 17017 -0.28 0.065 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: KEGG BASAL TRANSCRIPTION FACTORS.

Figure S54.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG BASAL TRANSCRIPTION FACTORS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA EGF PATHWAY

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 NRG4 NRG4 NRG4 50 0.52 0.12 YES
2 BTC BTC BTC 454 0.29 0.17 YES
3 EGF EGF EGF 621 0.25 0.23 YES
4 PIK3R1 PIK3R1 PIK3R1 834 0.22 0.27 YES
5 NRG2 NRG2 NRG2 1183 0.18 0.29 YES
6 ERBB4 ERBB4 ERBB4 1215 0.18 0.34 YES
7 ERBB3 ERBB3 ERBB3 1382 0.16 0.37 YES
8 HBEGF HBEGF HBEGF 2075 0.12 0.36 YES
9 THEM4 THEM4 THEM4 2491 0.1 0.36 YES
10 PDPK1 PDPK1 PDPK1 2713 0.094 0.37 YES
11 PHLPP1 PHLPP1 PHLPP1 3147 0.081 0.37 YES
12 EGFR EGFR EGFR 3272 0.077 0.38 YES
13 FOXO3 FOXO3 FOXO3 3342 0.075 0.39 YES
14 CASP9 CASP9 CASP9 3394 0.074 0.41 YES
15 RICTOR RICTOR RICTOR 3505 0.071 0.42 YES
16 CREB1 CREB1 CREB1 3783 0.066 0.42 YES
17 PIK3CA PIK3CA PIK3CA 4329 0.055 0.4 YES
18 MDM2 MDM2 MDM2 4403 0.053 0.41 YES
19 NRG1 NRG1 NRG1 4478 0.052 0.42 YES
20 TSC2 TSC2 TSC2 4709 0.047 0.42 NO
21 AKT1 AKT1 AKT1 5122 0.04 0.41 NO
22 AKT2 AKT2 AKT2 6478 0.021 0.34 NO
23 AKT1S1 AKT1S1 AKT1S1 6565 0.02 0.34 NO
24 MLST8 MLST8 MLST8 6616 0.019 0.34 NO
25 PTEN PTEN PTEN 6799 0.017 0.33 NO
26 MTOR MTOR MTOR 7088 0.013 0.32 NO
27 ERBB2 ERBB2 ERBB2 7249 0.011 0.31 NO
28 CDKN1A CDKN1A CDKN1A 7409 0.0091 0.31 NO
29 CDKN1B CDKN1B CDKN1B 7643 0.0062 0.3 NO
30 GSK3A GSK3A GSK3A 8407 -0.0033 0.26 NO
31 CHUK CHUK CHUK 9475 -0.017 0.2 NO
32 FOXO1 FOXO1 FOXO1 10812 -0.037 0.14 NO
33 GRB2 GRB2 GRB2 10838 -0.037 0.14 NO
34 FOXO4 FOXO4 FOXO4 10870 -0.038 0.15 NO
35 RPS6KB2 RPS6KB2 RPS6KB2 11247 -0.044 0.14 NO
36 BAD BAD BAD 11389 -0.047 0.14 NO
37 GAB1 GAB1 GAB1 12055 -0.06 0.12 NO
38 EREG EREG EREG 13183 -0.087 0.082 NO
39 MAPKAP1 MAPKAP1 MAPKAP1 13302 -0.091 0.098 NO
40 NR4A1 NR4A1 NR4A1 14579 -0.14 0.061 NO
41 TRIB3 TRIB3 TRIB3 16815 -0.27 0.0028 NO
42 AKT3 AKT3 AKT3 17239 -0.3 0.053 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: BIOCARTA EGF PATHWAY.

Figure S56.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA EGF 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 TRAIL PATHWAY

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 CLCA2 CLCA2 CLCA2 11 0.66 0.085 YES
2 SHH SHH SHH 115 0.45 0.14 YES
3 GPX2 GPX2 GPX2 121 0.45 0.2 YES
4 SERPINB5 SERPINB5 SERPINB5 154 0.43 0.25 YES
5 S100A2 S100A2 S100A2 184 0.4 0.3 YES
6 DHRS3 DHRS3 DHRS3 193 0.4 0.35 YES
7 TP63 TP63 TP63 215 0.38 0.4 YES
8 IGFBP3 IGFBP3 IGFBP3 775 0.23 0.4 YES
9 ITGB4 ITGB4 ITGB4 1244 0.17 0.4 YES
10 ITGA3 ITGA3 ITGA3 1268 0.17 0.42 YES
11 VDR VDR VDR 1292 0.17 0.44 YES
12 PRKCD PRKCD PRKCD 1730 0.14 0.43 YES
13 NQO1 NQO1 NQO1 1765 0.14 0.45 YES
14 PERP PERP PERP 2138 0.12 0.44 YES
15 IKBKB IKBKB IKBKB 2187 0.12 0.45 YES
16 EP300 EP300 EP300 2570 0.099 0.44 YES
17 SP1 SP1 SP1 2678 0.095 0.45 YES
18 FAS FAS FAS 2772 0.092 0.46 YES
19 GDF15 GDF15 GDF15 2992 0.085 0.46 NO
20 DST DST DST 3596 0.069 0.43 NO
21 PMAIP1 PMAIP1 PMAIP1 3724 0.067 0.44 NO
22 TFAP2C TFAP2C TFAP2C 4011 0.061 0.43 NO
23 SMARCD3 SMARCD3 SMARCD3 4064 0.06 0.43 NO
24 EVPL EVPL EVPL 4195 0.058 0.43 NO
25 WWP1 WWP1 WWP1 4214 0.057 0.44 NO
26 MDM2 MDM2 MDM2 4403 0.053 0.44 NO
27 JAG1 JAG1 JAG1 4925 0.044 0.41 NO
28 HBP1 HBP1 HBP1 5068 0.041 0.41 NO
29 DICER1 DICER1 DICER1 5917 0.029 0.37 NO
30 FLOT2 FLOT2 FLOT2 5956 0.028 0.37 NO
31 TP53I3 TP53I3 TP53I3 6035 0.027 0.37 NO
32 SPATA18 SPATA18 SPATA18 6686 0.018 0.33 NO
33 GADD45A GADD45A GADD45A 6909 0.015 0.32 NO
34 CDKN1A CDKN1A CDKN1A 7409 0.0091 0.3 NO
35 TRAF4 TRAF4 TRAF4 7759 0.0048 0.28 NO
36 PML PML PML 8155 -0.00014 0.26 NO
37 FDXR FDXR FDXR 8660 -0.0063 0.23 NO
38 ITCH ITCH ITCH 8689 -0.0067 0.23 NO
39 NOC2L NOC2L NOC2L 8776 -0.0078 0.23 NO
40 SSRP1 SSRP1 SSRP1 8835 -0.0085 0.22 NO
41 CHUK CHUK CHUK 9475 -0.017 0.19 NO
42 YWHAQ YWHAQ YWHAQ 9930 -0.023 0.17 NO
43 BAX BAX BAX 12824 -0.077 0.019 NO
44 AEN AEN AEN 13322 -0.091 0.0038 NO
45 ABL1 ABL1 ABL1 13630 -0.1 -0.00013 NO
46 PLK1 PLK1 PLK1 13754 -0.1 0.0067 NO
47 ADA ADA ADA 13940 -0.11 0.011 NO
48 BBC3 BBC3 BBC3 14001 -0.11 0.022 NO
49 MFGE8 MFGE8 MFGE8 14479 -0.13 0.013 NO
50 OGG1 OGG1 OGG1 15431 -0.18 -0.016 NO
51 SSPO SSPO SSPO 16111 -0.22 -0.025 NO
52 CABLES1 CABLES1 CABLES1 17182 -0.3 -0.046 NO
53 EGR2 EGR2 EGR2 17718 -0.36 -0.029 NO
54 CDKN2A CDKN2A CDKN2A 18047 -0.43 0.0083 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: PID TRAIL PATHWAY.

Figure S58.  Get High-res Image For the top 5 core enriched genes in the pathway: PID TRAIL 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 IGF1 PATHWAY

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 GNAI1 GNAI1 GNAI1 560 0.26 0.077 YES
2 EGF EGF EGF 621 0.25 0.18 YES
3 PIK3R1 PIK3R1 PIK3R1 834 0.22 0.26 YES
4 PAK1 PAK1 PAK1 1795 0.13 0.26 YES
5 NCK1 NCK1 NCK1 2126 0.12 0.29 YES
6 WASL WASL WASL 2265 0.11 0.32 YES
7 PTK2 PTK2 PTK2 2955 0.086 0.32 YES
8 EGFR EGFR EGFR 3272 0.077 0.34 YES
9 PIK3R2 PIK3R2 PIK3R2 3784 0.066 0.33 YES
10 SRC SRC SRC 3959 0.062 0.35 YES
11 PIK3CA PIK3CA PIK3CA 4329 0.055 0.35 YES
12 STAT3 STAT3 STAT3 4368 0.054 0.37 YES
13 PTPN6 PTPN6 PTPN6 4773 0.046 0.37 YES
14 SHC1 SHC1 SHC1 4846 0.045 0.38 YES
15 KRAS KRAS KRAS 4927 0.043 0.39 YES
16 PIK3R3 PIK3R3 PIK3R3 5459 0.035 0.38 NO
17 PTPN11 PTPN11 PTPN11 5472 0.035 0.39 NO
18 MAPK1 MAPK1 MAPK1 6298 0.023 0.36 NO
19 RASA1 RASA1 RASA1 6882 0.016 0.33 NO
20 GNAI3 GNAI3 GNAI3 7558 0.0074 0.3 NO
21 SOS1 SOS1 SOS1 7641 0.0062 0.3 NO
22 STAT1 STAT1 STAT1 7652 0.006 0.3 NO
23 PTPN1 PTPN1 PTPN1 8380 -0.0029 0.26 NO
24 NCK2 NCK2 NCK2 8479 -0.0044 0.26 NO
25 PIK3CB PIK3CB PIK3CB 9866 -0.022 0.19 NO
26 PIP5K1C PIP5K1C PIP5K1C 10162 -0.026 0.18 NO
27 NRAS NRAS NRAS 10172 -0.027 0.19 NO
28 HRAS HRAS HRAS 10770 -0.036 0.17 NO
29 GRB2 GRB2 GRB2 10838 -0.037 0.19 NO
30 PLCG1 PLCG1 PLCG1 11877 -0.056 0.15 NO
31 GAB1 GAB1 GAB1 12055 -0.06 0.17 NO
32 MAPK3 MAPK3 MAPK3 12494 -0.069 0.17 NO
33 TLN1 TLN1 TLN1 12750 -0.076 0.19 NO
34 PIK3CD PIK3CD PIK3CD 14383 -0.13 0.15 NO
35 GSN GSN GSN 14880 -0.15 0.18 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: PID IGF1 PATHWAY.

Figure S60.  Get High-res Image For the top 5 core enriched genes in the pathway: PID IGF1 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

Fold change

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

Expression level

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

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

Significant gene list

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

Subtype 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 97 genes.ES.table 0.41 1.8 0.012 0.11 0.65 0.36 0.25 0.27 0.036 0.019
KEGG DNA REPLICATION 36 genes.ES.table 0.61 1.6 0.078 0.2 0.92 0.75 0.31 0.52 0.1 0.022
KEGG PROTEASOME 43 genes.ES.table 0.6 1.8 0.018 0.11 0.59 0.63 0.3 0.44 0.031 0.023
KEGG NUCLEOTIDE EXCISION REPAIR 44 genes.ES.table 0.51 1.9 0.026 0.11 0.44 0.61 0.33 0.41 0 0.025
KEGG CELL CYCLE 118 genes.ES.table 0.47 1.6 0.074 0.18 0.9 0.43 0.22 0.34 0.09 0.022
KEGG SNARE INTERACTIONS IN VESICULAR TRANSPORT 38 genes.ES.table 0.44 1.7 0.033 0.15 0.81 0.1 0.046 0.1 0.064 0.02
KEGG ANTIGEN PROCESSING AND PRESENTATION 69 genes.ES.table 0.72 1.7 0.023 0.16 0.83 0.67 0.19 0.54 0.07 0.017
KEGG TOLL LIKE RECEPTOR SIGNALING PATHWAY 91 genes.ES.table 0.57 1.6 0.066 0.21 0.95 0.41 0.18 0.34 0.12 0.021
KEGG NOD LIKE RECEPTOR SIGNALING PATHWAY 61 genes.ES.table 0.65 1.7 0.014 0.16 0.82 0.33 0.072 0.3 0.067 0.02
KEGG RIG I LIKE RECEPTOR SIGNALING PATHWAY 58 genes.ES.table 0.54 1.8 0.014 0.11 0.64 0.38 0.18 0.31 0.035 0.02
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 PSMB9 PSMB9 PSMB9 452 0.41 0.049 YES
2 MYC MYC MYC 464 0.41 0.12 YES
3 CCNA1 CCNA1 CCNA1 928 0.31 0.15 YES
4 CCNE2 CCNE2 CCNE2 939 0.31 0.21 YES
5 PKMYT1 PKMYT1 PKMYT1 1218 0.27 0.24 YES
6 CCNA2 CCNA2 CCNA2 1288 0.26 0.28 YES
7 PSMB8 PSMB8 PSMB8 2450 0.16 0.25 YES
8 CKS1B CKS1B CKS1B 2531 0.15 0.27 YES
9 CDC25A CDC25A CDC25A 2583 0.15 0.3 YES
10 CDKN1A CDKN1A CDKN1A 2611 0.15 0.32 YES
11 PSMD5 PSMD5 PSMD5 2961 0.13 0.32 YES
12 PSMD2 PSMD2 PSMD2 3065 0.12 0.34 YES
13 PSMB7 PSMB7 PSMB7 3079 0.12 0.36 YES
14 MNAT1 MNAT1 MNAT1 3113 0.12 0.38 YES
15 PSMD1 PSMD1 PSMD1 3279 0.11 0.39 YES
16 PSME2 PSME2 PSME2 3319 0.11 0.41 YES
17 SKP2 SKP2 SKP2 3400 0.11 0.43 YES
18 PSMA6 PSMA6 PSMA6 3470 0.1 0.44 YES
19 PSMD11 PSMD11 PSMD11 3642 0.096 0.45 YES
20 PSMC3 PSMC3 PSMC3 3659 0.096 0.47 YES
21 PSMD12 PSMD12 PSMD12 3670 0.095 0.48 YES
22 PSMD14 PSMD14 PSMD14 3679 0.095 0.5 YES
23 PSMA2 PSMA2 PSMA2 3946 0.086 0.5 YES
24 CDK7 CDK7 CDK7 4010 0.084 0.51 YES
25 PSMB2 PSMB2 PSMB2 4022 0.084 0.53 YES
26 PSMA1 PSMA1 PSMA1 4030 0.084 0.54 YES
27 PSMD9 PSMD9 PSMD9 4214 0.078 0.55 YES
28 PSMC1 PSMC1 PSMC1 4267 0.077 0.56 YES
29 PSMA5 PSMA5 PSMA5 4396 0.073 0.56 YES
30 PSMD13 PSMD13 PSMD13 4482 0.07 0.57 YES
31 PSMB5 PSMB5 PSMB5 4512 0.07 0.58 YES
32 PSMA3 PSMA3 PSMA3 4651 0.066 0.59 YES
33 PSMD10 PSMD10 PSMD10 4675 0.065 0.6 YES
34 PSMC2 PSMC2 PSMC2 4795 0.062 0.6 YES
35 PSMA7 PSMA7 PSMA7 4815 0.061 0.61 YES
36 PSMB6 PSMB6 PSMB6 5279 0.05 0.6 YES
37 CCNE1 CCNE1 CCNE1 5381 0.048 0.6 YES
38 PSMF1 PSMF1 PSMF1 5449 0.047 0.6 YES
39 MAX MAX MAX 5453 0.046 0.61 YES
40 PSMB1 PSMB1 PSMB1 5457 0.046 0.62 YES
41 PSME1 PSME1 PSME1 5781 0.04 0.61 NO
42 PSMA4 PSMA4 PSMA4 6041 0.035 0.6 NO
43 CUL1 CUL1 CUL1 6076 0.034 0.6 NO
44 PSMC6 PSMC6 PSMC6 6178 0.032 0.61 NO
45 PSMD8 PSMD8 PSMD8 6408 0.028 0.6 NO
46 PSMB3 PSMB3 PSMB3 6607 0.025 0.59 NO
47 PSMD7 PSMD7 PSMD7 6770 0.022 0.59 NO
48 CDK2 CDK2 CDK2 6886 0.02 0.58 NO
49 PSMB10 PSMB10 PSMB10 6949 0.019 0.58 NO
50 RPS27A RPS27A RPS27A 7268 0.013 0.57 NO
51 PSMD3 PSMD3 PSMD3 7399 0.011 0.56 NO
52 PSMD6 PSMD6 PSMD6 7552 0.0082 0.56 NO
53 PSMB4 PSMB4 PSMB4 7561 0.008 0.56 NO
54 PSMD4 PSMD4 PSMD4 7680 0.0055 0.55 NO
55 PSMC5 PSMC5 PSMC5 7926 0.0018 0.54 NO
56 CCNH CCNH CCNH 8001 0.00045 0.54 NO
57 RB1 RB1 RB1 8407 -0.0068 0.51 NO
58 UBA52 UBA52 UBA52 8541 -0.0092 0.51 NO
59 PSMC4 PSMC4 PSMC4 9088 -0.019 0.48 NO
60 WEE1 WEE1 WEE1 9575 -0.028 0.46 NO
61 SKP1 SKP1 SKP1 9751 -0.031 0.46 NO
62 CDKN1B CDKN1B CDKN1B 11016 -0.055 0.4 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 DNA REPLICATION

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 PSMB9 PSMB9 PSMB9 452 0.41 0.062 YES
2 CCNA1 CCNA1 CCNA1 928 0.31 0.1 YES
3 CCNA2 CCNA2 CCNA2 1288 0.26 0.14 YES
4 PSMB8 PSMB8 PSMB8 2450 0.16 0.11 YES
5 MCM8 MCM8 MCM8 2577 0.15 0.13 YES
6 CDKN1A CDKN1A CDKN1A 2611 0.15 0.16 YES
7 MCM4 MCM4 MCM4 2655 0.14 0.19 YES
8 MCM6 MCM6 MCM6 2730 0.14 0.22 YES
9 CDT1 CDT1 CDT1 2746 0.14 0.24 YES
10 PSMD5 PSMD5 PSMD5 2961 0.13 0.26 YES
11 PSMD2 PSMD2 PSMD2 3065 0.12 0.28 YES
12 PSMB7 PSMB7 PSMB7 3079 0.12 0.31 YES
13 MCM2 MCM2 MCM2 3199 0.12 0.32 YES
14 PSMD1 PSMD1 PSMD1 3279 0.11 0.34 YES
15 PSME2 PSME2 PSME2 3319 0.11 0.36 YES
16 CDC6 CDC6 CDC6 3427 0.1 0.38 YES
17 PSMA6 PSMA6 PSMA6 3470 0.1 0.4 YES
18 PSMD11 PSMD11 PSMD11 3642 0.096 0.41 YES
19 PSMC3 PSMC3 PSMC3 3659 0.096 0.43 YES
20 PSMD12 PSMD12 PSMD12 3670 0.095 0.45 YES
21 PSMD14 PSMD14 PSMD14 3679 0.095 0.47 YES
22 PSMA2 PSMA2 PSMA2 3946 0.086 0.48 YES
23 PSMB2 PSMB2 PSMB2 4022 0.084 0.49 YES
24 PSMA1 PSMA1 PSMA1 4030 0.084 0.51 YES
25 PSMD9 PSMD9 PSMD9 4214 0.078 0.51 YES
26 PSMC1 PSMC1 PSMC1 4267 0.077 0.53 YES
27 PSMA5 PSMA5 PSMA5 4396 0.073 0.54 YES
28 PSMD13 PSMD13 PSMD13 4482 0.07 0.55 YES
29 PSMB5 PSMB5 PSMB5 4512 0.07 0.56 YES
30 MCM5 MCM5 MCM5 4634 0.066 0.57 YES
31 PSMA3 PSMA3 PSMA3 4651 0.066 0.58 YES
32 PSMD10 PSMD10 PSMD10 4675 0.065 0.59 YES
33 PSMC2 PSMC2 PSMC2 4795 0.062 0.6 YES
34 PSMA7 PSMA7 PSMA7 4815 0.061 0.61 YES
35 PSMB6 PSMB6 PSMB6 5279 0.05 0.6 NO
36 PSMF1 PSMF1 PSMF1 5449 0.047 0.6 NO
37 PSMB1 PSMB1 PSMB1 5457 0.046 0.61 NO
38 MCM7 MCM7 MCM7 5617 0.043 0.61 NO
39 PSME1 PSME1 PSME1 5781 0.04 0.61 NO
40 PSMA4 PSMA4 PSMA4 6041 0.035 0.6 NO
41 PSMC6 PSMC6 PSMC6 6178 0.032 0.6 NO
42 PSMD8 PSMD8 PSMD8 6408 0.028 0.59 NO
43 PSMB3 PSMB3 PSMB3 6607 0.025 0.59 NO
44 PSME4 PSME4 PSME4 6698 0.023 0.59 NO
45 PSMD7 PSMD7 PSMD7 6770 0.022 0.59 NO
46 CDK2 CDK2 CDK2 6886 0.02 0.59 NO
47 PSMB10 PSMB10 PSMB10 6949 0.019 0.59 NO
48 RPS27A RPS27A RPS27A 7268 0.013 0.57 NO
49 PSMD3 PSMD3 PSMD3 7399 0.011 0.57 NO
50 PSMD6 PSMD6 PSMD6 7552 0.0082 0.56 NO
51 PSMB4 PSMB4 PSMB4 7561 0.008 0.56 NO
52 PSMD4 PSMD4 PSMD4 7680 0.0055 0.56 NO
53 PSMC5 PSMC5 PSMC5 7926 0.0018 0.54 NO
54 PSMA8 PSMA8 PSMA8 8246 -0.0038 0.53 NO
55 RB1 RB1 RB1 8407 -0.0068 0.52 NO
56 UBA52 UBA52 UBA52 8541 -0.0092 0.51 NO
57 MCM3 MCM3 MCM3 8844 -0.015 0.5 NO
58 PSMC4 PSMC4 PSMC4 9088 -0.019 0.49 NO
59 CDKN1B CDKN1B CDKN1B 11016 -0.055 0.4 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 DNA REPLICATION.

Figure S64.  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 PROTEASOME

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 PSMB9 PSMB9 PSMB9 452 0.41 0.0053 YES
2 HCK HCK HCK 559 0.38 0.028 YES
3 TAF4B TAF4B TAF4B 572 0.38 0.056 YES
4 CCR5 CCR5 CCR5 684 0.36 0.076 YES
5 DOCK2 DOCK2 DOCK2 1214 0.27 0.067 YES
6 NMT2 NMT2 NMT2 1422 0.24 0.074 YES
7 TAF13 TAF13 TAF13 1490 0.24 0.088 YES
8 NUP155 NUP155 NUP155 1714 0.21 0.091 YES
9 CD247 CD247 CD247 1822 0.2 0.1 YES
10 GTF2H3 GTF2H3 GTF2H3 2010 0.19 0.1 YES
11 LCK LCK LCK 2427 0.16 0.093 YES
12 PSMB8 PSMB8 PSMB8 2450 0.16 0.1 YES
13 HMGA1 HMGA1 HMGA1 2514 0.15 0.11 YES
14 HLA-A HLA-A HLA-A 2515 0.15 0.12 YES
15 NUP188 NUP188 NUP188 2528 0.15 0.13 YES
16 CD8B CD8B CD8B 2563 0.15 0.14 YES
17 FEN1 FEN1 FEN1 2571 0.15 0.15 YES
18 CD28 CD28 CD28 2793 0.14 0.15 YES
19 B2M B2M B2M 2863 0.13 0.16 YES
20 PSMD5 PSMD5 PSMD5 2961 0.13 0.16 YES
21 CD4 CD4 CD4 2988 0.12 0.17 YES
22 PSMD2 PSMD2 PSMD2 3065 0.12 0.17 YES
23 PSMB7 PSMB7 PSMB7 3079 0.12 0.18 YES
24 XRCC4 XRCC4 XRCC4 3111 0.12 0.19 YES
25 MNAT1 MNAT1 MNAT1 3113 0.12 0.2 YES
26 COBRA1 COBRA1 COBRA1 3253 0.11 0.2 YES
27 PSMD1 PSMD1 PSMD1 3279 0.11 0.2 YES
28 RAN RAN RAN 3313 0.11 0.21 YES
29 PSME2 PSME2 PSME2 3319 0.11 0.22 YES
30 POLR2D POLR2D POLR2D 3322 0.11 0.23 YES
31 GTF2H1 GTF2H1 GTF2H1 3362 0.11 0.23 YES
32 SLC25A5 SLC25A5 SLC25A5 3408 0.11 0.24 YES
33 AP2S1 AP2S1 AP2S1 3416 0.11 0.25 YES
34 NUP205 NUP205 NUP205 3425 0.1 0.25 YES
35 PSMA6 PSMA6 PSMA6 3470 0.1 0.26 YES
36 NCBP1 NCBP1 NCBP1 3475 0.1 0.27 YES
37 TAF5 TAF5 TAF5 3555 0.1 0.27 YES
38 PSMD11 PSMD11 PSMD11 3642 0.096 0.27 YES
39 AP1S2 AP1S2 AP1S2 3655 0.096 0.28 YES
40 PSMC3 PSMC3 PSMC3 3659 0.096 0.28 YES
41 PSMD12 PSMD12 PSMD12 3670 0.095 0.29 YES
42 PSMD14 PSMD14 PSMD14 3679 0.095 0.3 YES
43 NUP37 NUP37 NUP37 3791 0.092 0.3 YES
44 GTF2A1 GTF2A1 GTF2A1 3843 0.09 0.3 YES
45 NUP153 NUP153 NUP153 3897 0.088 0.31 YES
46 PSMA2 PSMA2 PSMA2 3946 0.086 0.31 YES
47 CDK7 CDK7 CDK7 4010 0.084 0.31 YES
48 PSMB2 PSMB2 PSMB2 4022 0.084 0.32 YES
49 PSMA1 PSMA1 PSMA1 4030 0.084 0.32 YES
50 SEH1L SEH1L SEH1L 4047 0.083 0.33 YES
51 GTF2F2 GTF2F2 GTF2F2 4097 0.082 0.33 YES
52 SSRP1 SSRP1 SSRP1 4212 0.078 0.33 YES
53 PSMD9 PSMD9 PSMD9 4214 0.078 0.34 YES
54 RANBP1 RANBP1 RANBP1 4231 0.078 0.34 YES
55 PSMC1 PSMC1 PSMC1 4267 0.077 0.35 YES
56 TBP TBP TBP 4361 0.074 0.35 YES
57 PSMA5 PSMA5 PSMA5 4396 0.073 0.35 YES
58 PSMD13 PSMD13 PSMD13 4482 0.07 0.35 YES
59 PSMB5 PSMB5 PSMB5 4512 0.07 0.36 YES
60 GTF2H4 GTF2H4 GTF2H4 4536 0.069 0.36 YES
61 NUP93 NUP93 NUP93 4589 0.068 0.36 YES
62 PSMA3 PSMA3 PSMA3 4651 0.066 0.36 YES
63 PSMD10 PSMD10 PSMD10 4675 0.065 0.37 YES
64 CDK9 CDK9 CDK9 4730 0.064 0.37 YES
65 PSMC2 PSMC2 PSMC2 4795 0.062 0.37 YES
66 NUP54 NUP54 NUP54 4814 0.062 0.37 YES
67 PSMA7 PSMA7 PSMA7 4815 0.061 0.38 YES
68 PSIP1 PSIP1 PSIP1 4862 0.06 0.38 YES
69 RNGTT RNGTT RNGTT 4882 0.06 0.38 YES
70 RDBP RDBP RDBP 4884 0.06 0.39 YES
71 NPM1 NPM1 NPM1 4915 0.059 0.39 YES
72 SUPT16H SUPT16H SUPT16H 4924 0.059 0.39 YES
73 TCEB1 TCEB1 TCEB1 4933 0.058 0.4 YES
74 GTF2E1 GTF2E1 GTF2E1 4959 0.058 0.4 YES
75 POLR2L POLR2L POLR2L 4968 0.058 0.4 YES
76 NUP214 NUP214 NUP214 5004 0.057 0.41 YES
77 KPNB1 KPNB1 KPNB1 5094 0.054 0.4 YES
78 PPIA PPIA PPIA 5225 0.051 0.4 YES
79 PSMB6 PSMB6 PSMB6 5279 0.05 0.4 YES
80 NUPL1 NUPL1 NUPL1 5292 0.05 0.4 YES
81 PSMF1 PSMF1 PSMF1 5449 0.047 0.4 YES
82 PSMB1 PSMB1 PSMB1 5457 0.046 0.4 YES
83 TSG101 TSG101 TSG101 5464 0.046 0.41 YES
84 RANGAP1 RANGAP1 RANGAP1 5508 0.045 0.41 YES
85 XPO1 XPO1 XPO1 5530 0.045 0.41 YES
86 NUP85 NUP85 NUP85 5639 0.042 0.41 YES
87 TAF9 TAF9 TAF9 5661 0.042 0.41 YES
88 AP2A1 AP2A1 AP2A1 5760 0.04 0.41 YES
89 PSME1 PSME1 PSME1 5781 0.04 0.41 YES
90 RAC1 RAC1 RAC1 5910 0.038 0.4 YES
91 ELL ELL ELL 5922 0.038 0.41 YES
92 KPNA1 KPNA1 KPNA1 5965 0.037 0.41 YES
93 PAK2 PAK2 PAK2 6001 0.036 0.41 YES
94 PSMA4 PSMA4 PSMA4 6041 0.035 0.41 YES
95 NUP133 NUP133 NUP133 6085 0.034 0.41 YES
96 AP1M1 AP1M1 AP1M1 6086 0.034 0.41 YES
97 PSMC6 PSMC6 PSMC6 6178 0.032 0.41 YES
98 RANBP2 RANBP2 RANBP2 6217 0.032 0.41 YES
99 CCNT1 CCNT1 CCNT1 6224 0.032 0.41 YES
100 PACS1 PACS1 PACS1 6247 0.031 0.41 YES
101 RNMT RNMT RNMT 6250 0.031 0.41 YES
102 TAF12 TAF12 TAF12 6251 0.031 0.42 YES
103 PSMD8 PSMD8 PSMD8 6408 0.028 0.41 NO
104 NUP35 NUP35 NUP35 6450 0.027 0.41 NO
105 GTF2A2 GTF2A2 GTF2A2 6456 0.027 0.41 NO
106 TAF11 TAF11 TAF11 6515 0.026 0.41 NO
107 ATP6V1H ATP6V1H ATP6V1H 6594 0.025 0.41 NO
108 PSMB3 PSMB3 PSMB3 6607 0.025 0.41 NO
109 PSME4 PSME4 PSME4 6698 0.023 0.4 NO
110 PSMD7 PSMD7 PSMD7 6770 0.022 0.4 NO
111 AP1S1 AP1S1 AP1S1 6787 0.022 0.4 NO
112 NMT1 NMT1 NMT1 6818 0.021 0.4 NO
113 ERCC3 ERCC3 ERCC3 6858 0.02 0.4 NO
114 GTF2E2 GTF2E2 GTF2E2 6898 0.019 0.4 NO
115 PSMB10 PSMB10 PSMB10 6949 0.019 0.4 NO
116 FYN FYN FYN 6979 0.018 0.4 NO
117 NUP62 NUP62 NUP62 7256 0.013 0.38 NO
118 RPS27A RPS27A RPS27A 7268 0.013 0.39 NO
119 BANF1 BANF1 BANF1 7318 0.012 0.38 NO
120 RCC1 RCC1 RCC1 7334 0.012 0.38 NO
121 PSMD3 PSMD3 PSMD3 7399 0.011 0.38 NO
122 NUP88 NUP88 NUP88 7485 0.0093 0.38 NO
123 PSMD6 PSMD6 PSMD6 7552 0.0082 0.37 NO
124 PSMB4 PSMB4 PSMB4 7561 0.008 0.37 NO
125 POLR2G POLR2G POLR2G 7650 0.0061 0.37 NO
126 RAE1 RAE1 RAE1 7661 0.0059 0.37 NO
127 PSMD4 PSMD4 PSMD4 7680 0.0055 0.37 NO
128 AP2M1 AP2M1 AP2M1 7775 0.0038 0.36 NO
129 GTF2H2B GTF2H2B GTF2H2B 7844 0.0028 0.36 NO
130 PSMC5 PSMC5 PSMC5 7926 0.0018 0.36 NO
131 CCNH CCNH CCNH 8001 0.00045 0.35 NO
132 POLR2F POLR2F POLR2F 8004 0.00043 0.35 NO
133 POLR2C POLR2C POLR2C 8020 0.00016 0.35 NO
134 AP2A2 AP2A2 AP2A2 8028 -0.000026 0.35 NO
135 CTDP1 CTDP1 CTDP1 8120 -0.0015 0.35 NO
136 XRCC6 XRCC6 XRCC6 8166 -0.0024 0.34 NO
137 TAF6 TAF6 TAF6 8170 -0.0024 0.34 NO
138 TAF10 TAF10 TAF10 8195 -0.0029 0.34 NO
139 PSMA8 PSMA8 PSMA8 8246 -0.0038 0.34 NO
140 NUP50 NUP50 NUP50 8267 -0.0042 0.34 NO
141 VPS37A VPS37A VPS37A 8270 -0.0042 0.34 NO
142 ARF1 ARF1 ARF1 8288 -0.0046 0.34 NO
143 GTF2F1 GTF2F1 GTF2F1 8389 -0.0063 0.33 NO
144 NUP107 NUP107 NUP107 8423 -0.007 0.33 NO
145 BTRC BTRC BTRC 8507 -0.0085 0.33 NO
146 UBA52 UBA52 UBA52 8541 -0.0092 0.33 NO
147 XRCC5 XRCC5 XRCC5 8563 -0.0095 0.33 NO
148 POLR2A POLR2A POLR2A 8624 -0.011 0.32 NO
149 POLR2H POLR2H POLR2H 8669 -0.012 0.32 NO
150 POLR2E POLR2E POLR2E 8679 -0.012 0.32 NO
151 CUL5 CUL5 CUL5 8710 -0.012 0.32 NO
152 AP1G1 AP1G1 AP1G1 8712 -0.012 0.32 NO
153 TCEB3 TCEB3 TCEB3 8725 -0.013 0.32 NO
154 TPR TPR TPR 8843 -0.015 0.32 NO
155 TCEA1 TCEA1 TCEA1 8886 -0.015 0.32 NO
156 POLR2K POLR2K POLR2K 9063 -0.019 0.31 NO
157 RBX1 RBX1 RBX1 9072 -0.019 0.31 NO
158 PSMC4 PSMC4 PSMC4 9088 -0.019 0.31 NO
159 AP2B1 AP2B1 AP2B1 9132 -0.02 0.31 NO
160 SUPT5H SUPT5H SUPT5H 9166 -0.021 0.31 NO
161 NCBP2 NCBP2 NCBP2 9202 -0.021 0.31 NO
162 VPS37C VPS37C VPS37C 9250 -0.022 0.31 NO
163 CXCR4 CXCR4 CXCR4 9328 -0.024 0.3 NO
164 GTF2H2 GTF2H2 GTF2H2 9365 -0.024 0.3 NO
165 POLR2B POLR2B POLR2B 9366 -0.024 0.31 NO
166 LIG4 LIG4 LIG4 9388 -0.025 0.31 NO
167 LIG1 LIG1 LIG1 9455 -0.026 0.3 NO
168 POM121 POM121 POM121 9491 -0.026 0.3 NO
169 SUPT4H1 SUPT4H1 SUPT4H1 9644 -0.029 0.3 NO
170 SKP1 SKP1 SKP1 9751 -0.031 0.3 NO
171 VPS37B VPS37B VPS37B 9902 -0.033 0.29 NO
172 AAAS AAAS AAAS 10016 -0.035 0.29 NO
173 NUPL2 NUPL2 NUPL2 10024 -0.036 0.29 NO
174 TAF1 TAF1 TAF1 10346 -0.042 0.27 NO
175 POLR2I POLR2I POLR2I 10437 -0.044 0.27 NO
176 ERCC2 ERCC2 ERCC2 10475 -0.044 0.27 NO
177 SLC25A6 SLC25A6 SLC25A6 10703 -0.049 0.26 NO
178 NUP43 NUP43 NUP43 10911 -0.053 0.26 NO
179 TCEB2 TCEB2 TCEB2 10943 -0.054 0.26 NO
180 ELMO1 ELMO1 ELMO1 11311 -0.061 0.24 NO
181 POLR2J POLR2J POLR2J 11394 -0.063 0.24 NO
182 TH1L TH1L TH1L 11454 -0.064 0.24 NO
183 GTF2B GTF2B GTF2B 11801 -0.072 0.23 NO
184 VPS28 VPS28 VPS28 12265 -0.083 0.21 NO
185 TAF4 TAF4 TAF4 12350 -0.086 0.21 NO
186 AP1B1 AP1B1 AP1B1 12813 -0.099 0.2 NO
187 AP1M2 AP1M2 AP1M2 13157 -0.11 0.18 NO
188 WHSC2 WHSC2 WHSC2 13177 -0.11 0.19 NO
189 APOBEC3G APOBEC3G APOBEC3G 13754 -0.13 0.17 NO
190 SLC25A4 SLC25A4 SLC25A4 14553 -0.16 0.14 NO
191 CCNT2 CCNT2 CCNT2 15016 -0.19 0.12 NO
192 NUP210 NUP210 NUP210 16466 -0.28 0.065 NO
193 VPS37D VPS37D VPS37D 17462 -0.41 0.041 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 PROTEASOME.

Figure S66.  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 NUCLEOTIDE EXCISION REPAIR

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 452 0.41 0.056 YES
2 EXOSC3 EXOSC3 EXOSC3 2030 0.19 0.0058 YES
3 PSMB8 PSMB8 PSMB8 2450 0.16 0.014 YES
4 MAPK11 MAPK11 MAPK11 2620 0.15 0.033 YES
5 PSMD5 PSMD5 PSMD5 2961 0.13 0.039 YES
6 EXOSC2 EXOSC2 EXOSC2 3009 0.12 0.061 YES
7 PSMD2 PSMD2 PSMD2 3065 0.12 0.082 YES
8 PSMB7 PSMB7 PSMB7 3079 0.12 0.1 YES
9 HSPA8 HSPA8 HSPA8 3266 0.11 0.12 YES
10 PSMD1 PSMD1 PSMD1 3279 0.11 0.14 YES
11 PSME2 PSME2 PSME2 3319 0.11 0.16 YES
12 PSMA6 PSMA6 PSMA6 3470 0.1 0.17 YES
13 PSMD11 PSMD11 PSMD11 3642 0.096 0.18 YES
14 PSMC3 PSMC3 PSMC3 3659 0.096 0.2 YES
15 PSMD12 PSMD12 PSMD12 3670 0.095 0.22 YES
16 PSMD14 PSMD14 PSMD14 3679 0.095 0.23 YES
17 PSMA2 PSMA2 PSMA2 3946 0.086 0.24 YES
18 PSMB2 PSMB2 PSMB2 4022 0.084 0.25 YES
19 PSMA1 PSMA1 PSMA1 4030 0.084 0.26 YES
20 MAPK14 MAPK14 MAPK14 4124 0.081 0.28 YES
21 PSMD9 PSMD9 PSMD9 4214 0.078 0.29 YES
22 PSMC1 PSMC1 PSMC1 4267 0.077 0.3 YES
23 EIF4G1 EIF4G1 EIF4G1 4348 0.074 0.31 YES
24 PSMA5 PSMA5 PSMA5 4396 0.073 0.32 YES
25 PSMD13 PSMD13 PSMD13 4482 0.07 0.33 YES
26 PSMB5 PSMB5 PSMB5 4512 0.07 0.34 YES
27 EXOSC6 EXOSC6 EXOSC6 4607 0.067 0.35 YES
28 PSMA3 PSMA3 PSMA3 4651 0.066 0.36 YES
29 PSMD10 PSMD10 PSMD10 4675 0.065 0.37 YES
30 PSMC2 PSMC2 PSMC2 4795 0.062 0.38 YES
31 PSMA7 PSMA7 PSMA7 4815 0.061 0.39 YES
32 MAPKAPK2 MAPKAPK2 MAPKAPK2 4936 0.058 0.39 YES
33 EXOSC9 EXOSC9 EXOSC9 4952 0.058 0.4 YES
34 NUP214 NUP214 NUP214 5004 0.057 0.41 YES
35 YWHAZ YWHAZ YWHAZ 5119 0.054 0.42 YES
36 PSMB6 PSMB6 PSMB6 5279 0.05 0.42 YES
37 PSMF1 PSMF1 PSMF1 5449 0.047 0.42 YES
38 PSMB1 PSMB1 PSMB1 5457 0.046 0.43 YES
39 ZFP36 ZFP36 ZFP36 5472 0.046 0.44 YES
40 XPO1 XPO1 XPO1 5530 0.045 0.44 YES
41 ZFP36L1 ZFP36L1 ZFP36L1 5586 0.043 0.45 YES
42 PSME1 PSME1 PSME1 5781 0.04 0.44 YES
43 TNPO1 TNPO1 TNPO1 5921 0.038 0.44 YES
44 PSMA4 PSMA4 PSMA4 6041 0.035 0.44 YES
45 EXOSC4 EXOSC4 EXOSC4 6166 0.033 0.44 YES
46 PSMC6 PSMC6 PSMC6 6178 0.032 0.45 YES
47 XRN1 XRN1 XRN1 6339 0.03 0.45 YES
48 PSMD8 PSMD8 PSMD8 6408 0.028 0.45 YES
49 HNRNPD HNRNPD HNRNPD 6425 0.028 0.45 YES
50 DIS3 DIS3 DIS3 6509 0.026 0.45 YES
51 HSPA1B HSPA1B HSPA1B 6605 0.025 0.45 YES
52 PSMB3 PSMB3 PSMB3 6607 0.025 0.46 YES
53 PSME4 PSME4 PSME4 6698 0.023 0.46 NO
54 PSMD7 PSMD7 PSMD7 6770 0.022 0.46 NO
55 PSMB10 PSMB10 PSMB10 6949 0.019 0.45 NO
56 HSPB1 HSPB1 HSPB1 7108 0.016 0.45 NO
57 YWHAB YWHAB YWHAB 7122 0.016 0.45 NO
58 RPS27A RPS27A RPS27A 7268 0.013 0.44 NO
59 PSMD3 PSMD3 PSMD3 7399 0.011 0.44 NO
60 EXOSC8 EXOSC8 EXOSC8 7482 0.0093 0.44 NO
61 KHSRP KHSRP KHSRP 7505 0.0089 0.44 NO
62 PSMD6 PSMD6 PSMD6 7552 0.0082 0.44 NO
63 PSMB4 PSMB4 PSMB4 7561 0.008 0.44 NO
64 AKT1 AKT1 AKT1 7646 0.0062 0.43 NO
65 PSMD4 PSMD4 PSMD4 7680 0.0055 0.43 NO
66 PSMC5 PSMC5 PSMC5 7926 0.0018 0.42 NO
67 PSMA8 PSMA8 PSMA8 8246 -0.0038 0.4 NO
68 UBA52 UBA52 UBA52 8541 -0.0092 0.39 NO
69 PARN PARN PARN 9048 -0.019 0.36 NO
70 PRKCA PRKCA PRKCA 9052 -0.019 0.37 NO
71 PSMC4 PSMC4 PSMC4 9088 -0.019 0.37 NO
72 EXOSC1 EXOSC1 EXOSC1 9614 -0.028 0.34 NO
73 ELAVL1 ELAVL1 ELAVL1 10109 -0.037 0.32 NO
74 EXOSC7 EXOSC7 EXOSC7 10199 -0.039 0.33 NO
75 ANP32A ANP32A ANP32A 10209 -0.039 0.34 NO
76 DCP2 DCP2 DCP2 10828 -0.051 0.31 NO
77 EXOSC5 EXOSC5 EXOSC5 11149 -0.058 0.3 NO
78 DCP1A DCP1A DCP1A 11940 -0.076 0.28 NO
79 TNFSF13 TNFSF13 TNFSF13 12773 -0.098 0.25 NO
80 PABPC1 PABPC1 PABPC1 13120 -0.11 0.25 NO
81 PRKCD PRKCD PRKCD 14012 -0.14 0.23 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 NUCLEOTIDE EXCISION REPAIR.

Figure S68.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG NUCLEOTIDE EXCISION REPAIR, 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 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 PSMB9 PSMB9 PSMB9 452 0.41 0.068 YES
2 CCNA1 CCNA1 CCNA1 928 0.31 0.11 YES
3 CCNE2 CCNE2 CCNE2 939 0.31 0.18 YES
4 CCNA2 CCNA2 CCNA2 1288 0.26 0.22 YES
5 PSMB8 PSMB8 PSMB8 2450 0.16 0.19 YES
6 CKS1B CKS1B CKS1B 2531 0.15 0.22 YES
7 CDKN1A CDKN1A CDKN1A 2611 0.15 0.25 YES
8 PSMD5 PSMD5 PSMD5 2961 0.13 0.26 YES
9 PSMD2 PSMD2 PSMD2 3065 0.12 0.28 YES
10 PSMB7 PSMB7 PSMB7 3079 0.12 0.31 YES
11 PSMD1 PSMD1 PSMD1 3279 0.11 0.32 YES
12 PSME2 PSME2 PSME2 3319 0.11 0.35 YES
13 SKP2 SKP2 SKP2 3400 0.11 0.37 YES
14 PSMA6 PSMA6 PSMA6 3470 0.1 0.39 YES
15 PSMD11 PSMD11 PSMD11 3642 0.096 0.4 YES
16 PSMC3 PSMC3 PSMC3 3659 0.096 0.42 YES
17 PSMD12 PSMD12 PSMD12 3670 0.095 0.44 YES
18 PSMD14 PSMD14 PSMD14 3679 0.095 0.46 YES
19 PSMA2 PSMA2 PSMA2 3946 0.086 0.47 YES
20 PSMB2 PSMB2 PSMB2 4022 0.084 0.48 YES
21 PSMA1 PSMA1 PSMA1 4030 0.084 0.5 YES
22 PSMD9 PSMD9 PSMD9 4214 0.078 0.51 YES
23 PSMC1 PSMC1 PSMC1 4267 0.077 0.52 YES
24 PSMA5 PSMA5 PSMA5 4396 0.073 0.53 YES
25 PSMD13 PSMD13 PSMD13 4482 0.07 0.54 YES
26 PSMB5 PSMB5 PSMB5 4512 0.07 0.56 YES
27 PSMA3 PSMA3 PSMA3 4651 0.066 0.56 YES
28 PSMD10 PSMD10 PSMD10 4675 0.065 0.58 YES
29 PSMC2 PSMC2 PSMC2 4795 0.062 0.58 YES
30 PSMA7 PSMA7 PSMA7 4815 0.061 0.6 YES
31 PSMB6 PSMB6 PSMB6 5279 0.05 0.58 YES
32 CCNE1 CCNE1 CCNE1 5381 0.048 0.59 YES
33 PSMF1 PSMF1 PSMF1 5449 0.047 0.6 YES
34 PSMB1 PSMB1 PSMB1 5457 0.046 0.61 YES
35 PSME1 PSME1 PSME1 5781 0.04 0.6 NO
36 PSMA4 PSMA4 PSMA4 6041 0.035 0.59 NO
37 CUL1 CUL1 CUL1 6076 0.034 0.6 NO
38 PSMC6 PSMC6 PSMC6 6178 0.032 0.6 NO
39 PSMD8 PSMD8 PSMD8 6408 0.028 0.59 NO
40 PSMB3 PSMB3 PSMB3 6607 0.025 0.59 NO
41 PSMD7 PSMD7 PSMD7 6770 0.022 0.58 NO
42 CDK2 CDK2 CDK2 6886 0.02 0.58 NO
43 PSMB10 PSMB10 PSMB10 6949 0.019 0.58 NO
44 RPS27A RPS27A RPS27A 7268 0.013 0.57 NO
45 PSMD3 PSMD3 PSMD3 7399 0.011 0.56 NO
46 PSMD6 PSMD6 PSMD6 7552 0.0082 0.56 NO
47 PSMB4 PSMB4 PSMB4 7561 0.008 0.56 NO
48 PSMD4 PSMD4 PSMD4 7680 0.0055 0.55 NO
49 PSMC5 PSMC5 PSMC5 7926 0.0018 0.54 NO
50 UBA52 UBA52 UBA52 8541 -0.0092 0.51 NO
51 PSMC4 PSMC4 PSMC4 9088 -0.019 0.48 NO
52 SKP1 SKP1 SKP1 9751 -0.031 0.45 NO
53 CDKN1B CDKN1B CDKN1B 11016 -0.055 0.4 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 CELL CYCLE.

Figure S70.  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: KEGG SNARE INTERACTIONS IN VESICULAR TRANSPORT

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 PSMB9 PSMB9 PSMB9 452 0.41 0.02 YES
2 MYC MYC MYC 464 0.41 0.064 YES
3 CDC25B CDC25B CDC25B 709 0.36 0.09 YES
4 POLE2 POLE2 POLE2 904 0.31 0.11 YES
5 CCNA1 CCNA1 CCNA1 928 0.31 0.15 YES
6 CCNE2 CCNE2 CCNE2 939 0.31 0.18 YES
7 CCNA2 CCNA2 CCNA2 1288 0.26 0.19 YES
8 CDC45 CDC45 CDC45 2025 0.19 0.17 YES
9 PSMB8 PSMB8 PSMB8 2450 0.16 0.16 YES
10 CKS1B CKS1B CKS1B 2531 0.15 0.17 YES
11 FEN1 FEN1 FEN1 2571 0.15 0.19 YES
12 MCM8 MCM8 MCM8 2577 0.15 0.2 YES
13 CDC25A CDC25A CDC25A 2583 0.15 0.22 YES
14 CDKN1A CDKN1A CDKN1A 2611 0.15 0.24 YES
15 PRIM1 PRIM1 PRIM1 2624 0.15 0.25 YES
16 MCM4 MCM4 MCM4 2655 0.14 0.26 YES
17 GINS1 GINS1 GINS1 2663 0.14 0.28 YES
18 RFC4 RFC4 RFC4 2688 0.14 0.3 YES
19 MCM6 MCM6 MCM6 2730 0.14 0.31 YES
20 CDT1 CDT1 CDT1 2746 0.14 0.32 YES
21 POLD2 POLD2 POLD2 2778 0.14 0.34 YES
22 PRIM2 PRIM2 PRIM2 2914 0.13 0.34 YES
23 PSMD5 PSMD5 PSMD5 2961 0.13 0.35 YES
24 PSMD2 PSMD2 PSMD2 3065 0.12 0.36 YES
25 PSMB7 PSMB7 PSMB7 3079 0.12 0.37 YES
26 MNAT1 MNAT1 MNAT1 3113 0.12 0.38 YES
27 GINS2 GINS2 GINS2 3143 0.12 0.4 YES
28 MCM2 MCM2 MCM2 3199 0.12 0.41 YES
29 RPA3 RPA3 RPA3 3236 0.11 0.42 YES
30 PSMD1 PSMD1 PSMD1 3279 0.11 0.43 YES
31 PSME2 PSME2 PSME2 3319 0.11 0.44 YES
32 POLA1 POLA1 POLA1 3384 0.11 0.44 YES
33 SKP2 SKP2 SKP2 3400 0.11 0.46 YES
34 POLA2 POLA2 POLA2 3412 0.11 0.47 YES
35 CDC6 CDC6 CDC6 3427 0.1 0.48 YES
36 PSMA6 PSMA6 PSMA6 3470 0.1 0.49 YES
37 RFC3 RFC3 RFC3 3547 0.1 0.49 YES
38 PCNA PCNA PCNA 3569 0.1 0.5 YES
39 PSMD11 PSMD11 PSMD11 3642 0.096 0.51 YES
40 PSMC3 PSMC3 PSMC3 3659 0.096 0.52 YES
41 PSMD12 PSMD12 PSMD12 3670 0.095 0.53 YES
42 PSMD14 PSMD14 PSMD14 3679 0.095 0.54 YES
43 POLD1 POLD1 POLD1 3802 0.091 0.54 YES
44 PSMA2 PSMA2 PSMA2 3946 0.086 0.54 YES
45 CDK7 CDK7 CDK7 4010 0.084 0.55 YES
46 PSMB2 PSMB2 PSMB2 4022 0.084 0.56 YES
47 PSMA1 PSMA1 PSMA1 4030 0.084 0.57 YES
48 PSMD9 PSMD9 PSMD9 4214 0.078 0.56 YES
49 RFC2 RFC2 RFC2 4253 0.077 0.57 YES
50 PSMC1 PSMC1 PSMC1 4267 0.077 0.58 YES
51 PSMA5 PSMA5 PSMA5 4396 0.073 0.58 YES
52 GINS4 GINS4 GINS4 4468 0.07 0.58 YES
53 POLD3 POLD3 POLD3 4477 0.07 0.59 YES
54 PSMD13 PSMD13 PSMD13 4482 0.07 0.6 YES
55 PSMB5 PSMB5 PSMB5 4512 0.07 0.6 YES
56 MCM5 MCM5 MCM5 4634 0.066 0.6 YES
57 PSMA3 PSMA3 PSMA3 4651 0.066 0.61 YES
58 PSMD10 PSMD10 PSMD10 4675 0.065 0.62 YES
59 PSMC2 PSMC2 PSMC2 4795 0.062 0.62 YES
60 PSMA7 PSMA7 PSMA7 4815 0.061 0.62 YES
61 DNA2 DNA2 DNA2 4995 0.057 0.62 YES
62 PSMB6 PSMB6 PSMB6 5279 0.05 0.61 YES
63 CCNE1 CCNE1 CCNE1 5381 0.048 0.61 YES
64 POLD4 POLD4 POLD4 5387 0.048 0.61 YES
65 PSMF1 PSMF1 PSMF1 5449 0.047 0.62 YES
66 MAX MAX MAX 5453 0.046 0.62 YES
67 PSMB1 PSMB1 PSMB1 5457 0.046 0.63 YES
68 MCM7 MCM7 MCM7 5617 0.043 0.62 NO
69 PSME1 PSME1 PSME1 5781 0.04 0.62 NO
70 RPA1 RPA1 RPA1 5947 0.037 0.61 NO
71 PSMA4 PSMA4 PSMA4 6041 0.035 0.61 NO
72 CUL1 CUL1 CUL1 6076 0.034 0.61 NO
73 PSMC6 PSMC6 PSMC6 6178 0.032 0.61 NO
74 CCND1 CCND1 CCND1 6367 0.029 0.6 NO
75 PSMD8 PSMD8 PSMD8 6408 0.028 0.6 NO
76 PSMB3 PSMB3 PSMB3 6607 0.025 0.6 NO
77 PSME4 PSME4 PSME4 6698 0.023 0.59 NO
78 PSMD7 PSMD7 PSMD7 6770 0.022 0.59 NO
79 CDK2 CDK2 CDK2 6886 0.02 0.59 NO
80 PSMB10 PSMB10 PSMB10 6949 0.019 0.59 NO
81 RFC5 RFC5 RFC5 7040 0.017 0.58 NO
82 CDK4 CDK4 CDK4 7255 0.013 0.57 NO
83 RPS27A RPS27A RPS27A 7268 0.013 0.57 NO
84 PSMD3 PSMD3 PSMD3 7399 0.011 0.57 NO
85 POLE POLE POLE 7478 0.0094 0.56 NO
86 PSMD6 PSMD6 PSMD6 7552 0.0082 0.56 NO
87 PSMB4 PSMB4 PSMB4 7561 0.008 0.56 NO
88 PSMD4 PSMD4 PSMD4 7680 0.0055 0.56 NO
89 PSMC5 PSMC5 PSMC5 7926 0.0018 0.54 NO
90 CCNH CCNH CCNH 8001 0.00045 0.54 NO
91 PSMA8 PSMA8 PSMA8 8246 -0.0038 0.53 NO
92 RB1 RB1 RB1 8407 -0.0068 0.52 NO
93 UBA52 UBA52 UBA52 8541 -0.0092 0.51 NO
94 MCM3 MCM3 MCM3 8844 -0.015 0.5 NO
95 PSMC4 PSMC4 PSMC4 9088 -0.019 0.48 NO
96 LIG1 LIG1 LIG1 9455 -0.026 0.47 NO
97 RPA2 RPA2 RPA2 9515 -0.027 0.47 NO
98 WEE1 WEE1 WEE1 9575 -0.028 0.47 NO
99 SKP1 SKP1 SKP1 9751 -0.031 0.46 NO
100 CDKN1B CDKN1B CDKN1B 11016 -0.055 0.4 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 SNARE INTERACTIONS IN VESICULAR TRANSPORT.

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

genes ES table in pathway: KEGG ANTIGEN PROCESSING AND PRESENTATION

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 452 0.41 0.032 YES
2 POLE2 POLE2 POLE2 904 0.31 0.051 YES
3 CCNA1 CCNA1 CCNA1 928 0.31 0.092 YES
4 CCNA2 CCNA2 CCNA2 1288 0.26 0.11 YES
5 CDC45 CDC45 CDC45 2025 0.19 0.094 YES
6 PSMB8 PSMB8 PSMB8 2450 0.16 0.092 YES
7 FEN1 FEN1 FEN1 2571 0.15 0.11 YES
8 MCM8 MCM8 MCM8 2577 0.15 0.13 YES
9 CDKN1A CDKN1A CDKN1A 2611 0.15 0.14 YES
10 PRIM1 PRIM1 PRIM1 2624 0.15 0.16 YES
11 MCM4 MCM4 MCM4 2655 0.14 0.18 YES
12 GINS1 GINS1 GINS1 2663 0.14 0.2 YES
13 RFC4 RFC4 RFC4 2688 0.14 0.22 YES
14 MCM6 MCM6 MCM6 2730 0.14 0.24 YES
15 CDT1 CDT1 CDT1 2746 0.14 0.26 YES
16 POLD2 POLD2 POLD2 2778 0.14 0.27 YES
17 PRIM2 PRIM2 PRIM2 2914 0.13 0.28 YES
18 PSMD5 PSMD5 PSMD5 2961 0.13 0.3 YES
19 PSMD2 PSMD2 PSMD2 3065 0.12 0.31 YES
20 PSMB7 PSMB7 PSMB7 3079 0.12 0.33 YES
21 GINS2 GINS2 GINS2 3143 0.12 0.34 YES
22 MCM2 MCM2 MCM2 3199 0.12 0.35 YES
23 RPA3 RPA3 RPA3 3236 0.11 0.37 YES
24 PSMD1 PSMD1 PSMD1 3279 0.11 0.38 YES
25 PSME2 PSME2 PSME2 3319 0.11 0.39 YES
26 POLA1 POLA1 POLA1 3384 0.11 0.4 YES
27 POLA2 POLA2 POLA2 3412 0.11 0.42 YES
28 CDC6 CDC6 CDC6 3427 0.1 0.43 YES
29 PSMA6 PSMA6 PSMA6 3470 0.1 0.44 YES
30 RFC3 RFC3 RFC3 3547 0.1 0.45 YES
31 PCNA PCNA PCNA 3569 0.1 0.47 YES
32 PSMD11 PSMD11 PSMD11 3642 0.096 0.48 YES
33 PSMC3 PSMC3 PSMC3 3659 0.096 0.49 YES
34 PSMD12 PSMD12 PSMD12 3670 0.095 0.5 YES
35 PSMD14 PSMD14 PSMD14 3679 0.095 0.51 YES
36 POLD1 POLD1 POLD1 3802 0.091 0.52 YES
37 PSMA2 PSMA2 PSMA2 3946 0.086 0.52 YES
38 PSMB2 PSMB2 PSMB2 4022 0.084 0.53 YES
39 PSMA1 PSMA1 PSMA1 4030 0.084 0.54 YES
40 PSMD9 PSMD9 PSMD9 4214 0.078 0.54 YES
41 RFC2 RFC2 RFC2 4253 0.077 0.55 YES
42 PSMC1 PSMC1 PSMC1 4267 0.077 0.56 YES
43 PSMA5 PSMA5 PSMA5 4396 0.073 0.56 YES
44 GINS4 GINS4 GINS4 4468 0.07 0.57 YES
45 POLD3 POLD3 POLD3 4477 0.07 0.58 YES
46 PSMD13 PSMD13 PSMD13 4482 0.07 0.59 YES
47 PSMB5 PSMB5 PSMB5 4512 0.07 0.6 YES
48 MCM5 MCM5 MCM5 4634 0.066 0.6 YES
49 PSMA3 PSMA3 PSMA3 4651 0.066 0.61 YES
50 PSMD10 PSMD10 PSMD10 4675 0.065 0.62 YES
51 PSMC2 PSMC2 PSMC2 4795 0.062 0.62 YES
52 PSMA7 PSMA7 PSMA7 4815 0.061 0.62 YES
53 DNA2 DNA2 DNA2 4995 0.057 0.62 NO
54 PSMB6 PSMB6 PSMB6 5279 0.05 0.61 NO
55 POLD4 POLD4 POLD4 5387 0.048 0.62 NO
56 PSMF1 PSMF1 PSMF1 5449 0.047 0.62 NO
57 PSMB1 PSMB1 PSMB1 5457 0.046 0.62 NO
58 MCM7 MCM7 MCM7 5617 0.043 0.62 NO
59 PSME1 PSME1 PSME1 5781 0.04 0.62 NO
60 RPA1 RPA1 RPA1 5947 0.037 0.61 NO
61 PSMA4 PSMA4 PSMA4 6041 0.035 0.61 NO
62 PSMC6 PSMC6 PSMC6 6178 0.032 0.61 NO
63 PSMD8 PSMD8 PSMD8 6408 0.028 0.6 NO
64 PSMB3 PSMB3 PSMB3 6607 0.025 0.6 NO
65 PSME4 PSME4 PSME4 6698 0.023 0.59 NO
66 PSMD7 PSMD7 PSMD7 6770 0.022 0.59 NO
67 CDK2 CDK2 CDK2 6886 0.02 0.59 NO
68 PSMB10 PSMB10 PSMB10 6949 0.019 0.59 NO
69 RFC5 RFC5 RFC5 7040 0.017 0.58 NO
70 RPS27A RPS27A RPS27A 7268 0.013 0.57 NO
71 PSMD3 PSMD3 PSMD3 7399 0.011 0.57 NO
72 POLE POLE POLE 7478 0.0094 0.57 NO
73 PSMD6 PSMD6 PSMD6 7552 0.0082 0.56 NO
74 PSMB4 PSMB4 PSMB4 7561 0.008 0.56 NO
75 PSMD4 PSMD4 PSMD4 7680 0.0055 0.56 NO
76 PSMC5 PSMC5 PSMC5 7926 0.0018 0.54 NO
77 PSMA8 PSMA8 PSMA8 8246 -0.0038 0.53 NO
78 RB1 RB1 RB1 8407 -0.0068 0.52 NO
79 UBA52 UBA52 UBA52 8541 -0.0092 0.51 NO
80 MCM3 MCM3 MCM3 8844 -0.015 0.5 NO
81 PSMC4 PSMC4 PSMC4 9088 -0.019 0.49 NO
82 LIG1 LIG1 LIG1 9455 -0.026 0.47 NO
83 RPA2 RPA2 RPA2 9515 -0.027 0.47 NO
84 CDKN1B CDKN1B CDKN1B 11016 -0.055 0.4 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 ANTIGEN PROCESSING AND PRESENTATION.

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

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

Table 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 PSMB9 PSMB9 PSMB9 452 0.41 0.023 YES
2 HCK HCK HCK 559 0.38 0.063 YES
3 DOCK2 DOCK2 DOCK2 1214 0.27 0.058 YES
4 NUP155 NUP155 NUP155 1714 0.21 0.056 YES
5 CD247 CD247 CD247 1822 0.2 0.074 YES
6 LCK LCK LCK 2427 0.16 0.06 YES
7 PSMB8 PSMB8 PSMB8 2450 0.16 0.077 YES
8 HMGA1 HMGA1 HMGA1 2514 0.15 0.092 YES
9 HLA-A HLA-A HLA-A 2515 0.15 0.11 YES
10 NUP188 NUP188 NUP188 2528 0.15 0.13 YES
11 CD8B CD8B CD8B 2563 0.15 0.14 YES
12 CD28 CD28 CD28 2793 0.14 0.15 YES
13 B2M B2M B2M 2863 0.13 0.16 YES
14 PSMD5 PSMD5 PSMD5 2961 0.13 0.17 YES
15 CD4 CD4 CD4 2988 0.12 0.18 YES
16 PSMD2 PSMD2 PSMD2 3065 0.12 0.19 YES
17 PSMB7 PSMB7 PSMB7 3079 0.12 0.2 YES
18 PSMD1 PSMD1 PSMD1 3279 0.11 0.21 YES
19 RAN RAN RAN 3313 0.11 0.22 YES
20 PSME2 PSME2 PSME2 3319 0.11 0.23 YES
21 SLC25A5 SLC25A5 SLC25A5 3408 0.11 0.24 YES
22 AP2S1 AP2S1 AP2S1 3416 0.11 0.25 YES
23 NUP205 NUP205 NUP205 3425 0.1 0.26 YES
24 PSMA6 PSMA6 PSMA6 3470 0.1 0.27 YES
25 PSMD11 PSMD11 PSMD11 3642 0.096 0.27 YES
26 AP1S2 AP1S2 AP1S2 3655 0.096 0.28 YES
27 PSMC3 PSMC3 PSMC3 3659 0.096 0.3 YES
28 PSMD12 PSMD12 PSMD12 3670 0.095 0.31 YES
29 PSMD14 PSMD14 PSMD14 3679 0.095 0.32 YES
30 NUP37 NUP37 NUP37 3791 0.092 0.32 YES
31 NUP153 NUP153 NUP153 3897 0.088 0.33 YES
32 PSMA2 PSMA2 PSMA2 3946 0.086 0.33 YES
33 PSMB2 PSMB2 PSMB2 4022 0.084 0.34 YES
34 PSMA1 PSMA1 PSMA1 4030 0.084 0.35 YES
35 SEH1L SEH1L SEH1L 4047 0.083 0.36 YES
36 PSMD9 PSMD9 PSMD9 4214 0.078 0.36 YES
37 RANBP1 RANBP1 RANBP1 4231 0.078 0.37 YES
38 PSMC1 PSMC1 PSMC1 4267 0.077 0.37 YES
39 PSMA5 PSMA5 PSMA5 4396 0.073 0.38 YES
40 PSMD13 PSMD13 PSMD13 4482 0.07 0.38 YES
41 PSMB5 PSMB5 PSMB5 4512 0.07 0.38 YES
42 NUP93 NUP93 NUP93 4589 0.068 0.39 YES
43 PSMA3 PSMA3 PSMA3 4651 0.066 0.39 YES
44 PSMD10 PSMD10 PSMD10 4675 0.065 0.4 YES
45 CDK9 CDK9 CDK9 4730 0.064 0.4 YES
46 PSMC2 PSMC2 PSMC2 4795 0.062 0.41 YES
47 NUP54 NUP54 NUP54 4814 0.062 0.41 YES
48 PSMA7 PSMA7 PSMA7 4815 0.061 0.42 YES
49 PSIP1 PSIP1 PSIP1 4862 0.06 0.43 YES
50 NPM1 NPM1 NPM1 4915 0.059 0.43 YES
51 TCEB1 TCEB1 TCEB1 4933 0.058 0.44 YES
52 NUP214 NUP214 NUP214 5004 0.057 0.44 YES
53 KPNB1 KPNB1 KPNB1 5094 0.054 0.44 YES
54 PPIA PPIA PPIA 5225 0.051 0.44 YES
55 PSMB6 PSMB6 PSMB6 5279 0.05 0.44 YES
56 NUPL1 NUPL1 NUPL1 5292 0.05 0.45 YES
57 PSMF1 PSMF1 PSMF1 5449 0.047 0.44 YES
58 PSMB1 PSMB1 PSMB1 5457 0.046 0.45 YES
59 RANGAP1 RANGAP1 RANGAP1 5508 0.045 0.45 YES
60 XPO1 XPO1 XPO1 5530 0.045 0.46 YES
61 NUP85 NUP85 NUP85 5639 0.042 0.46 YES
62 AP2A1 AP2A1 AP2A1 5760 0.04 0.45 YES
63 PSME1 PSME1 PSME1 5781 0.04 0.46 YES
64 RAC1 RAC1 RAC1 5910 0.038 0.45 YES
65 KPNA1 KPNA1 KPNA1 5965 0.037 0.46 YES
66 PAK2 PAK2 PAK2 6001 0.036 0.46 YES
67 PSMA4 PSMA4 PSMA4 6041 0.035 0.46 YES
68 NUP133 NUP133 NUP133 6085 0.034 0.46 YES
69 AP1M1 AP1M1 AP1M1 6086 0.034 0.47 YES
70 PSMC6 PSMC6 PSMC6 6178 0.032 0.46 YES
71 RANBP2 RANBP2 RANBP2 6217 0.032 0.47 YES
72 CCNT1 CCNT1 CCNT1 6224 0.032 0.47 YES
73 PACS1 PACS1 PACS1 6247 0.031 0.47 YES
74 PSMD8 PSMD8 PSMD8 6408 0.028 0.47 NO
75 NUP35 NUP35 NUP35 6450 0.027 0.47 NO
76 ATP6V1H ATP6V1H ATP6V1H 6594 0.025 0.46 NO
77 PSMB3 PSMB3 PSMB3 6607 0.025 0.46 NO
78 PSME4 PSME4 PSME4 6698 0.023 0.46 NO
79 PSMD7 PSMD7 PSMD7 6770 0.022 0.46 NO
80 AP1S1 AP1S1 AP1S1 6787 0.022 0.46 NO
81 PSMB10 PSMB10 PSMB10 6949 0.019 0.46 NO
82 FYN FYN FYN 6979 0.018 0.46 NO
83 NUP62 NUP62 NUP62 7256 0.013 0.44 NO
84 RPS27A RPS27A RPS27A 7268 0.013 0.44 NO
85 BANF1 BANF1 BANF1 7318 0.012 0.44 NO
86 RCC1 RCC1 RCC1 7334 0.012 0.44 NO
87 PSMD3 PSMD3 PSMD3 7399 0.011 0.44 NO
88 NUP88 NUP88 NUP88 7485 0.0093 0.44 NO
89 PSMD6 PSMD6 PSMD6 7552 0.0082 0.44 NO
90 PSMB4 PSMB4 PSMB4 7561 0.008 0.44 NO
91 RAE1 RAE1 RAE1 7661 0.0059 0.43 NO
92 PSMD4 PSMD4 PSMD4 7680 0.0055 0.43 NO
93 AP2M1 AP2M1 AP2M1 7775 0.0038 0.42 NO
94 PSMC5 PSMC5 PSMC5 7926 0.0018 0.42 NO
95 AP2A2 AP2A2 AP2A2 8028 -0.000026 0.41 NO
96 PSMA8 PSMA8 PSMA8 8246 -0.0038 0.4 NO
97 NUP50 NUP50 NUP50 8267 -0.0042 0.4 NO
98 ARF1 ARF1 ARF1 8288 -0.0046 0.4 NO
99 NUP107 NUP107 NUP107 8423 -0.007 0.39 NO
100 BTRC BTRC BTRC 8507 -0.0085 0.39 NO
101 UBA52 UBA52 UBA52 8541 -0.0092 0.39 NO
102 CUL5 CUL5 CUL5 8710 -0.012 0.38 NO
103 AP1G1 AP1G1 AP1G1 8712 -0.012 0.38 NO
104 TPR TPR TPR 8843 -0.015 0.38 NO
105 RBX1 RBX1 RBX1 9072 -0.019 0.37 NO
106 PSMC4 PSMC4 PSMC4 9088 -0.019 0.37 NO
107 AP2B1 AP2B1 AP2B1 9132 -0.02 0.37 NO
108 POM121 POM121 POM121 9491 -0.026 0.35 NO
109 SKP1 SKP1 SKP1 9751 -0.031 0.34 NO
110 AAAS AAAS AAAS 10016 -0.035 0.33 NO
111 NUPL2 NUPL2 NUPL2 10024 -0.036 0.33 NO
112 SLC25A6 SLC25A6 SLC25A6 10703 -0.049 0.3 NO
113 NUP43 NUP43 NUP43 10911 -0.053 0.3 NO
114 TCEB2 TCEB2 TCEB2 10943 -0.054 0.3 NO
115 ELMO1 ELMO1 ELMO1 11311 -0.061 0.29 NO
116 AP1B1 AP1B1 AP1B1 12813 -0.099 0.22 NO
117 AP1M2 AP1M2 AP1M2 13157 -0.11 0.21 NO
118 APOBEC3G APOBEC3G APOBEC3G 13754 -0.13 0.19 NO
119 SLC25A4 SLC25A4 SLC25A4 14553 -0.16 0.17 NO
120 NUP210 NUP210 NUP210 16466 -0.28 0.096 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 TOLL LIKE RECEPTOR SIGNALING PATHWAY.

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

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

Table 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 NCF2 NCF2 NCF2 145 0.57 0.065 YES
2 PSMB9 PSMB9 PSMB9 452 0.41 0.1 YES
3 FCGR1A FCGR1A FCGR1A 633 0.37 0.14 YES
4 FCGR1B FCGR1B FCGR1B 716 0.35 0.18 YES
5 CYBB CYBB CYBB 751 0.34 0.22 YES
6 MRC1 MRC1 MRC1 807 0.33 0.26 YES
7 TAP1 TAP1 TAP1 891 0.32 0.3 YES
8 HLA-F HLA-F HLA-F 960 0.3 0.33 YES
9 TAP2 TAP2 TAP2 1021 0.3 0.37 YES
10 LNPEP LNPEP LNPEP 1846 0.2 0.35 YES
11 MRC2 MRC2 MRC2 1962 0.19 0.36 YES
12 HLA-G HLA-G HLA-G 2001 0.19 0.39 YES
13 HLA-B HLA-B HLA-B 2192 0.18 0.4 YES
14 ITGB5 ITGB5 ITGB5 2442 0.16 0.41 YES
15 PSMB8 PSMB8 PSMB8 2450 0.16 0.43 YES
16 HLA-A HLA-A HLA-A 2515 0.15 0.44 YES
17 B2M B2M B2M 2863 0.13 0.44 YES
18 SEC61G SEC61G SEC61G 2915 0.13 0.45 YES
19 PSMD5 PSMD5 PSMD5 2961 0.13 0.47 YES
20 ITGAV ITGAV ITGAV 3023 0.12 0.48 YES
21 PSMD2 PSMD2 PSMD2 3065 0.12 0.49 YES
22 PSMB7 PSMB7 PSMB7 3079 0.12 0.51 YES
23 PSMD1 PSMD1 PSMD1 3279 0.11 0.51 YES
24 PSME2 PSME2 PSME2 3319 0.11 0.52 YES
25 HLA-C HLA-C HLA-C 3406 0.11 0.53 YES
26 PSMA6 PSMA6 PSMA6 3470 0.1 0.54 YES
27 PSMD11 PSMD11 PSMD11 3642 0.096 0.55 YES
28 PSMC3 PSMC3 PSMC3 3659 0.096 0.56 YES
29 PSMD12 PSMD12 PSMD12 3670 0.095 0.57 YES
30 PSMD14 PSMD14 PSMD14 3679 0.095 0.58 YES
31 PSMA2 PSMA2 PSMA2 3946 0.086 0.58 YES
32 PSMB2 PSMB2 PSMB2 4022 0.084 0.58 YES
33 PSMA1 PSMA1 PSMA1 4030 0.084 0.59 YES
34 SEC61B SEC61B SEC61B 4195 0.079 0.59 YES
35 PSMD9 PSMD9 PSMD9 4214 0.078 0.6 YES
36 PSMC1 PSMC1 PSMC1 4267 0.077 0.61 YES
37 PSMA5 PSMA5 PSMA5 4396 0.073 0.61 YES
38 PSMD13 PSMD13 PSMD13 4482 0.07 0.62 YES
39 PSMB5 PSMB5 PSMB5 4512 0.07 0.62 YES
40 PSMA3 PSMA3 PSMA3 4651 0.066 0.62 YES
41 PSMD10 PSMD10 PSMD10 4675 0.065 0.63 YES
42 CD36 CD36 CD36 4685 0.065 0.64 YES
43 PSMC2 PSMC2 PSMC2 4795 0.062 0.64 YES
44 PSMA7 PSMA7 PSMA7 4815 0.061 0.65 YES
45 CD207 CD207 CD207 5078 0.055 0.64 NO
46 PSMB6 PSMB6 PSMB6 5279 0.05 0.64 NO
47 PSMF1 PSMF1 PSMF1 5449 0.047 0.63 NO
48 PSMB1 PSMB1 PSMB1 5457 0.046 0.64 NO
49 PSME1 PSME1 PSME1 5781 0.04 0.63 NO
50 PSMA4 PSMA4 PSMA4 6041 0.035 0.62 NO
51 PSMC6 PSMC6 PSMC6 6178 0.032 0.61 NO
52 CALR CALR CALR 6186 0.032 0.62 NO
53 PSMD8 PSMD8 PSMD8 6408 0.028 0.61 NO
54 PSMB3 PSMB3 PSMB3 6607 0.025 0.6 NO
55 PSME4 PSME4 PSME4 6698 0.023 0.6 NO
56 PSMD7 PSMD7 PSMD7 6770 0.022 0.6 NO
57 NCF4 NCF4 NCF4 6868 0.02 0.59 NO
58 PSMB10 PSMB10 PSMB10 6949 0.019 0.59 NO
59 RPS27A RPS27A RPS27A 7268 0.013 0.58 NO
60 PSMD3 PSMD3 PSMD3 7399 0.011 0.57 NO
61 SEC61A1 SEC61A1 SEC61A1 7422 0.01 0.57 NO
62 PDIA3 PDIA3 PDIA3 7428 0.01 0.57 NO
63 PSMD6 PSMD6 PSMD6 7552 0.0082 0.57 NO
64 PSMB4 PSMB4 PSMB4 7561 0.008 0.57 NO
65 PSMD4 PSMD4 PSMD4 7680 0.0055 0.56 NO
66 CYBA CYBA CYBA 7885 0.0023 0.55 NO
67 PSMC5 PSMC5 PSMC5 7926 0.0018 0.55 NO
68 PSMA8 PSMA8 PSMA8 8246 -0.0038 0.53 NO
69 UBA52 UBA52 UBA52 8541 -0.0092 0.52 NO
70 PSMC4 PSMC4 PSMC4 9088 -0.019 0.49 NO
71 CTSS CTSS CTSS 9298 -0.023 0.48 NO
72 SEC61A2 SEC61A2 SEC61A2 12503 -0.09 0.31 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 NOD LIKE RECEPTOR SIGNALING PATHWAY.

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

genes ES table in pathway: KEGG RIG I LIKE RECEPTOR SIGNALING PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 SPHK1 SPHK1 SPHK1 84 0.63 0.26 YES
2 KIF13A KIF13A KIF13A 2513 0.15 0.19 YES
3 KIFC3 KIFC3 KIFC3 2582 0.15 0.25 YES
4 CCT4 CCT4 CCT4 3166 0.12 0.26 YES
5 FKBP9 FKBP9 FKBP9 3274 0.11 0.31 YES
6 CCT6A CCT6A CCT6A 3302 0.11 0.35 YES
7 FBXW2 FBXW2 FBXW2 3355 0.11 0.39 YES
8 FBXO6 FBXO6 FBXO6 3519 0.1 0.43 YES
9 CCT5 CCT5 CCT5 3525 0.1 0.47 YES
10 FBXW5 FBXW5 FBXW5 3758 0.092 0.49 YES
11 NOP56 NOP56 NOP56 4647 0.066 0.47 YES
12 FBXO4 FBXO4 FBXO4 5126 0.054 0.47 YES
13 TCP1 TCP1 TCP1 5293 0.05 0.48 YES
14 XRN2 XRN2 XRN2 5406 0.047 0.49 YES
15 CCT7 CCT7 CCT7 5633 0.043 0.5 YES
16 CCT3 CCT3 CCT3 6142 0.033 0.49 NO
17 CCT2 CCT2 CCT2 7770 0.0039 0.4 NO
18 CCT8 CCT8 CCT8 7939 0.0015 0.39 NO
19 FBXL3 FBXL3 FBXL3 8121 -0.0015 0.38 NO
20 LONP2 LONP2 LONP2 9852 -0.033 0.3 NO
21 AP3M1 AP3M1 AP3M1 10040 -0.036 0.3 NO
22 FBXW7 FBXW7 FBXW7 10575 -0.046 0.29 NO
23 FBXL5 FBXL5 FBXL5 10949 -0.054 0.3 NO
24 ARFGEF2 ARFGEF2 ARFGEF2 10985 -0.054 0.32 NO
25 USP11 USP11 USP11 12579 -0.092 0.27 NO
26 FBXW4 FBXW4 FBXW4 12903 -0.1 0.29 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 RIG I LIKE RECEPTOR SIGNALING PATHWAY.

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

Fold change

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

Expression level

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

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

Significant gene list

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

Subtype clus5 enriched pathways

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

GeneSet(GS) Size(#genes) genes.ES.table ES NES NOM.p.val FDR.q.val FWER.p.val Tag.. Gene.. Signal FDR..median. glob.p.val
KEGG LYSINE DEGRADATION 44 genes.ES.table 0.42 1.7 0.019 0.17 0.83 0.46 0.32 0.31 0.07 0.021
KEGG RNA DEGRADATION 56 genes.ES.table 0.39 1.9 0.027 0.093 0.45 0.62 0.44 0.35 0 0.017
KEGG DNA REPLICATION 36 genes.ES.table 0.58 1.6 0.091 0.23 0.94 0.67 0.26 0.5 0.14 0.026
KEGG SPLICEOSOME 114 genes.ES.table 0.43 1.8 0.036 0.094 0.5 0.88 0.51 0.44 0 0.014
KEGG NUCLEOTIDE EXCISION REPAIR 44 genes.ES.table 0.4 1.5 0.1 0.25 0.96 0.46 0.33 0.3 0.16 0.025
KEGG HOMOLOGOUS RECOMBINATION 26 genes.ES.table 0.6 1.7 0.041 0.17 0.84 0.58 0.24 0.44 0.074 0.022
KEGG CELL CYCLE 118 genes.ES.table 0.45 1.6 0.076 0.18 0.9 0.39 0.2 0.31 0.091 0.021
KEGG OOCYTE MEIOSIS 106 genes.ES.table 0.41 1.6 0.022 0.18 0.88 0.24 0.16 0.21 0.086 0.021
BIOCARTA CHREBP2 PATHWAY 41 genes.ES.table 0.39 1.5 0.056 0.24 0.95 0.24 0.25 0.18 0.15 0.029
PID FANCONI PATHWAY 46 genes.ES.table 0.65 1.9 0.0062 0.097 0.4 0.63 0.24 0.48 0 0.02
genes ES table in pathway: KEGG LYSINE DEGRADATION

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 VPS37D VPS37D VPS37D 141 0.43 0.064 YES
2 NUP210 NUP210 NUP210 733 0.29 0.079 YES
3 GTF2H2B GTF2H2B GTF2H2B 1681 0.2 0.06 YES
4 TAF5 TAF5 TAF5 1709 0.2 0.092 YES
5 TAF4B TAF4B TAF4B 2166 0.17 0.095 YES
6 CCNT1 CCNT1 CCNT1 2192 0.17 0.12 YES
7 GTF2H2 GTF2H2 GTF2H2 2413 0.16 0.14 YES
8 NMT2 NMT2 NMT2 2443 0.16 0.16 YES
9 NUP107 NUP107 NUP107 2789 0.14 0.16 YES
10 GTF2A1 GTF2A1 GTF2A1 2814 0.14 0.19 YES
11 NUP155 NUP155 NUP155 2998 0.13 0.2 YES
12 NUP88 NUP88 NUP88 3301 0.12 0.2 YES
13 NUP35 NUP35 NUP35 4155 0.093 0.17 YES
14 POLR2D POLR2D POLR2D 4417 0.086 0.17 YES
15 NUP85 NUP85 NUP85 4536 0.084 0.18 YES
16 NUP153 NUP153 NUP153 4570 0.084 0.19 YES
17 GTF2E1 GTF2E1 GTF2E1 4680 0.081 0.2 YES
18 NUP205 NUP205 NUP205 4793 0.079 0.2 YES
19 TAF11 TAF11 TAF11 4898 0.077 0.21 YES
20 RNMT RNMT RNMT 4920 0.076 0.22 YES
21 AAAS AAAS AAAS 4926 0.076 0.24 YES
22 NUP62 NUP62 NUP62 5042 0.074 0.24 YES
23 NCBP1 NCBP1 NCBP1 5048 0.074 0.25 YES
24 RANBP1 RANBP1 RANBP1 5130 0.072 0.26 YES
25 RAE1 RAE1 RAE1 5134 0.072 0.27 YES
26 SSRP1 SSRP1 SSRP1 5143 0.072 0.28 YES
27 SEH1L SEH1L SEH1L 5148 0.072 0.3 YES
28 SUPT16H SUPT16H SUPT16H 5162 0.072 0.31 YES
29 GTF2H3 GTF2H3 GTF2H3 5174 0.072 0.32 YES
30 XPO1 XPO1 XPO1 5201 0.071 0.33 YES
31 ERCC2 ERCC2 ERCC2 5202 0.071 0.34 YES
32 NUP188 NUP188 NUP188 5287 0.07 0.35 YES
33 NUP43 NUP43 NUP43 5341 0.069 0.36 YES
34 NUPL1 NUPL1 NUPL1 5385 0.068 0.36 YES
35 RNGTT RNGTT RNGTT 5466 0.067 0.37 YES
36 NUP133 NUP133 NUP133 5469 0.067 0.38 YES
37 NUP93 NUP93 NUP93 5703 0.062 0.38 YES
38 TBP TBP TBP 5738 0.062 0.39 YES
39 GTF2H4 GTF2H4 GTF2H4 5786 0.061 0.4 YES
40 TH1L TH1L TH1L 6006 0.057 0.39 YES
41 TPR TPR TPR 6132 0.056 0.39 YES
42 TAF6 TAF6 TAF6 6269 0.054 0.4 YES
43 RAN RAN RAN 6301 0.053 0.4 YES
44 ERCC3 ERCC3 ERCC3 6396 0.051 0.41 YES
45 TAF4 TAF4 TAF4 6424 0.051 0.41 YES
46 WHSC2 WHSC2 WHSC2 6527 0.05 0.42 YES
47 POM121 POM121 POM121 6584 0.049 0.42 YES
48 CCNT2 CCNT2 CCNT2 6594 0.049 0.43 YES
49 NUP214 NUP214 NUP214 6775 0.046 0.43 YES
50 GTF2B GTF2B GTF2B 6778 0.046 0.43 YES
51 POLR2K POLR2K POLR2K 6816 0.046 0.44 YES
52 POLR2A POLR2A POLR2A 6847 0.046 0.44 YES
53 POLR2H POLR2H POLR2H 6986 0.044 0.44 YES
54 POLR2B POLR2B POLR2B 7039 0.043 0.45 YES
55 NCBP2 NCBP2 NCBP2 7125 0.042 0.45 YES
56 TCEA1 TCEA1 TCEA1 7514 0.037 0.44 YES
57 POLR2G POLR2G POLR2G 7535 0.037 0.44 YES
58 POLR2I POLR2I POLR2I 7592 0.036 0.44 YES
59 TCEB1 TCEB1 TCEB1 7638 0.036 0.45 YES
60 POLR2F POLR2F POLR2F 7659 0.036 0.45 YES
61 SUPT5H SUPT5H SUPT5H 7748 0.035 0.45 YES
62 TAF9 TAF9 TAF9 7780 0.034 0.46 YES
63 SUPT4H1 SUPT4H1 SUPT4H1 7836 0.033 0.46 YES
64 MNAT1 MNAT1 MNAT1 7881 0.033 0.46 YES
65 TAF1 TAF1 TAF1 7984 0.032 0.46 NO
66 NMT1 NMT1 NMT1 8126 0.03 0.46 NO
67 RDBP RDBP RDBP 8180 0.029 0.46 NO
68 NUP37 NUP37 NUP37 8539 0.024 0.44 NO
69 RANBP2 RANBP2 RANBP2 8540 0.024 0.45 NO
70 RCC1 RCC1 RCC1 8563 0.024 0.45 NO
71 GTF2F1 GTF2F1 GTF2F1 8685 0.023 0.45 NO
72 TCEB3 TCEB3 TCEB3 9016 0.019 0.43 NO
73 POLR2J POLR2J POLR2J 9105 0.018 0.43 NO
74 NUP50 NUP50 NUP50 9163 0.017 0.43 NO
75 CCNH CCNH CCNH 9276 0.016 0.43 NO
76 NUPL2 NUPL2 NUPL2 9400 0.014 0.42 NO
77 POLR2E POLR2E POLR2E 9636 0.011 0.41 NO
78 TSG101 TSG101 TSG101 9770 0.0094 0.41 NO
79 TAF10 TAF10 TAF10 10039 0.0053 0.39 NO
80 POLR2C POLR2C POLR2C 10233 0.0026 0.38 NO
81 COBRA1 COBRA1 COBRA1 10333 0.0013 0.38 NO
82 CDK9 CDK9 CDK9 10380 0.00073 0.38 NO
83 NUP54 NUP54 NUP54 10498 -0.00092 0.37 NO
84 CTDP1 CTDP1 CTDP1 10512 -0.0011 0.37 NO
85 VPS28 VPS28 VPS28 10569 -0.0018 0.36 NO
86 RANGAP1 RANGAP1 RANGAP1 10615 -0.0024 0.36 NO
87 UBA52 UBA52 UBA52 10678 -0.0032 0.36 NO
88 GTF2H1 GTF2H1 GTF2H1 10692 -0.0034 0.36 NO
89 GTF2A2 GTF2A2 GTF2A2 10712 -0.0036 0.36 NO
90 RPS27A RPS27A RPS27A 10955 -0.007 0.35 NO
91 GTF2E2 GTF2E2 GTF2E2 10996 -0.0075 0.35 NO
92 POLR2L POLR2L POLR2L 11114 -0.0093 0.34 NO
93 CDK7 CDK7 CDK7 11456 -0.014 0.32 NO
94 GTF2F2 GTF2F2 GTF2F2 11530 -0.016 0.32 NO
95 VPS37C VPS37C VPS37C 11574 -0.016 0.32 NO
96 TAF12 TAF12 TAF12 11800 -0.02 0.32 NO
97 VPS37B VPS37B VPS37B 12186 -0.026 0.3 NO
98 TCEB2 TCEB2 TCEB2 12628 -0.035 0.28 NO
99 VPS37A VPS37A VPS37A 13051 -0.044 0.26 NO
100 TAF13 TAF13 TAF13 13316 -0.05 0.26 NO
101 ELL ELL ELL 14165 -0.075 0.22 NO

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

Figure S82.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG LYSINE DEGRADATION, 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 DEGRADATION

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 NUP210 NUP210 NUP210 733 0.29 -0.0026 YES
2 GTF2H2B GTF2H2B GTF2H2B 1681 0.2 -0.028 YES
3 ZNF473 ZNF473 ZNF473 2257 0.17 -0.038 YES
4 GTF2H2 GTF2H2 GTF2H2 2413 0.16 -0.026 YES
5 NUP107 NUP107 NUP107 2789 0.14 -0.028 YES
6 NUP155 NUP155 NUP155 2998 0.13 -0.022 YES
7 NUP88 NUP88 NUP88 3301 0.12 -0.023 YES
8 CSTF3 CSTF3 CSTF3 4054 0.096 -0.052 YES
9 SNRPA SNRPA SNRPA 4071 0.096 -0.04 YES
10 NUP35 NUP35 NUP35 4155 0.093 -0.032 YES
11 THOC4 THOC4 THOC4 4346 0.088 -0.031 YES
12 POLR2D POLR2D POLR2D 4417 0.086 -0.023 YES
13 SNRPD1 SNRPD1 SNRPD1 4459 0.086 -0.014 YES
14 CPSF3 CPSF3 CPSF3 4513 0.085 -0.006 YES
15 NUP85 NUP85 NUP85 4536 0.084 0.0039 YES
16 NUP153 NUP153 NUP153 4570 0.084 0.013 YES
17 RBMX RBMX RBMX 4586 0.083 0.023 YES
18 SNRNP40 SNRNP40 SNRNP40 4632 0.082 0.032 YES
19 SNRPB2 SNRPB2 SNRPB2 4747 0.08 0.036 YES
20 NUP205 NUP205 NUP205 4793 0.079 0.044 YES
21 SMC1A SMC1A SMC1A 4888 0.077 0.049 YES
22 RNMT RNMT RNMT 4920 0.076 0.057 YES
23 AAAS AAAS AAAS 4926 0.076 0.067 YES
24 SNRPE SNRPE SNRPE 4974 0.075 0.075 YES
25 NUP62 NUP62 NUP62 5042 0.074 0.081 YES
26 NCBP1 NCBP1 NCBP1 5048 0.074 0.09 YES
27 SNRNP200 SNRNP200 SNRNP200 5067 0.074 0.099 YES
28 DHX9 DHX9 DHX9 5118 0.072 0.11 YES
29 RAE1 RAE1 RAE1 5134 0.072 0.11 YES
30 SEH1L SEH1L SEH1L 5148 0.072 0.12 YES
31 HNRNPA0 HNRNPA0 HNRNPA0 5154 0.072 0.13 YES
32 GTF2H3 GTF2H3 GTF2H3 5174 0.072 0.14 YES
33 ERCC2 ERCC2 ERCC2 5202 0.071 0.15 YES
34 EFTUD2 EFTUD2 EFTUD2 5215 0.071 0.16 YES
35 UPF3B UPF3B UPF3B 5253 0.07 0.16 YES
36 METTL3 METTL3 METTL3 5256 0.07 0.17 YES
37 NUP188 NUP188 NUP188 5287 0.07 0.18 YES
38 TXNL4A TXNL4A TXNL4A 5301 0.07 0.19 YES
39 NUP43 NUP43 NUP43 5341 0.069 0.2 YES
40 NUPL1 NUPL1 NUPL1 5385 0.068 0.2 YES
41 FUS FUS FUS 5399 0.068 0.21 YES
42 CSTF1 CSTF1 CSTF1 5421 0.068 0.22 YES
43 RNGTT RNGTT RNGTT 5466 0.067 0.23 YES
44 NUP133 NUP133 NUP133 5469 0.067 0.24 YES
45 CPSF1 CPSF1 CPSF1 5511 0.066 0.24 YES
46 HNRNPR HNRNPR HNRNPR 5567 0.065 0.25 YES
47 NUP93 NUP93 NUP93 5703 0.062 0.25 YES
48 GTF2H4 GTF2H4 GTF2H4 5786 0.061 0.25 YES
49 HNRNPM HNRNPM HNRNPM 5817 0.06 0.26 YES
50 SF3B4 SF3B4 SF3B4 5863 0.06 0.26 YES
51 HNRNPH1 HNRNPH1 HNRNPH1 5970 0.058 0.26 YES
52 HNRNPU HNRNPU HNRNPU 6002 0.057 0.27 YES
53 CLP1 CLP1 CLP1 6120 0.056 0.27 YES
54 TPR TPR TPR 6132 0.056 0.28 YES
55 PRPF8 PRPF8 PRPF8 6164 0.055 0.28 YES
56 SF3A2 SF3A2 SF3A2 6272 0.053 0.28 YES
57 YBX1 YBX1 YBX1 6322 0.053 0.29 YES
58 HNRNPUL1 HNRNPUL1 HNRNPUL1 6388 0.052 0.29 YES
59 ERCC3 ERCC3 ERCC3 6396 0.051 0.3 YES
60 HNRNPC HNRNPC HNRNPC 6421 0.051 0.3 YES
61 LSM2 LSM2 LSM2 6542 0.05 0.3 YES
62 SNRPA1 SNRPA1 SNRPA1 6552 0.049 0.31 YES
63 POM121 POM121 POM121 6584 0.049 0.32 YES
64 CPSF7 CPSF7 CPSF7 6645 0.048 0.32 YES
65 SF3A1 SF3A1 SF3A1 6676 0.048 0.32 YES
66 RBM8A RBM8A RBM8A 6683 0.048 0.33 YES
67 ADAR ADAR ADAR 6692 0.048 0.34 YES
68 PRPF4 PRPF4 PRPF4 6715 0.047 0.34 YES
69 HNRNPL HNRNPL HNRNPL 6750 0.047 0.34 YES
70 HNRNPD HNRNPD HNRNPD 6751 0.047 0.35 YES
71 HNRNPA3 HNRNPA3 HNRNPA3 6759 0.047 0.36 YES
72 SNRPF SNRPF SNRPF 6768 0.047 0.36 YES
73 NUP214 NUP214 NUP214 6775 0.046 0.37 YES
74 POLR2K POLR2K POLR2K 6816 0.046 0.37 YES
75 SF3B5 SF3B5 SF3B5 6834 0.046 0.38 YES
76 POLR2A POLR2A POLR2A 6847 0.046 0.38 YES
77 PABPN1 PABPN1 PABPN1 6896 0.045 0.38 YES
78 POLR2H POLR2H POLR2H 6986 0.044 0.39 YES
79 CDC40 CDC40 CDC40 7000 0.044 0.39 YES
80 U2AF1 U2AF1 U2AF1 7033 0.043 0.4 YES
81 POLR2B POLR2B POLR2B 7039 0.043 0.4 YES
82 PTBP1 PTBP1 PTBP1 7056 0.043 0.4 YES
83 CCAR1 CCAR1 CCAR1 7061 0.043 0.41 YES
84 SF3A3 SF3A3 SF3A3 7079 0.043 0.42 YES
85 PHF5A PHF5A PHF5A 7116 0.042 0.42 YES
86 NCBP2 NCBP2 NCBP2 7125 0.042 0.42 YES
87 HNRNPA2B1 HNRNPA2B1 HNRNPA2B1 7149 0.042 0.43 YES
88 SNRPG SNRPG SNRPG 7291 0.04 0.43 YES
89 PCBP2 PCBP2 PCBP2 7332 0.04 0.43 YES
90 HNRNPA1 HNRNPA1 HNRNPA1 7344 0.039 0.43 YES
91 SF3B3 SF3B3 SF3B3 7368 0.039 0.44 YES
92 U2AF2 U2AF2 U2AF2 7455 0.038 0.44 YES
93 SRRM1 SRRM1 SRRM1 7464 0.038 0.44 YES
94 DDX23 DDX23 DDX23 7467 0.038 0.45 YES
95 POLR2G POLR2G POLR2G 7535 0.037 0.45 YES
96 POLR2I POLR2I POLR2I 7592 0.036 0.45 YES
97 POLR2F POLR2F POLR2F 7659 0.036 0.45 YES
98 CSTF2 CSTF2 CSTF2 7697 0.035 0.45 YES
99 SUPT5H SUPT5H SUPT5H 7748 0.035 0.46 YES
100 HNRNPK HNRNPK HNRNPK 7770 0.034 0.46 YES
101 PRPF6 PRPF6 PRPF6 7818 0.034 0.46 YES
102 MNAT1 MNAT1 MNAT1 7881 0.033 0.46 YES
103 SNRPB SNRPB SNRPB 7934 0.032 0.46 YES
104 MAGOH MAGOH MAGOH 7944 0.032 0.47 YES
105 SLBP SLBP SLBP 8014 0.031 0.47 YES
106 SNRPD2 SNRPD2 SNRPD2 8030 0.031 0.47 YES
107 RNPS1 RNPS1 RNPS1 8089 0.03 0.47 YES
108 LSM11 LSM11 LSM11 8182 0.029 0.47 YES
109 LSM10 LSM10 LSM10 8255 0.028 0.47 YES
110 SF3B2 SF3B2 SF3B2 8294 0.028 0.47 YES
111 NUP37 NUP37 NUP37 8539 0.024 0.46 NO
112 RANBP2 RANBP2 RANBP2 8540 0.024 0.46 NO
113 CD2BP2 CD2BP2 CD2BP2 8657 0.023 0.46 NO
114 GTF2F1 GTF2F1 GTF2F1 8685 0.023 0.46 NO
115 NUDT21 NUDT21 NUDT21 8742 0.022 0.46 NO
116 SNRNP70 SNRNP70 SNRNP70 8868 0.02 0.46 NO
117 SNRPD3 SNRPD3 SNRPD3 8946 0.02 0.46 NO
118 POLR2J POLR2J POLR2J 9105 0.018 0.45 NO
119 EIF4E EIF4E EIF4E 9127 0.018 0.45 NO
120 NUP50 NUP50 NUP50 9163 0.017 0.45 NO
121 SF3B1 SF3B1 SF3B1 9180 0.017 0.45 NO
122 CPSF2 CPSF2 CPSF2 9258 0.016 0.45 NO
123 CCNH CCNH CCNH 9276 0.016 0.45 NO
124 DNAJC8 DNAJC8 DNAJC8 9305 0.016 0.45 NO
125 NUPL2 NUPL2 NUPL2 9400 0.014 0.45 NO
126 NFX1 NFX1 NFX1 9413 0.014 0.45 NO
127 RBM5 RBM5 RBM5 9518 0.013 0.45 NO
128 PAPOLA PAPOLA PAPOLA 9629 0.011 0.44 NO
129 POLR2E POLR2E POLR2E 9636 0.011 0.44 NO
130 SF3B14 SF3B14 SF3B14 9742 0.0096 0.44 NO
131 HNRNPF HNRNPF HNRNPF 9819 0.0088 0.44 NO
132 DHX38 DHX38 DHX38 9942 0.007 0.43 NO
133 PCBP1 PCBP1 PCBP1 9956 0.0067 0.43 NO
134 NHP2L1 NHP2L1 NHP2L1 10151 0.0038 0.42 NO
135 POLR2C POLR2C POLR2C 10233 0.0026 0.42 NO
136 NUP54 NUP54 NUP54 10498 -0.00092 0.4 NO
137 NXF1 NXF1 NXF1 10548 -0.0016 0.4 NO
138 GTF2H1 GTF2H1 GTF2H1 10692 -0.0034 0.39 NO
139 POLR2L POLR2L POLR2L 11114 -0.0093 0.37 NO
140 PCF11 PCF11 PCF11 11378 -0.013 0.36 NO
141 CDK7 CDK7 CDK7 11456 -0.014 0.35 NO
142 GTF2F2 GTF2F2 GTF2F2 11530 -0.016 0.35 NO
143 HNRNPH2 HNRNPH2 HNRNPH2 12916 -0.041 0.28 NO
144 ADARB1 ADARB1 ADARB1 14766 -0.097 0.19 NO

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

Figure S84.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG RNA DEGRADATION, 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 DNA REPLICATION

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 GTF2H2B GTF2H2B GTF2H2B 1681 0.2 -0.05 YES
2 TAF5 TAF5 TAF5 1709 0.2 -0.0087 YES
3 TAF4B TAF4B TAF4B 2166 0.17 0.003 YES
4 CCNT1 CCNT1 CCNT1 2192 0.17 0.038 YES
5 ZNF473 ZNF473 ZNF473 2257 0.17 0.07 YES
6 GTF2H2 GTF2H2 GTF2H2 2413 0.16 0.096 YES
7 GTF2A1 GTF2A1 GTF2A1 2814 0.14 0.1 YES
8 CSTF3 CSTF3 CSTF3 4054 0.096 0.056 YES
9 THOC4 THOC4 THOC4 4346 0.088 0.058 YES
10 POLR2D POLR2D POLR2D 4417 0.086 0.073 YES
11 CPSF3 CPSF3 CPSF3 4513 0.085 0.086 YES
12 GTF2E1 GTF2E1 GTF2E1 4680 0.081 0.094 YES
13 TAF11 TAF11 TAF11 4898 0.077 0.098 YES
14 RNMT RNMT RNMT 4920 0.076 0.11 YES
15 SNRPE SNRPE SNRPE 4974 0.075 0.13 YES
16 NCBP1 NCBP1 NCBP1 5048 0.074 0.14 YES
17 SSRP1 SSRP1 SSRP1 5143 0.072 0.15 YES
18 SUPT16H SUPT16H SUPT16H 5162 0.072 0.16 YES
19 GTF2H3 GTF2H3 GTF2H3 5174 0.072 0.18 YES
20 ERCC2 ERCC2 ERCC2 5202 0.071 0.19 YES
21 UPF3B UPF3B UPF3B 5253 0.07 0.2 YES
22 CSTF1 CSTF1 CSTF1 5421 0.068 0.21 YES
23 RNGTT RNGTT RNGTT 5466 0.067 0.22 YES
24 CPSF1 CPSF1 CPSF1 5511 0.066 0.23 YES
25 TBP TBP TBP 5738 0.062 0.23 YES
26 GTF2H4 GTF2H4 GTF2H4 5786 0.061 0.24 YES
27 TH1L TH1L TH1L 6006 0.057 0.24 YES
28 CLP1 CLP1 CLP1 6120 0.056 0.25 YES
29 TAF6 TAF6 TAF6 6269 0.054 0.25 YES
30 ERCC3 ERCC3 ERCC3 6396 0.051 0.26 YES
31 TAF4 TAF4 TAF4 6424 0.051 0.27 YES
32 WHSC2 WHSC2 WHSC2 6527 0.05 0.27 YES
33 CCNT2 CCNT2 CCNT2 6594 0.049 0.28 YES
34 CPSF7 CPSF7 CPSF7 6645 0.048 0.28 YES
35 RBM8A RBM8A RBM8A 6683 0.048 0.29 YES
36 SNRPF SNRPF SNRPF 6768 0.047 0.3 YES
37 GTF2B GTF2B GTF2B 6778 0.046 0.31 YES
38 POLR2K POLR2K POLR2K 6816 0.046 0.32 YES
39 POLR2A POLR2A POLR2A 6847 0.046 0.32 YES
40 PABPN1 PABPN1 PABPN1 6896 0.045 0.33 YES
41 POLR2H POLR2H POLR2H 6986 0.044 0.34 YES
42 CDC40 CDC40 CDC40 7000 0.044 0.34 YES
43 U2AF1 U2AF1 U2AF1 7033 0.043 0.35 YES
44 POLR2B POLR2B POLR2B 7039 0.043 0.36 YES
45 NCBP2 NCBP2 NCBP2 7125 0.042 0.36 YES
46 SNRPG SNRPG SNRPG 7291 0.04 0.36 YES
47 U2AF2 U2AF2 U2AF2 7455 0.038 0.36 YES
48 SRRM1 SRRM1 SRRM1 7464 0.038 0.37 YES
49 TCEA1 TCEA1 TCEA1 7514 0.037 0.38 YES
50 POLR2G POLR2G POLR2G 7535 0.037 0.38 YES
51 POLR2I POLR2I POLR2I 7592 0.036 0.39 YES
52 TCEB1 TCEB1 TCEB1 7638 0.036 0.39 YES
53 POLR2F POLR2F POLR2F 7659 0.036 0.4 YES
54 CSTF2 CSTF2 CSTF2 7697 0.035 0.4 YES
55 SUPT5H SUPT5H SUPT5H 7748 0.035 0.41 YES
56 TAF9 TAF9 TAF9 7780 0.034 0.42 YES
57 SUPT4H1 SUPT4H1 SUPT4H1 7836 0.033 0.42 YES
58 MNAT1 MNAT1 MNAT1 7881 0.033 0.42 YES
59 SNRPB SNRPB SNRPB 7934 0.032 0.43 YES
60 MAGOH MAGOH MAGOH 7944 0.032 0.43 YES
61 TAF1 TAF1 TAF1 7984 0.032 0.44 YES
62 SLBP SLBP SLBP 8014 0.031 0.44 YES
63 RNPS1 RNPS1 RNPS1 8089 0.03 0.45 YES
64 RDBP RDBP RDBP 8180 0.029 0.45 YES
65 LSM11 LSM11 LSM11 8182 0.029 0.45 YES
66 LSM10 LSM10 LSM10 8255 0.028 0.46 YES
67 GTF2F1 GTF2F1 GTF2F1 8685 0.023 0.44 NO
68 NUDT21 NUDT21 NUDT21 8742 0.022 0.44 NO
69 SNRPD3 SNRPD3 SNRPD3 8946 0.02 0.43 NO
70 TCEB3 TCEB3 TCEB3 9016 0.019 0.43 NO
71 POLR2J POLR2J POLR2J 9105 0.018 0.43 NO
72 CPSF2 CPSF2 CPSF2 9258 0.016 0.42 NO
73 CCNH CCNH CCNH 9276 0.016 0.43 NO
74 NFX1 NFX1 NFX1 9413 0.014 0.42 NO
75 PAPOLA PAPOLA PAPOLA 9629 0.011 0.41 NO
76 POLR2E POLR2E POLR2E 9636 0.011 0.42 NO
77 DHX38 DHX38 DHX38 9942 0.007 0.4 NO
78 TAF10 TAF10 TAF10 10039 0.0053 0.4 NO
79 POLR2C POLR2C POLR2C 10233 0.0026 0.39 NO
80 COBRA1 COBRA1 COBRA1 10333 0.0013 0.38 NO
81 CDK9 CDK9 CDK9 10380 0.00073 0.38 NO
82 CTDP1 CTDP1 CTDP1 10512 -0.0011 0.37 NO
83 GTF2H1 GTF2H1 GTF2H1 10692 -0.0034 0.36 NO
84 GTF2A2 GTF2A2 GTF2A2 10712 -0.0036 0.36 NO
85 GTF2E2 GTF2E2 GTF2E2 10996 -0.0075 0.35 NO
86 POLR2L POLR2L POLR2L 11114 -0.0093 0.34 NO
87 PCF11 PCF11 PCF11 11378 -0.013 0.33 NO
88 CDK7 CDK7 CDK7 11456 -0.014 0.33 NO
89 GTF2F2 GTF2F2 GTF2F2 11530 -0.016 0.33 NO
90 TAF12 TAF12 TAF12 11800 -0.02 0.32 NO
91 TCEB2 TCEB2 TCEB2 12628 -0.035 0.28 NO
92 TAF13 TAF13 TAF13 13316 -0.05 0.25 NO
93 ELL ELL ELL 14165 -0.075 0.22 NO

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

Figure S86.  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 SPLICEOSOME

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 POU2F1 POU2F1 POU2F1 2180 0.17 -0.035 YES
2 NFIB NFIB NFIB 2893 0.14 -0.0072 YES
3 GTF3C5 GTF3C5 GTF3C5 2899 0.14 0.06 YES
4 LZTS1 LZTS1 LZTS1 3402 0.12 0.089 YES
5 GTF3C4 GTF3C4 GTF3C4 3551 0.11 0.14 YES
6 SNAPC3 SNAPC3 SNAPC3 3556 0.11 0.19 YES
7 POLR3E POLR3E POLR3E 4399 0.087 0.19 YES
8 SNAPC4 SNAPC4 SNAPC4 4643 0.082 0.21 YES
9 POLR3F POLR3F POLR3F 4666 0.081 0.25 YES
10 POLR3K POLR3K POLR3K 4880 0.077 0.28 YES
11 POLR3A POLR3A POLR3A 5153 0.072 0.3 YES
12 POLR3C POLR3C POLR3C 5292 0.07 0.33 YES
13 GTF3C2 GTF3C2 GTF3C2 5573 0.065 0.34 YES
14 BRF2 BRF2 BRF2 5666 0.063 0.37 YES
15 TBP TBP TBP 5738 0.062 0.4 YES
16 GTF3C3 GTF3C3 GTF3C3 5841 0.06 0.42 YES
17 SSB SSB SSB 6189 0.055 0.43 YES
18 POLR2K POLR2K POLR2K 6816 0.046 0.42 YES
19 BRF1 BRF1 BRF1 6826 0.046 0.44 YES
20 POLR3B POLR3B POLR3B 6870 0.045 0.46 YES
21 POLR3D POLR3D POLR3D 6908 0.045 0.48 YES
22 POLR2H POLR2H POLR2H 6986 0.044 0.49 YES
23 POLR3H POLR3H POLR3H 7397 0.039 0.49 YES
24 POLR2F POLR2F POLR2F 7659 0.036 0.49 YES
25 POLR1C POLR1C POLR1C 7786 0.034 0.5 YES
26 ZNF143 ZNF143 ZNF143 8278 0.028 0.49 NO
27 SNAPC5 SNAPC5 SNAPC5 9474 0.013 0.43 NO
28 POLR2E POLR2E POLR2E 9636 0.011 0.43 NO
29 SNAPC2 SNAPC2 SNAPC2 9730 0.0099 0.43 NO
30 POLR1D POLR1D POLR1D 10986 -0.0074 0.36 NO
31 POLR2L POLR2L POLR2L 11114 -0.0093 0.36 NO
32 SNAPC1 SNAPC1 SNAPC1 11869 -0.021 0.33 NO
33 POLR3GL POLR3GL POLR3GL 12883 -0.04 0.29 NO

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

Figure S88.  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: KEGG NUCLEOTIDE EXCISION REPAIR

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 NINL NINL NINL 53 0.5 0.064 YES
2 CDC25C CDC25C CDC25C 372 0.36 0.094 YES
3 CEP72 CEP72 CEP72 862 0.27 0.1 YES
4 E2F1 E2F1 E2F1 1053 0.25 0.13 YES
5 NEK2 NEK2 NEK2 1140 0.24 0.15 YES
6 E2F3 E2F3 E2F3 1210 0.24 0.18 YES
7 PLK1 PLK1 PLK1 1306 0.23 0.21 YES
8 PLK4 PLK4 PLK4 1327 0.23 0.24 YES
9 CENPJ CENPJ CENPJ 1364 0.22 0.26 YES
10 PRKAR2B PRKAR2B PRKAR2B 1491 0.22 0.28 YES
11 CDC25A CDC25A CDC25A 1568 0.21 0.31 YES
12 TUBA1A TUBA1A TUBA1A 1700 0.2 0.33 YES
13 CCNB2 CCNB2 CCNB2 1811 0.19 0.35 YES
14 CEP76 CEP76 CEP76 2022 0.18 0.36 YES
15 CCNB1 CCNB1 CCNB1 2120 0.18 0.38 YES
16 CCNA2 CCNA2 CCNA2 2311 0.16 0.39 YES
17 CEP135 CEP135 CEP135 2459 0.16 0.4 YES
18 CDK5RAP2 CDK5RAP2 CDK5RAP2 2608 0.15 0.41 YES
19 AZI1 AZI1 AZI1 2655 0.15 0.43 YES
20 CDK1 CDK1 CDK1 2869 0.14 0.44 YES
21 CKAP5 CKAP5 CKAP5 3030 0.13 0.45 YES
22 ALMS1 ALMS1 ALMS1 3192 0.12 0.45 YES
23 PKMYT1 PKMYT1 PKMYT1 3213 0.12 0.47 YES
24 NEDD1 NEDD1 NEDD1 3601 0.11 0.46 YES
25 CDC25B CDC25B CDC25B 3643 0.11 0.47 YES
26 CCNA1 CCNA1 CCNA1 3698 0.11 0.48 YES
27 CDK2 CDK2 CDK2 3706 0.11 0.5 YES
28 CEP70 CEP70 CEP70 4036 0.097 0.49 YES
29 CEP192 CEP192 CEP192 4142 0.094 0.5 YES
30 FGFR1OP FGFR1OP FGFR1OP 4283 0.09 0.5 YES
31 PCNT PCNT PCNT 4416 0.087 0.51 YES
32 CEP164 CEP164 CEP164 4596 0.083 0.51 YES
33 CEP290 CEP290 CEP290 4731 0.08 0.51 YES
34 TUBGCP3 TUBGCP3 TUBGCP3 4922 0.076 0.51 YES
35 XPO1 XPO1 XPO1 5201 0.071 0.51 YES
36 CEP250 CEP250 CEP250 5203 0.071 0.52 YES
37 TUBB TUBB TUBB 5219 0.071 0.52 YES
38 CLASP1 CLASP1 CLASP1 5410 0.068 0.52 NO
39 YWHAE YWHAE YWHAE 6083 0.056 0.49 NO
40 TUBG1 TUBG1 TUBG1 6283 0.053 0.49 NO
41 AKAP9 AKAP9 AKAP9 6336 0.052 0.5 NO
42 CEP57 CEP57 CEP57 6477 0.05 0.49 NO
43 PCM1 PCM1 PCM1 6515 0.05 0.5 NO
44 TUBGCP5 TUBGCP5 TUBGCP5 6672 0.048 0.5 NO
45 DCTN1 DCTN1 DCTN1 6960 0.044 0.49 NO
46 CEP63 CEP63 CEP63 7822 0.034 0.44 NO
47 CSNK1E CSNK1E CSNK1E 7849 0.033 0.45 NO
48 MNAT1 MNAT1 MNAT1 7881 0.033 0.45 NO
49 HSP90AA1 HSP90AA1 HSP90AA1 8009 0.031 0.45 NO
50 CSNK1D CSNK1D CSNK1D 8478 0.025 0.42 NO
51 DYNC1H1 DYNC1H1 DYNC1H1 8587 0.024 0.42 NO
52 DCTN2 DCTN2 DCTN2 8645 0.023 0.42 NO
53 MAPRE1 MAPRE1 MAPRE1 8717 0.022 0.42 NO
54 YWHAG YWHAG YWHAG 8786 0.021 0.42 NO
55 HAUS2 HAUS2 HAUS2 9064 0.018 0.41 NO
56 DCTN3 DCTN3 DCTN3 9216 0.016 0.4 NO
57 CCNH CCNH CCNH 9276 0.016 0.4 NO
58 PPP2R1A PPP2R1A PPP2R1A 9280 0.016 0.4 NO
59 ACTR1A ACTR1A ACTR1A 9909 0.0075 0.37 NO
60 PAFAH1B1 PAFAH1B1 PAFAH1B1 9943 0.007 0.37 NO
61 SDCCAG8 SDCCAG8 SDCCAG8 10196 0.0032 0.35 NO
62 NUMA1 NUMA1 NUMA1 10645 -0.0028 0.33 NO
63 PRKACA PRKACA PRKACA 10747 -0.0041 0.32 NO
64 DYNC1I2 DYNC1I2 DYNC1I2 10776 -0.0044 0.32 NO
65 OFD1 OFD1 OFD1 10873 -0.006 0.32 NO
66 WEE1 WEE1 WEE1 11056 -0.0084 0.31 NO
67 TUBGCP2 TUBGCP2 TUBGCP2 11149 -0.0097 0.3 NO
68 DYNLL1 DYNLL1 DYNLL1 11168 -0.0099 0.3 NO
69 TUBGCP6 TUBGCP6 TUBGCP6 11366 -0.013 0.3 NO
70 CDK7 CDK7 CDK7 11456 -0.014 0.29 NO
71 CETN2 CETN2 CETN2 11926 -0.022 0.27 NO
72 SSNA1 SSNA1 SSNA1 12150 -0.026 0.26 NO
73 TUBG2 TUBG2 TUBG2 14633 -0.092 0.14 NO
74 TUBA4A TUBA4A TUBA4A 18113 -0.45 0.0046 NO

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

Figure S90.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG NUCLEOTIDE EXCISION REPAIR, 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 S46.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 NINL NINL NINL 53 0.5 0.089 YES
2 CEP72 CEP72 CEP72 862 0.27 0.093 YES
3 NEK2 NEK2 NEK2 1140 0.24 0.12 YES
4 PLK1 PLK1 PLK1 1306 0.23 0.15 YES
5 PLK4 PLK4 PLK4 1327 0.23 0.19 YES
6 CENPJ CENPJ CENPJ 1364 0.22 0.23 YES
7 PRKAR2B PRKAR2B PRKAR2B 1491 0.22 0.26 YES
8 TUBA1A TUBA1A TUBA1A 1700 0.2 0.29 YES
9 CEP76 CEP76 CEP76 2022 0.18 0.3 YES
10 CCNB1 CCNB1 CCNB1 2120 0.18 0.33 YES
11 CEP135 CEP135 CEP135 2459 0.16 0.34 YES
12 CDK5RAP2 CDK5RAP2 CDK5RAP2 2608 0.15 0.36 YES
13 AZI1 AZI1 AZI1 2655 0.15 0.38 YES
14 CDK1 CDK1 CDK1 2869 0.14 0.4 YES
15 CKAP5 CKAP5 CKAP5 3030 0.13 0.41 YES
16 ALMS1 ALMS1 ALMS1 3192 0.12 0.42 YES
17 NEDD1 NEDD1 NEDD1 3601 0.11 0.42 YES
18 CEP70 CEP70 CEP70 4036 0.097 0.42 YES
19 CEP192 CEP192 CEP192 4142 0.094 0.43 YES
20 FGFR1OP FGFR1OP FGFR1OP 4283 0.09 0.44 YES
21 PCNT PCNT PCNT 4416 0.087 0.44 YES
22 CEP164 CEP164 CEP164 4596 0.083 0.45 YES
23 CEP290 CEP290 CEP290 4731 0.08 0.46 YES
24 TUBGCP3 TUBGCP3 TUBGCP3 4922 0.076 0.46 YES
25 CEP250 CEP250 CEP250 5203 0.071 0.46 YES
26 TUBB TUBB TUBB 5219 0.071 0.47 YES
27 CLASP1 CLASP1 CLASP1 5410 0.068 0.47 YES
28 YWHAE YWHAE YWHAE 6083 0.056 0.44 NO
29 TUBG1 TUBG1 TUBG1 6283 0.053 0.44 NO
30 AKAP9 AKAP9 AKAP9 6336 0.052 0.45 NO
31 CEP57 CEP57 CEP57 6477 0.05 0.45 NO
32 PCM1 PCM1 PCM1 6515 0.05 0.46 NO
33 TUBGCP5 TUBGCP5 TUBGCP5 6672 0.048 0.46 NO
34 DCTN1 DCTN1 DCTN1 6960 0.044 0.45 NO
35 CEP63 CEP63 CEP63 7822 0.034 0.41 NO
36 CSNK1E CSNK1E CSNK1E 7849 0.033 0.41 NO
37 HSP90AA1 HSP90AA1 HSP90AA1 8009 0.031 0.41 NO
38 CSNK1D CSNK1D CSNK1D 8478 0.025 0.39 NO
39 DYNC1H1 DYNC1H1 DYNC1H1 8587 0.024 0.39 NO
40 DCTN2 DCTN2 DCTN2 8645 0.023 0.39 NO
41 MAPRE1 MAPRE1 MAPRE1 8717 0.022 0.39 NO
42 YWHAG YWHAG YWHAG 8786 0.021 0.39 NO
43 HAUS2 HAUS2 HAUS2 9064 0.018 0.38 NO
44 DCTN3 DCTN3 DCTN3 9216 0.016 0.37 NO
45 PPP2R1A PPP2R1A PPP2R1A 9280 0.016 0.37 NO
46 ACTR1A ACTR1A ACTR1A 9909 0.0075 0.34 NO
47 PAFAH1B1 PAFAH1B1 PAFAH1B1 9943 0.007 0.34 NO
48 SDCCAG8 SDCCAG8 SDCCAG8 10196 0.0032 0.32 NO
49 NUMA1 NUMA1 NUMA1 10645 -0.0028 0.3 NO
50 PRKACA PRKACA PRKACA 10747 -0.0041 0.3 NO
51 DYNC1I2 DYNC1I2 DYNC1I2 10776 -0.0044 0.29 NO
52 OFD1 OFD1 OFD1 10873 -0.006 0.29 NO
53 TUBGCP2 TUBGCP2 TUBGCP2 11149 -0.0097 0.28 NO
54 DYNLL1 DYNLL1 DYNLL1 11168 -0.0099 0.28 NO
55 TUBGCP6 TUBGCP6 TUBGCP6 11366 -0.013 0.27 NO
56 CETN2 CETN2 CETN2 11926 -0.022 0.24 NO
57 SSNA1 SSNA1 SSNA1 12150 -0.026 0.24 NO
58 TUBG2 TUBG2 TUBG2 14633 -0.092 0.11 NO
59 TUBA4A TUBA4A TUBA4A 18113 -0.45 0.0046 NO

Figure S91.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG HOMOLOGOUS RECOMBINATION.

Figure S92.  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 S47.  Get Full Table This table shows a Running Enrichment Score (RES) of each gene in this pathway, that is, the enrichment score at this point in the ranked list of genes. All genes are ranked by Signal-to-Noise (S2N), a measure of similarity as default and are used to obtain ES matrix of all genes. In this way, GSEA tool uses expression pattern of not only overlapped genes but also not-overlapped genes to produce ES matrix.

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 NUP210 NUP210 NUP210 733 0.29 0.05 YES
2 SMN1 SMN1 SMN1 1848 0.19 0.049 YES
3 NUP107 NUP107 NUP107 2789 0.14 0.042 YES
4 NUP155 NUP155 NUP155 2998 0.13 0.072 YES
5 NUP88 NUP88 NUP88 3301 0.12 0.093 YES
6 NUP35 NUP35 NUP35 4155 0.093 0.076 YES
7 TGS1 TGS1 TGS1 4202 0.092 0.1 YES
8 DDX20 DDX20 DDX20 4216 0.091 0.13 YES
9 GEMIN5 GEMIN5 GEMIN5 4403 0.087 0.15 YES
10 SNRPD1 SNRPD1 SNRPD1 4459 0.086 0.17 YES
11 NUP85 NUP85 NUP85 4536 0.084 0.19 YES
12 NUP153 NUP153 NUP153 4570 0.084 0.22 YES
13 SMN2 SMN2 SMN2 4574 0.084 0.24 YES
14 NUP205 NUP205 NUP205 4793 0.079 0.26 YES
15 PRMT5 PRMT5 PRMT5 4896 0.077 0.28 YES
16 AAAS AAAS AAAS 4926 0.076 0.3 YES
17 GEMIN6 GEMIN6 GEMIN6 4948 0.076 0.32 YES
18 SNRPE SNRPE SNRPE 4974 0.075 0.34 YES
19 NUP62 NUP62 NUP62 5042 0.074 0.36 YES
20 NCBP1 NCBP1 NCBP1 5048 0.074 0.39 YES
21 RAE1 RAE1 RAE1 5134 0.072 0.4 YES
22 SEH1L SEH1L SEH1L 5148 0.072 0.43 YES
23 NUP188 NUP188 NUP188 5287 0.07 0.44 YES
24 NUP43 NUP43 NUP43 5341 0.069 0.46 YES
25 NUPL1 NUPL1 NUPL1 5385 0.068 0.48 YES
26 NUP133 NUP133 NUP133 5469 0.067 0.5 YES
27 NUP93 NUP93 NUP93 5703 0.062 0.5 YES
28 PHAX PHAX PHAX 5776 0.061 0.52 YES
29 TPR TPR TPR 6132 0.056 0.52 YES
30 POM121 POM121 POM121 6584 0.049 0.51 YES
31 SNRPF SNRPF SNRPF 6768 0.047 0.51 YES
32 NUP214 NUP214 NUP214 6775 0.046 0.53 YES
33 GEMIN4 GEMIN4 GEMIN4 7043 0.043 0.52 YES
34 NCBP2 NCBP2 NCBP2 7125 0.042 0.53 YES
35 SNRPG SNRPG SNRPG 7291 0.04 0.54 YES
36 SNRPB SNRPB SNRPB 7934 0.032 0.51 NO
37 SNRPD2 SNRPD2 SNRPD2 8030 0.031 0.52 NO
38 NUP37 NUP37 NUP37 8539 0.024 0.5 NO
39 RANBP2 RANBP2 RANBP2 8540 0.024 0.5 NO
40 SNRPD3 SNRPD3 SNRPD3 8946 0.02 0.49 NO
41 NUP50 NUP50 NUP50 9163 0.017 0.48 NO
42 NUPL2 NUPL2 NUPL2 9400 0.014 0.47 NO
43 CLNS1A CLNS1A CLNS1A 9685 0.01 0.46 NO
44 GEMIN7 GEMIN7 GEMIN7 10412 0.0002 0.42 NO
45 SNUPN SNUPN SNUPN 10471 -0.00058 0.42 NO
46 NUP54 NUP54 NUP54 10498 -0.00092 0.42 NO
47 WDR77 WDR77 WDR77 11950 -0.022 0.34 NO

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

Figure S94.  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: KEGG OOCYTE MEIOSIS

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 NUP210 NUP210 NUP210 733 0.29 0.0048 YES
2 NUP107 NUP107 NUP107 2789 0.14 -0.086 YES
3 NUP155 NUP155 NUP155 2998 0.13 -0.077 YES
4 NUP88 NUP88 NUP88 3301 0.12 -0.075 YES
5 CSTF3 CSTF3 CSTF3 4054 0.096 -0.1 YES
6 SNRPA SNRPA SNRPA 4071 0.096 -0.087 YES
7 NUP35 NUP35 NUP35 4155 0.093 -0.077 YES
8 THOC4 THOC4 THOC4 4346 0.088 -0.074 YES
9 POLR2D POLR2D POLR2D 4417 0.086 -0.064 YES
10 SNRPD1 SNRPD1 SNRPD1 4459 0.086 -0.053 YES
11 CPSF3 CPSF3 CPSF3 4513 0.085 -0.042 YES
12 NUP85 NUP85 NUP85 4536 0.084 -0.03 YES
13 NUP153 NUP153 NUP153 4570 0.084 -0.019 YES
14 RBMX RBMX RBMX 4586 0.083 -0.0063 YES
15 SNRNP40 SNRNP40 SNRNP40 4632 0.082 0.0042 YES
16 SNRPB2 SNRPB2 SNRPB2 4747 0.08 0.01 YES
17 NUP205 NUP205 NUP205 4793 0.079 0.02 YES
18 SMC1A SMC1A SMC1A 4888 0.077 0.028 YES
19 AAAS AAAS AAAS 4926 0.076 0.038 YES
20 SNRPE SNRPE SNRPE 4974 0.075 0.047 YES
21 NUP62 NUP62 NUP62 5042 0.074 0.055 YES
22 NCBP1 NCBP1 NCBP1 5048 0.074 0.066 YES
23 SNRNP200 SNRNP200 SNRNP200 5067 0.074 0.077 YES
24 DHX9 DHX9 DHX9 5118 0.072 0.086 YES
25 RAE1 RAE1 RAE1 5134 0.072 0.096 YES
26 SEH1L SEH1L SEH1L 5148 0.072 0.11 YES
27 HNRNPA0 HNRNPA0 HNRNPA0 5154 0.072 0.12 YES
28 EFTUD2 EFTUD2 EFTUD2 5215 0.071 0.13 YES
29 UPF3B UPF3B UPF3B 5253 0.07 0.14 YES
30 METTL3 METTL3 METTL3 5256 0.07 0.15 YES
31 NUP188 NUP188 NUP188 5287 0.07 0.16 YES
32 TXNL4A TXNL4A TXNL4A 5301 0.07 0.17 YES
33 NUP43 NUP43 NUP43 5341 0.069 0.17 YES
34 NUPL1 NUPL1 NUPL1 5385 0.068 0.18 YES
35 FUS FUS FUS 5399 0.068 0.19 YES
36 CSTF1 CSTF1 CSTF1 5421 0.068 0.2 YES
37 NUP133 NUP133 NUP133 5469 0.067 0.21 YES
38 CPSF1 CPSF1 CPSF1 5511 0.066 0.22 YES
39 HNRNPR HNRNPR HNRNPR 5567 0.065 0.23 YES
40 NUP93 NUP93 NUP93 5703 0.062 0.23 YES
41 HNRNPM HNRNPM HNRNPM 5817 0.06 0.23 YES
42 SF3B4 SF3B4 SF3B4 5863 0.06 0.24 YES
43 HNRNPH1 HNRNPH1 HNRNPH1 5970 0.058 0.24 YES
44 HNRNPU HNRNPU HNRNPU 6002 0.057 0.25 YES
45 CLP1 CLP1 CLP1 6120 0.056 0.25 YES
46 TPR TPR TPR 6132 0.056 0.26 YES
47 PRPF8 PRPF8 PRPF8 6164 0.055 0.27 YES
48 SF3A2 SF3A2 SF3A2 6272 0.053 0.27 YES
49 YBX1 YBX1 YBX1 6322 0.053 0.27 YES
50 HNRNPUL1 HNRNPUL1 HNRNPUL1 6388 0.052 0.28 YES
51 HNRNPC HNRNPC HNRNPC 6421 0.051 0.28 YES
52 LSM2 LSM2 LSM2 6542 0.05 0.29 YES
53 SNRPA1 SNRPA1 SNRPA1 6552 0.049 0.29 YES
54 POM121 POM121 POM121 6584 0.049 0.3 YES
55 CPSF7 CPSF7 CPSF7 6645 0.048 0.3 YES
56 SF3A1 SF3A1 SF3A1 6676 0.048 0.31 YES
57 RBM8A RBM8A RBM8A 6683 0.048 0.32 YES
58 PRPF4 PRPF4 PRPF4 6715 0.047 0.32 YES
59 HNRNPL HNRNPL HNRNPL 6750 0.047 0.33 YES
60 HNRNPD HNRNPD HNRNPD 6751 0.047 0.34 YES
61 HNRNPA3 HNRNPA3 HNRNPA3 6759 0.047 0.34 YES
62 SNRPF SNRPF SNRPF 6768 0.047 0.35 YES
63 NUP214 NUP214 NUP214 6775 0.046 0.36 YES
64 POLR2K POLR2K POLR2K 6816 0.046 0.36 YES
65 SF3B5 SF3B5 SF3B5 6834 0.046 0.37 YES
66 POLR2A POLR2A POLR2A 6847 0.046 0.38 YES
67 PABPN1 PABPN1 PABPN1 6896 0.045 0.38 YES
68 POLR2H POLR2H POLR2H 6986 0.044 0.38 YES
69 CDC40 CDC40 CDC40 7000 0.044 0.39 YES
70 U2AF1 U2AF1 U2AF1 7033 0.043 0.39 YES
71 POLR2B POLR2B POLR2B 7039 0.043 0.4 YES
72 PTBP1 PTBP1 PTBP1 7056 0.043 0.4 YES
73 CCAR1 CCAR1 CCAR1 7061 0.043 0.41 YES
74 SF3A3 SF3A3 SF3A3 7079 0.043 0.42 YES
75 PHF5A PHF5A PHF5A 7116 0.042 0.42 YES
76 NCBP2 NCBP2 NCBP2 7125 0.042 0.43 YES
77 HNRNPA2B1 HNRNPA2B1 HNRNPA2B1 7149 0.042 0.43 YES
78 SNRPG SNRPG SNRPG 7291 0.04 0.43 YES
79 PCBP2 PCBP2 PCBP2 7332 0.04 0.44 YES
80 HNRNPA1 HNRNPA1 HNRNPA1 7344 0.039 0.44 YES
81 SF3B3 SF3B3 SF3B3 7368 0.039 0.45 YES
82 U2AF2 U2AF2 U2AF2 7455 0.038 0.45 YES
83 SRRM1 SRRM1 SRRM1 7464 0.038 0.45 YES
84 DDX23 DDX23 DDX23 7467 0.038 0.46 YES
85 POLR2G POLR2G POLR2G 7535 0.037 0.46 YES
86 POLR2I POLR2I POLR2I 7592 0.036 0.46 YES
87 POLR2F POLR2F POLR2F 7659 0.036 0.47 YES
88 CSTF2 CSTF2 CSTF2 7697 0.035 0.47 YES
89 HNRNPK HNRNPK HNRNPK 7770 0.034 0.47 YES
90 PRPF6 PRPF6 PRPF6 7818 0.034 0.47 YES
91 SNRPB SNRPB SNRPB 7934 0.032 0.47 YES
92 MAGOH MAGOH MAGOH 7944 0.032 0.48 YES
93 SLBP SLBP SLBP 8014 0.031 0.48 YES
94 SNRPD2 SNRPD2 SNRPD2 8030 0.031 0.48 YES
95 RNPS1 RNPS1 RNPS1 8089 0.03 0.48 YES
96 SF3B2 SF3B2 SF3B2 8294 0.028 0.48 NO
97 NUP37 NUP37 NUP37 8539 0.024 0.47 NO
98 RANBP2 RANBP2 RANBP2 8540 0.024 0.47 NO
99 CD2BP2 CD2BP2 CD2BP2 8657 0.023 0.47 NO
100 GTF2F1 GTF2F1 GTF2F1 8685 0.023 0.47 NO
101 NUDT21 NUDT21 NUDT21 8742 0.022 0.47 NO
102 SNRNP70 SNRNP70 SNRNP70 8868 0.02 0.47 NO
103 SNRPD3 SNRPD3 SNRPD3 8946 0.02 0.47 NO
104 POLR2J POLR2J POLR2J 9105 0.018 0.46 NO
105 EIF4E EIF4E EIF4E 9127 0.018 0.46 NO
106 NUP50 NUP50 NUP50 9163 0.017 0.46 NO
107 SF3B1 SF3B1 SF3B1 9180 0.017 0.46 NO
108 CPSF2 CPSF2 CPSF2 9258 0.016 0.46 NO
109 DNAJC8 DNAJC8 DNAJC8 9305 0.016 0.46 NO
110 NUPL2 NUPL2 NUPL2 9400 0.014 0.46 NO
111 NFX1 NFX1 NFX1 9413 0.014 0.46 NO
112 RBM5 RBM5 RBM5 9518 0.013 0.46 NO
113 PAPOLA PAPOLA PAPOLA 9629 0.011 0.45 NO
114 POLR2E POLR2E POLR2E 9636 0.011 0.45 NO
115 SF3B14 SF3B14 SF3B14 9742 0.0096 0.45 NO
116 HNRNPF HNRNPF HNRNPF 9819 0.0088 0.45 NO
117 DHX38 DHX38 DHX38 9942 0.007 0.44 NO
118 PCBP1 PCBP1 PCBP1 9956 0.0067 0.44 NO
119 NHP2L1 NHP2L1 NHP2L1 10151 0.0038 0.43 NO
120 POLR2C POLR2C POLR2C 10233 0.0026 0.43 NO
121 NUP54 NUP54 NUP54 10498 -0.00092 0.41 NO
122 NXF1 NXF1 NXF1 10548 -0.0016 0.41 NO
123 POLR2L POLR2L POLR2L 11114 -0.0093 0.38 NO
124 PCF11 PCF11 PCF11 11378 -0.013 0.37 NO
125 GTF2F2 GTF2F2 GTF2F2 11530 -0.016 0.36 NO
126 HNRNPH2 HNRNPH2 HNRNPH2 12916 -0.041 0.29 NO

Figure S95.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: KEGG OOCYTE MEIOSIS.

Figure S96.  Get High-res Image For the top 5 core enriched genes in the pathway: KEGG OOCYTE MEIOSIS, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA CHREBP2 PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 NUP210 NUP210 NUP210 733 0.29 0.084 YES
2 GCK GCK GCK 931 0.26 0.19 YES
3 GCKR GCKR GCKR 2527 0.15 0.17 YES
4 NUP107 NUP107 NUP107 2789 0.14 0.21 YES
5 NUP155 NUP155 NUP155 2998 0.13 0.26 YES
6 NUP88 NUP88 NUP88 3301 0.12 0.3 YES
7 NUP35 NUP35 NUP35 4155 0.093 0.29 YES
8 NUP85 NUP85 NUP85 4536 0.084 0.3 YES
9 NUP153 NUP153 NUP153 4570 0.084 0.34 YES
10 NUP205 NUP205 NUP205 4793 0.079 0.36 YES
11 AAAS AAAS AAAS 4926 0.076 0.39 YES
12 NUP62 NUP62 NUP62 5042 0.074 0.41 YES
13 RAE1 RAE1 RAE1 5134 0.072 0.44 YES
14 SEH1L SEH1L SEH1L 5148 0.072 0.47 YES
15 NUP188 NUP188 NUP188 5287 0.07 0.49 YES
16 NUP43 NUP43 NUP43 5341 0.069 0.52 YES
17 NUPL1 NUPL1 NUPL1 5385 0.068 0.55 YES
18 NUP133 NUP133 NUP133 5469 0.067 0.57 YES
19 NUP93 NUP93 NUP93 5703 0.062 0.59 YES
20 TPR TPR TPR 6132 0.056 0.59 YES
21 POM121 POM121 POM121 6584 0.049 0.58 YES
22 NUP214 NUP214 NUP214 6775 0.046 0.59 YES
23 NUP37 NUP37 NUP37 8539 0.024 0.51 NO
24 RANBP2 RANBP2 RANBP2 8540 0.024 0.52 NO
25 NUP50 NUP50 NUP50 9163 0.017 0.49 NO
26 NUPL2 NUPL2 NUPL2 9400 0.014 0.48 NO
27 NUP54 NUP54 NUP54 10498 -0.00092 0.42 NO

Figure S97.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: BIOCARTA CHREBP2 PATHWAY.

Figure S98.  Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA CHREBP2 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: PID FANCONI PATHWAY

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

Rank GENE SYMBOL DESC LIST.LOC S2N RES CORE_ENRICHMENT
1 NINL NINL NINL 53 0.5 0.096 YES
2 CEP72 CEP72 CEP72 862 0.27 0.1 YES
3 NEK2 NEK2 NEK2 1140 0.24 0.14 YES
4 PLK1 PLK1 PLK1 1306 0.23 0.17 YES
5 PLK4 PLK4 PLK4 1327 0.23 0.22 YES
6 CENPJ CENPJ CENPJ 1364 0.22 0.26 YES
7 PRKAR2B PRKAR2B PRKAR2B 1491 0.22 0.29 YES
8 TUBA1A TUBA1A TUBA1A 1700 0.2 0.32 YES
9 CEP76 CEP76 CEP76 2022 0.18 0.34 YES
10 CEP135 CEP135 CEP135 2459 0.16 0.35 YES
11 CDK5RAP2 CDK5RAP2 CDK5RAP2 2608 0.15 0.37 YES
12 AZI1 AZI1 AZI1 2655 0.15 0.39 YES
13 CDK1 CDK1 CDK1 2869 0.14 0.41 YES
14 CKAP5 CKAP5 CKAP5 3030 0.13 0.42 YES
15 ALMS1 ALMS1 ALMS1 3192 0.12 0.44 YES
16 NEDD1 NEDD1 NEDD1 3601 0.11 0.44 YES
17 CEP70 CEP70 CEP70 4036 0.097 0.43 YES
18 CEP192 CEP192 CEP192 4142 0.094 0.45 YES
19 FGFR1OP FGFR1OP FGFR1OP 4283 0.09 0.46 YES
20 PCNT PCNT PCNT 4416 0.087 0.47 YES
21 CEP164 CEP164 CEP164 4596 0.083 0.47 YES
22 CEP290 CEP290 CEP290 4731 0.08 0.48 YES
23 CEP250 CEP250 CEP250 5203 0.071 0.47 YES
24 TUBB TUBB TUBB 5219 0.071 0.48 YES
25 CLASP1 CLASP1 CLASP1 5410 0.068 0.48 YES
26 YWHAE YWHAE YWHAE 6083 0.056 0.46 NO
27 TUBG1 TUBG1 TUBG1 6283 0.053 0.46 NO
28 AKAP9 AKAP9 AKAP9 6336 0.052 0.47 NO
29 CEP57 CEP57 CEP57 6477 0.05 0.47 NO
30 PCM1 PCM1 PCM1 6515 0.05 0.48 NO
31 DCTN1 DCTN1 DCTN1 6960 0.044 0.46 NO
32 CEP63 CEP63 CEP63 7822 0.034 0.42 NO
33 CSNK1E CSNK1E CSNK1E 7849 0.033 0.42 NO
34 HSP90AA1 HSP90AA1 HSP90AA1 8009 0.031 0.42 NO
35 CSNK1D CSNK1D CSNK1D 8478 0.025 0.4 NO
36 DYNC1H1 DYNC1H1 DYNC1H1 8587 0.024 0.4 NO
37 DCTN2 DCTN2 DCTN2 8645 0.023 0.4 NO
38 MAPRE1 MAPRE1 MAPRE1 8717 0.022 0.4 NO
39 YWHAG YWHAG YWHAG 8786 0.021 0.4 NO
40 HAUS2 HAUS2 HAUS2 9064 0.018 0.39 NO
41 DCTN3 DCTN3 DCTN3 9216 0.016 0.38 NO
42 PPP2R1A PPP2R1A PPP2R1A 9280 0.016 0.38 NO
43 ACTR1A ACTR1A ACTR1A 9909 0.0075 0.35 NO
44 PAFAH1B1 PAFAH1B1 PAFAH1B1 9943 0.007 0.35 NO
45 SDCCAG8 SDCCAG8 SDCCAG8 10196 0.0032 0.34 NO
46 PRKACA PRKACA PRKACA 10747 -0.0041 0.31 NO
47 DYNC1I2 DYNC1I2 DYNC1I2 10776 -0.0044 0.31 NO
48 OFD1 OFD1 OFD1 10873 -0.006 0.3 NO
49 DYNLL1 DYNLL1 DYNLL1 11168 -0.0099 0.29 NO
50 CETN2 CETN2 CETN2 11926 -0.022 0.25 NO
51 SSNA1 SSNA1 SSNA1 12150 -0.026 0.24 NO
52 TUBA4A TUBA4A TUBA4A 18113 -0.45 0.0046 NO

Figure S99.  Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID FANCONI PATHWAY.

Figure S100.  Get High-res Image For the top 5 core enriched genes in the pathway: PID FANCONI PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

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 = BLCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt

  • Phenotype data file = BLCA-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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