GSEA Class2: Canonical Pathways enriched in each subtypes of mRNAseq_cNMF in LAML-TB
Acute Myeloid Leukemia (Primary blood derived cancer - Peripheral blood)
28 January 2016 | analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1R78DNT
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 LAML-TB. Broad Institute of MIT and Harvard. doi:10.7908/C1R78DNT
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 "LAML-TB.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: 692
Number of samples: 173
Original number of Gene Sets: 1320
Maximum gene set size: 933

Table 2. Get Full Table pheno data info

phenotype info
pheno.type: 1 - 3 :[ clus1 ] 75
pheno.type: 2 - 3 :[ clus2 ] 52
pheno.type: 3 - 3 :[ clus3 ] 46

For the expression subtypes of 17276 genes in 174 samples, GSEA found enriched gene sets in each cluster using 173 gene sets in MSigDB canonical pathways. Top enriched gene sets are listed as below.

- clus1

- Top enriched gene sets are KEGG N GLYCAN BIOSYNTHESIS, KEGG MTOR SIGNALING PATHWAY, KEGG ADHERENS JUNCTION, KEGG RENAL CELL CARCINOMA, KEGG PANCREATIC CANCER, KEGG ENDOMETRIAL CANCER, KEGG PROSTATE CANCER, KEGG THYROID CANCER, KEGG MELANOMA, KEGG NON SMALL CELL LUNG CANCER

- And common core enriched genes are EGF, EGFR, CCND1, CDH1, MGAT3, ESR1, IFNG, NR2F2, TERT, AKT3

- clus2

- Top enriched gene sets are KEGG LYSOSOME, KEGG FC GAMMA R MEDIATED PHAGOCYTOSIS, BIOCARTA HIVNEF PATHWAY, BIOCARTA PYK2 PATHWAY, BIOCARTA TOLL PATHWAY, ST TUMOR NECROSIS FACTOR PATHWAY, PID IL1PATHWAY, PID IFNGPATHWAY, PID IL8CXCR2 PATHWAY, PID MAPKTRKPATHWAY

- And common core enriched genes are FOS, MAP2K1, MAP2K6, MAPK7, MEF2C, DUSP6, IRAK3, LY96, MYD88, NFKB2

- clus3

- Top enriched gene sets are KEGG GLYCOSYLPHOSPHATIDYLINOSITOL GPI ANCHOR BIOSYNTHESIS, KEGG AMINOACYL TRNA BIOSYNTHESIS, KEGG RIBOSOME, KEGG RNA POLYMERASE, PID MYC PATHWAY, REACTOME TRANSLATION, REACTOME FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX, REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE, REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S, REACTOME PEPTIDE CHAIN ELONGATION

- And common core enriched genes are POLR1C, POLR1D, POLR2F, POLR2H, POLR2L, POLR3B, POLR3D, POLR3H, POLR3K, CDKN2A

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 N GLYCAN BIOSYNTHESIS | 46 | genes.ES.table | 0.48 | 1.9 | 0.002 | 0.53 | 0.26 | 0.28 | 0.28 | 0.2 | 0 | 0.1
KEGG MTOR SIGNALING PATHWAY | 49 | genes.ES.table | 0.48 | 1.7 | 0.012 | 0.47 | 0.65 | 0.2 | 0.17 | 0.17 | 0.16 | 0.12
KEGG ADHERENS JUNCTION | 72 | genes.ES.table | 0.57 | 1.7 | 0.0061 | 0.68 | 0.61 | 0.24 | 0.092 | 0.22 | 0.22 | 0.16
KEGG RENAL CELL CARCINOMA | 69 | genes.ES.table | 0.46 | 1.7 | 0.004 | 0.48 | 0.73 | 0.23 | 0.18 | 0.19 | 0.19 | 0.12
KEGG PANCREATIC CANCER | 70 | genes.ES.table | 0.43 | 1.7 | 0.0019 | 0.55 | 0.62 | 0.17 | 0.15 | 0.15 | 0.18 | 0.13
KEGG ENDOMETRIAL CANCER | 51 | genes.ES.table | 0.54 | 1.9 | 0.002 | 0.79 | 0.26 | 0.2 | 0.15 | 0.17 | 0 | 0.15
KEGG PROSTATE CANCER | 87 | genes.ES.table | 0.5 | 1.8 | 0.004 | 0.5 | 0.42 | 0.23 | 0.17 | 0.19 | 0 | 0.11
KEGG THYROID CANCER | 28 | genes.ES.table | 0.57 | 1.7 | 0.002 | 0.45 | 0.65 | 0.18 | 0.14 | 0.15 | 0.16 | 0.12
KEGG MELANOMA | 60 | genes.ES.table | 0.58 | 1.7 | 0.0019 | 0.47 | 0.69 | 0.35 | 0.17 | 0.29 | 0.17 | 0.13
KEGG NON SMALL CELL LUNG CANCER | 53 | genes.ES.table | 0.45 | 1.7 | 0.0039 | 0.6 | 0.61 | 0.15 | 0.15 | 0.13 | 0.19 | 0.14

genes ES table in pathway: KEGG N GLYCAN BIOSYNTHESIS

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 | CCND1 | CCND1 | CCND1 | 63 | 0.61 | 0.1 | YES
2 | TERT | TERT | TERT | 143 | 0.56 | 0.19 | YES
3 | EGFR | EGFR | EGFR | 177 | 0.54 | 0.28 | YES
4 | EGF | EGF | EGF | 253 | 0.51 | 0.36 | YES
5 | ESR1 | ESR1 | ESR1 | 652 | 0.42 | 0.41 | YES
6 | NR2F2 | NR2F2 | NR2F2 | 881 | 0.38 | 0.46 | YES
7 | IFNG | IFNG | IFNG | 1523 | 0.31 | 0.47 | YES
8 | PIF1 | PIF1 | PIF1 | 2377 | 0.23 | 0.46 | NO
9 | WRN | WRN | WRN | 4085 | 0.14 | 0.39 | NO
10 | MYC | MYC | MYC | 5427 | 0.09 | 0.32 | NO
11 | PARP2 | PARP2 | PARP2 | 5487 | 0.089 | 0.34 | NO
12 | DKC1 | DKC1 | DKC1 | 6217 | 0.071 | 0.31 | NO
13 | MRE11A | MRE11A | MRE11A | 6287 | 0.07 | 0.31 | NO
14 | TNKS | TNKS | TNKS | 6339 | 0.069 | 0.32 | NO
15 | POT1 | POT1 | POT1 | 7074 | 0.054 | 0.29 | NO
16 | RBBP4 | RBBP4 | RBBP4 | 7161 | 0.053 | 0.29 | NO
17 | NBN | NBN | NBN | 7211 | 0.052 | 0.3 | NO
18 | WT1 | WT1 | WT1 | 7320 | 0.05 | 0.3 | NO
19 | HDAC2 | HDAC2 | HDAC2 | 7479 | 0.048 | 0.3 | NO
20 | SIN3A | SIN3A | SIN3A | 7537 | 0.047 | 0.3 | NO
21 | SMAD3 | SMAD3 | SMAD3 | 7609 | 0.046 | 0.31 | NO
22 | SP3 | SP3 | SP3 | 7672 | 0.045 | 0.31 | NO
23 | RAD9A | RAD9A | RAD9A | 7969 | 0.04 | 0.3 | NO
24 | TERF1 | TERF1 | TERF1 | 7990 | 0.04 | 0.31 | NO
25 | SMG6 | SMG6 | SMG6 | 8042 | 0.04 | 0.31 | NO
26 | IRF1 | IRF1 | IRF1 | 8060 | 0.039 | 0.32 | NO
27 | E2F1 | E2F1 | E2F1 | 8092 | 0.039 | 0.32 | NO
28 | MAX | MAX | MAX | 8131 | 0.038 | 0.32 | NO
29 | ABL1 | ABL1 | ABL1 | 8189 | 0.038 | 0.33 | NO
30 | ATM | ATM | ATM | 8222 | 0.037 | 0.33 | NO
31 | RAD1 | RAD1 | RAD1 | 8267 | 0.037 | 0.34 | NO
32 | TERF2IP | TERF2IP | TERF2IP | 8441 | 0.034 | 0.33 | NO
33 | UBE3A | UBE3A | UBE3A | 8508 | 0.033 | 0.33 | NO
34 | BLM | BLM | BLM | 8557 | 0.033 | 0.34 | NO
35 | SIN3B | SIN3B | SIN3B | 8587 | 0.032 | 0.34 | NO
36 | HDAC1 | HDAC1 | HDAC1 | 8625 | 0.032 | 0.34 | NO
37 | NCL | NCL | NCL | 8824 | 0.029 | 0.34 | NO
38 | SMG5 | SMG5 | SMG5 | 8854 | 0.029 | 0.34 | NO
39 | RPS6KB1 | RPS6KB1 | RPS6KB1 | 8933 | 0.028 | 0.34 | NO
40 | RBBP7 | RBBP7 | RBBP7 | 9094 | 0.026 | 0.34 | NO
41 | XRCC5 | XRCC5 | XRCC5 | 9106 | 0.026 | 0.34 | NO
42 | MTOR | MTOR | MTOR | 9420 | 0.022 | 0.32 | NO
43 | MAPK1 | MAPK1 | MAPK1 | 10305 | 0.011 | 0.28 | NO
44 | XRCC6 | XRCC6 | XRCC6 | 10472 | 0.0086 | 0.27 | NO
45 | CDKN1B | CDKN1B | CDKN1B | 10668 | 0.0064 | 0.26 | NO
46 | HSP90AA1 | HSP90AA1 | HSP90AA1 | 10748 | 0.0052 | 0.25 | NO
47 | RAD50 | RAD50 | RAD50 | 10917 | 0.0032 | 0.24 | NO
48 | SP1 | SP1 | SP1 | 11371 | -0.0029 | 0.22 | NO
49 | HNRNPC | HNRNPC | HNRNPC | 11479 | -0.0043 | 0.21 | NO
50 | TERF2 | TERF2 | TERF2 | 11563 | -0.0054 | 0.21 | NO
51 | ZNFX1 | ZNFX1 | ZNFX1 | 11635 | -0.0066 | 0.21 | NO
52 | SAP18 | SAP18 | SAP18 | 12010 | -0.012 | 0.19 | NO
53 | PTGES3 | PTGES3 | PTGES3 | 12348 | -0.017 | 0.17 | NO
54 | IFNAR2 | IFNAR2 | IFNAR2 | 12351 | -0.017 | 0.17 | NO
55 | MAPK3 | MAPK3 | MAPK3 | 12736 | -0.023 | 0.15 | NO
56 | TINF2 | TINF2 | TINF2 | 12819 | -0.025 | 0.15 | NO
57 | HUS1 | HUS1 | HUS1 | 12925 | -0.027 | 0.15 | NO
58 | NFKB1 | NFKB1 | NFKB1 | 13189 | -0.031 | 0.14 | NO
59 | YWHAE | YWHAE | YWHAE | 13424 | -0.036 | 0.13 | NO
60 | ACD | ACD | ACD | 13800 | -0.044 | 0.12 | NO
61 | FOS | FOS | FOS | 13848 | -0.045 | 0.12 | NO
62 | PINX1 | PINX1 | PINX1 | 13893 | -0.046 | 0.13 | NO
63 | TGFB1 | TGFB1 | TGFB1 | 14565 | -0.064 | 0.1 | NO
64 | AKT1 | AKT1 | AKT1 | 14735 | -0.07 | 0.1 | NO
65 | JUN | JUN | JUN | 14997 | -0.078 | 0.1 | NO
66 | MXD1 | MXD1 | MXD1 | 15005 | -0.078 | 0.11 | NO
67 | SAP30 | SAP30 | SAP30 | 15505 | -0.1 | 0.1 | 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 N GLYCAN BIOSYNTHESIS.

Figure S2. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG N 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 MTOR SIGNALING PATHWAY

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 | CCND1 | CCND1 | CCND1 | 63 | 0.61 | 0.1 | YES
2 | CDH1 | CDH1 | CDH1 | 140 | 0.56 | 0.2 | YES
3 | EGFR | EGFR | EGFR | 177 | 0.54 | 0.29 | YES
4 | EGF | EGF | EGF | 253 | 0.51 | 0.38 | YES
5 | LEF1 | LEF1 | LEF1 | 642 | 0.42 | 0.43 | YES
6 | TCF7 | TCF7 | TCF7 | 1589 | 0.3 | 0.42 | YES
7 | AXIN2 | AXIN2 | AXIN2 | 1885 | 0.27 | 0.45 | YES
8 | AKT3 | AKT3 | AKT3 | 2347 | 0.24 | 0.47 | YES
9 | PIK3R3 | PIK3R3 | PIK3R3 | 2395 | 0.23 | 0.51 | YES
10 | ERBB2 | ERBB2 | ERBB2 | 2526 | 0.22 | 0.54 | YES
11 | CTNNA3 | CTNNA3 | CTNNA3 | 3921 | 0.14 | 0.48 | NO
12 | PIK3CA | PIK3CA | PIK3CA | 5255 | 0.095 | 0.42 | NO
13 | MYC | MYC | MYC | 5427 | 0.09 | 0.43 | NO
14 | FOXO3 | FOXO3 | FOXO3 | 5514 | 0.088 | 0.44 | NO
15 | SOS1 | SOS1 | SOS1 | 5782 | 0.081 | 0.44 | NO
16 | BRAF | BRAF | BRAF | 6025 | 0.075 | 0.44 | NO
17 | TCF7L2 | TCF7L2 | TCF7L2 | 6035 | 0.075 | 0.45 | NO
18 | PIK3R1 | PIK3R1 | PIK3R1 | 6522 | 0.065 | 0.43 | NO
19 | APC | APC | APC | 8151 | 0.038 | 0.34 | NO
20 | NRAS | NRAS | NRAS | 8475 | 0.034 | 0.33 | NO
21 | AXIN1 | AXIN1 | AXIN1 | 8762 | 0.03 | 0.32 | NO
22 | PTEN | PTEN | PTEN | 8964 | 0.028 | 0.31 | NO
23 | PIK3CG | PIK3CG | PIK3CG | 9829 | 0.017 | 0.26 | NO
24 | GSK3B | GSK3B | GSK3B | 10065 | 0.014 | 0.25 | NO
25 | MAPK1 | MAPK1 | MAPK1 | 10305 | 0.011 | 0.24 | NO
26 | MAP2K2 | MAP2K2 | MAP2K2 | 10714 | 0.0058 | 0.22 | NO
27 | AKT2 | AKT2 | AKT2 | 11099 | 0.0008 | 0.2 | NO
28 | MLH1 | MLH1 | MLH1 | 11261 | -0.0013 | 0.19 | NO
29 | PIK3CD | PIK3CD | PIK3CD | 11292 | -0.0018 | 0.19 | NO
30 | RAF1 | RAF1 | RAF1 | 11328 | -0.0022 | 0.18 | NO
31 | ELK1 | ELK1 | ELK1 | 11412 | -0.0034 | 0.18 | NO
32 | PDPK1 | PDPK1 | PDPK1 | 11511 | -0.0048 | 0.18 | NO
33 | KRAS | KRAS | KRAS | 11523 | -0.0049 | 0.18 | NO
34 | APC2 | APC2 | APC2 | 11737 | -0.008 | 0.16 | NO
35 | TP53 | TP53 | TP53 | 11867 | -0.0098 | 0.16 | NO
36 | SOS2 | SOS2 | SOS2 | 12356 | -0.017 | 0.13 | NO
37 | CTNNB1 | CTNNB1 | CTNNB1 | 12367 | -0.018 | 0.14 | NO
38 | MAPK3 | MAPK3 | MAPK3 | 12736 | -0.023 | 0.12 | NO
39 | ARAF | ARAF | ARAF | 12866 | -0.026 | 0.12 | NO
40 | PIK3R2 | PIK3R2 | PIK3R2 | 12876 | -0.026 | 0.12 | NO
41 | TCF7L1 | TCF7L1 | TCF7L1 | 13041 | -0.028 | 0.12 | NO
42 | HRAS | HRAS | HRAS | 14457 | -0.061 | 0.044 | NO
43 | BAD | BAD | BAD | 14488 | -0.062 | 0.053 | NO
44 | PIK3CB | PIK3CB | PIK3CB | 14720 | -0.069 | 0.052 | NO
45 | AKT1 | AKT1 | AKT1 | 14735 | -0.07 | 0.063 | NO
46 | PIK3R5 | PIK3R5 | PIK3R5 | 14762 | -0.07 | 0.074 | NO
47 | GRB2 | GRB2 | GRB2 | 14763 | -0.07 | 0.086 | NO
48 | MAP2K1 | MAP2K1 | MAP2K1 | 14788 | -0.071 | 0.097 | NO
49 | CASP9 | CASP9 | CASP9 | 14790 | -0.072 | 0.11 | NO
50 | ILK | ILK | ILK | 14911 | -0.075 | 0.12 | NO
51 | CTNNA1 | CTNNA1 | CTNNA1 | 15811 | -0.12 | 0.084 | 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 MTOR SIGNALING PATHWAY.

Figure S4. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG MTOR 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 ADHERENS JUNCTION

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 | MGAT5B | MGAT5B | MGAT5B | 379 | 0.48 | 0.096 | YES
2 | TUSC3 | TUSC3 | TUSC3 | 635 | 0.42 | 0.18 | YES
3 | MAN1A1 | MAN1A1 | MAN1A1 | 683 | 0.41 | 0.28 | YES
4 | MGAT3 | MGAT3 | MGAT3 | 830 | 0.39 | 0.37 | YES
5 | MAN1C1 | MAN1C1 | MAN1C1 | 2381 | 0.23 | 0.34 | YES
6 | ALG11 | ALG11 | ALG11 | 2649 | 0.22 | 0.38 | YES
7 | MGAT4A | MGAT4A | MGAT4A | 2656 | 0.22 | 0.43 | YES
8 | FUT8 | FUT8 | FUT8 | 4002 | 0.14 | 0.39 | YES
9 | ALG10B | ALG10B | ALG10B | 4364 | 0.13 | 0.4 | YES
10 | MGAT5 | MGAT5 | MGAT5 | 4738 | 0.11 | 0.4 | YES
11 | ALG10 | ALG10 | ALG10 | 4828 | 0.11 | 0.43 | YES
12 | STT3B | STT3B | STT3B | 4859 | 0.11 | 0.45 | YES
13 | ST6GAL1 | ST6GAL1 | ST6GAL1 | 4885 | 0.11 | 0.48 | YES
14 | ALG14 | ALG14 | ALG14 | 5754 | 0.082 | 0.45 | NO
15 | ALG9 | ALG9 | ALG9 | 5935 | 0.078 | 0.46 | NO
16 | MAN1A2 | MAN1A2 | MAN1A2 | 6416 | 0.067 | 0.44 | NO
17 | ALG13 | ALG13 | ALG13 | 7480 | 0.048 | 0.4 | NO
18 | MAN2A2 | MAN2A2 | MAN2A2 | 8725 | 0.031 | 0.33 | NO
19 | B4GALT3 | B4GALT3 | B4GALT3 | 8994 | 0.027 | 0.32 | NO
20 | GANAB | GANAB | GANAB | 9154 | 0.025 | 0.32 | NO
21 | ALG12 | ALG12 | ALG12 | 9264 | 0.024 | 0.32 | NO
22 | STT3A | STT3A | STT3A | 9421 | 0.022 | 0.31 | NO
23 | ALG6 | ALG6 | ALG6 | 9753 | 0.018 | 0.3 | NO
24 | MAN1B1 | MAN1B1 | MAN1B1 | 10415 | 0.0093 | 0.26 | NO
25 | DOLPP1 | DOLPP1 | DOLPP1 | 10894 | 0.0034 | 0.24 | NO
26 | ALG3 | ALG3 | ALG3 | 11016 | 0.0019 | 0.23 | NO
27 | ALG2 | ALG2 | ALG2 | 11114 | 0.00064 | 0.22 | NO
28 | B4GALT2 | B4GALT2 | B4GALT2 | 11144 | 0.00024 | 0.22 | NO
29 | DPAGT1 | DPAGT1 | DPAGT1 | 11443 | -0.0038 | 0.21 | NO
30 | DPM1 | DPM1 | DPM1 | 11584 | -0.0057 | 0.2 | NO
31 | RPN1 | RPN1 | RPN1 | 11601 | -0.006 | 0.2 | NO
32 | DDOST | DDOST | DDOST | 11611 | -0.0062 | 0.2 | NO
33 | RPN2 | RPN2 | RPN2 | 11711 | -0.0077 | 0.2 | NO
34 | ALG5 | ALG5 | ALG5 | 11834 | -0.0095 | 0.19 | NO
35 | RFT1 | RFT1 | RFT1 | 11950 | -0.011 | 0.19 | NO
36 | DPM2 | DPM2 | DPM2 | 12120 | -0.014 | 0.18 | NO
37 | DPM3 | DPM3 | DPM3 | 12196 | -0.015 | 0.18 | NO
38 | MAN2A1 | MAN2A1 | MAN2A1 | 12276 | -0.016 | 0.18 | NO
39 | ALG8 | ALG8 | ALG8 | 13317 | -0.033 | 0.13 | NO
40 | MOGS | MOGS | MOGS | 13384 | -0.035 | 0.13 | NO
41 | MGAT2 | MGAT2 | MGAT2 | 13674 | -0.041 | 0.13 | NO
42 | ALG1 | ALG1 | ALG1 | 13998 | -0.048 | 0.12 | NO
43 | DAD1 | DAD1 | DAD1 | 14564 | -0.064 | 0.1 | NO
44 | B4GALT1 | B4GALT1 | B4GALT1 | 14731 | -0.069 | 0.11 | NO
45 | MGAT1 | MGAT1 | MGAT1 | 14769 | -0.071 | 0.13 | NO
46 | MGAT4B | MGAT4B | MGAT4B | 14806 | -0.072 | 0.14 | 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 ADHERENS JUNCTION.

Figure S6. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG ADHERENS JUNCTION, 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 RENAL CELL CARCINOMA

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 | EFNA1 | EFNA1 | EFNA1 | 97 | 0.58 | 0.076 | YES
2 | CDH1 | CDH1 | CDH1 | 140 | 0.56 | 0.15 | YES
3 | EGFR | EGFR | EGFR | 177 | 0.54 | 0.22 | YES
4 | EGF | EGF | EGF | 253 | 0.51 | 0.29 | YES
5 | NCKAP1 | NCKAP1 | NCKAP1 | 279 | 0.5 | 0.36 | YES
6 | IGF1 | IGF1 | IGF1 | 303 | 0.49 | 0.43 | YES
7 | MET | MET | MET | 676 | 0.41 | 0.46 | YES
8 | MGAT3 | MGAT3 | MGAT3 | 830 | 0.39 | 0.51 | YES
9 | EPHA2 | EPHA2 | EPHA2 | 846 | 0.38 | 0.56 | YES
10 | IGF1R | IGF1R | IGF1R | 1338 | 0.32 | 0.58 | YES
11 | MLLT4 | MLLT4 | MLLT4 | 1552 | 0.3 | 0.61 | YES
12 | ENAH | ENAH | ENAH | 1569 | 0.3 | 0.65 | YES
13 | MYO6 | MYO6 | MYO6 | 1895 | 0.27 | 0.67 | YES
14 | HGF | HGF | HGF | 1998 | 0.26 | 0.7 | YES
15 | CYFIP2 | CYFIP2 | CYFIP2 | 3423 | 0.17 | 0.64 | NO
16 | LIMA1 | LIMA1 | LIMA1 | 4705 | 0.11 | 0.58 | NO
17 | NCK1 | NCK1 | NCK1 | 5874 | 0.079 | 0.52 | NO
18 | PVRL2 | PVRL2 | PVRL2 | 5898 | 0.078 | 0.53 | NO
19 | VCL | VCL | VCL | 7723 | 0.044 | 0.43 | NO
20 | KIFC3 | KIFC3 | KIFC3 | 9476 | 0.021 | 0.33 | NO
21 | GIT1 | GIT1 | GIT1 | 9582 | 0.02 | 0.33 | NO
22 | ABI1 | ABI1 | ABI1 | 10350 | 0.01 | 0.29 | NO
23 | ROCK1 | ROCK1 | ROCK1 | 10445 | 0.0089 | 0.28 | NO
24 | CTNND1 | CTNND1 | CTNND1 | 11596 | -0.0059 | 0.22 | NO
25 | DIAPH1 | DIAPH1 | DIAPH1 | 11675 | -0.0072 | 0.21 | NO
26 | EXOC4 | EXOC4 | EXOC4 | 12044 | -0.013 | 0.19 | NO
27 | ACTN1 | ACTN1 | ACTN1 | 12073 | -0.013 | 0.19 | NO
28 | CTNNB1 | CTNNB1 | CTNNB1 | 12367 | -0.018 | 0.18 | NO
29 | EXOC3 | EXOC3 | EXOC3 | 12836 | -0.025 | 0.16 | NO
30 | PIP5K1C | PIP5K1C | PIP5K1C | 13328 | -0.034 | 0.13 | NO
31 | AQP3 | AQP3 | AQP3 | 13411 | -0.036 | 0.13 | NO
32 | STX4 | STX4 | STX4 | 13984 | -0.048 | 0.1 | NO
33 | RHOA | RHOA | RHOA | 14076 | -0.05 | 0.11 | NO
34 | ARF6 | ARF6 | ARF6 | 14406 | -0.06 | 0.096 | NO
35 | LPP | LPP | LPP | 14440 | -0.06 | 0.1 | NO
36 | VASP | VASP | VASP | 14643 | -0.066 | 0.1 | NO
37 | ZYX | ZYX | ZYX | 15455 | -0.097 | 0.066 | NO
38 | CTNNA1 | CTNNA1 | CTNNA1 | 15811 | -0.12 | 0.062 | NO
39 | PLEKHA7 | PLEKHA7 | PLEKHA7 | 16259 | -0.16 | 0.058 | 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 RENAL CELL CARCINOMA.

Figure S8. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG RENAL CELL CARCINOMA, 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 PANCREATIC CANCER

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 | FLT4 | FLT4 | FLT4 | 114 | 0.58 | 0.16 | YES
2 | KDR | KDR | KDR | 437 | 0.46 | 0.28 | YES
3 | PTK2 | PTK2 | PTK2 | 483 | 0.45 | 0.41 | YES
4 | FLT1 | FLT1 | FLT1 | 624 | 0.42 | 0.53 | YES
5 | PLCG1 | PLCG1 | PLCG1 | 686 | 0.41 | 0.65 | YES
6 | VEGFA | VEGFA | VEGFA | 1915 | 0.27 | 0.66 | YES
7 | NOS3 | NOS3 | NOS3 | 3357 | 0.17 | 0.62 | NO
8 | PIK3CA | PIK3CA | PIK3CA | 5255 | 0.095 | 0.54 | NO
9 | HIF1A | HIF1A | HIF1A | 6016 | 0.076 | 0.52 | NO
10 | PIK3R1 | PIK3R1 | PIK3R1 | 6522 | 0.065 | 0.51 | NO
11 | PRKCB | PRKCB | PRKCB | 7241 | 0.052 | 0.48 | NO
12 | EIF1AX | EIF1AX | EIF1AX | 8181 | 0.038 | 0.44 | NO
13 | EIF2S1 | EIF2S1 | EIF2S1 | 8669 | 0.032 | 0.42 | NO
14 | ELAVL1 | ELAVL1 | ELAVL1 | 9051 | 0.027 | 0.41 | NO
15 | PXN | PXN | PXN | 9697 | 0.018 | 0.38 | NO
16 | PIK3CG | PIK3CG | PIK3CG | 9829 | 0.017 | 0.37 | NO
17 | EIF2B5 | EIF2B5 | EIF2B5 | 10791 | 0.0047 | 0.32 | NO
18 | SHC1 | SHC1 | SHC1 | 10856 | 0.0039 | 0.32 | NO
19 | EIF2B3 | EIF2B3 | EIF2B3 | 11005 | 0.0021 | 0.31 | NO
20 | VHL | VHL | VHL | 11033 | 0.0017 | 0.31 | NO
21 | EIF2S3 | EIF2S3 | EIF2S3 | 11203 | -0.00066 | 0.3 | NO
22 | PRKCA | PRKCA | PRKCA | 11637 | -0.0066 | 0.27 | NO
23 | EIF2S2 | EIF2S2 | EIF2S2 | 11692 | -0.0074 | 0.27 | NO
24 | EIF2B4 | EIF2B4 | EIF2B4 | 11756 | -0.0082 | 0.27 | NO
25 | EIF2B1 | EIF2B1 | EIF2B1 | 12294 | -0.016 | 0.25 | NO
26 | EIF2B2 | EIF2B2 | EIF2B2 | 12737 | -0.023 | 0.23 | NO
27 | ARNT | ARNT | ARNT | 12811 | -0.024 | 0.23 | NO
28 | EIF1 | EIF1 | EIF1 | 13335 | -0.034 | 0.21 | NO
29 | HRAS | HRAS | HRAS | 14457 | -0.061 | 0.16 | 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 PANCREATIC CANCER.

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

genes ES table in pathway: KEGG ENDOMETRIAL CANCER

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 | CCND1 | CCND1 | CCND1 | 63 | 0.61 | 0.056 | YES
2 | EGFR | EGFR | EGFR | 177 | 0.54 | 0.1 | YES
3 | EGF | EGF | EGF | 253 | 0.51 | 0.15 | YES
4 | IGF1 | IGF1 | IGF1 | 303 | 0.49 | 0.19 | YES
5 | FGFR2 | FGFR2 | FGFR2 | 509 | 0.44 | 0.22 | YES
6 | LEF1 | LEF1 | LEF1 | 642 | 0.42 | 0.26 | YES
7 | PDGFRA | PDGFRA | PDGFRA | 718 | 0.4 | 0.29 | YES
8 | FGFR1 | FGFR1 | FGFR1 | 776 | 0.4 | 0.32 | YES
9 | IGF1R | IGF1R | IGF1R | 1338 | 0.32 | 0.32 | YES
10 | PDGFB | PDGFB | PDGFB | 1444 | 0.31 | 0.35 | YES
11 | PDGFRB | PDGFRB | PDGFRB | 1498 | 0.31 | 0.37 | YES
12 | FOXO1 | FOXO1 | FOXO1 | 1581 | 0.3 | 0.4 | YES
13 | TCF7 | TCF7 | TCF7 | 1589 | 0.3 | 0.43 | YES
14 | CREB3L3 | CREB3L3 | CREB3L3 | 1888 | 0.27 | 0.44 | YES
15 | AR | AR | AR | 2130 | 0.25 | 0.45 | YES
16 | AKT3 | AKT3 | AKT3 | 2347 | 0.24 | 0.46 | YES
17 | PIK3R3 | PIK3R3 | PIK3R3 | 2395 | 0.23 | 0.48 | YES
18 | ERBB2 | ERBB2 | ERBB2 | 2526 | 0.22 | 0.49 | YES
19 | PDGFC | PDGFC | PDGFC | 2757 | 0.21 | 0.5 | YES
20 | PDGFA | PDGFA | PDGFA | 3008 | 0.19 | 0.5 | YES
21 | CREB3L1 | CREB3L1 | CREB3L1 | 3380 | 0.17 | 0.5 | NO
22 | BCL2 | BCL2 | BCL2 | 3993 | 0.14 | 0.47 | NO
23 | CREB3L4 | CREB3L4 | CREB3L4 | 4227 | 0.13 | 0.47 | NO
24 | PIK3CA | PIK3CA | PIK3CA | 5255 | 0.095 | 0.42 | NO
25 | E2F2 | E2F2 | E2F2 | 5441 | 0.09 | 0.42 | NO
26 | SRD5A2 | SRD5A2 | SRD5A2 | 5723 | 0.083 | 0.41 | NO
27 | SOS1 | SOS1 | SOS1 | 5782 | 0.081 | 0.42 | NO
28 | BRAF | BRAF | BRAF | 6025 | 0.075 | 0.41 | NO
29 | TCF7L2 | TCF7L2 | TCF7L2 | 6035 | 0.075 | 0.42 | NO
30 | CCNE2 | CCNE2 | CCNE2 | 6124 | 0.073 | 0.42 | NO
31 | CCNE1 | CCNE1 | CCNE1 | 6133 | 0.073 | 0.42 | NO
32 | PIK3R1 | PIK3R1 | PIK3R1 | 6522 | 0.065 | 0.41 | NO
33 | RB1 | RB1 | RB1 | 7562 | 0.047 | 0.35 | NO
34 | CREB1 | CREB1 | CREB1 | 7684 | 0.045 | 0.35 | NO
35 | E2F1 | E2F1 | E2F1 | 8092 | 0.039 | 0.33 | NO
36 | CREBBP | CREBBP | CREBBP | 8220 | 0.037 | 0.33 | NO
37 | NRAS | NRAS | NRAS | 8475 | 0.034 | 0.32 | NO
38 | CREB3L2 | CREB3L2 | CREB3L2 | 8600 | 0.032 | 0.31 | NO
39 | PTEN | PTEN | PTEN | 8964 | 0.028 | 0.29 | NO
40 | CDK2 | CDK2 | CDK2 | 9134 | 0.025 | 0.28 | NO
41 | HSP90AB1 | HSP90AB1 | HSP90AB1 | 9180 | 0.025 | 0.28 | NO
42 | MTOR | MTOR | MTOR | 9420 | 0.022 | 0.27 | NO
43 | EP300 | EP300 | EP300 | 9530 | 0.02 | 0.27 | NO
44 | E2F3 | E2F3 | E2F3 | 9827 | 0.017 | 0.25 | NO
45 | PIK3CG | PIK3CG | PIK3CG | 9829 | 0.017 | 0.25 | NO
46 | IKBKB | IKBKB | IKBKB | 9869 | 0.016 | 0.25 | NO
47 | GSK3B | GSK3B | GSK3B | 10065 | 0.014 | 0.24 | NO
48 | ATF4 | ATF4 | ATF4 | 10071 | 0.014 | 0.24 | NO
49 | HSP90B1 | HSP90B1 | HSP90B1 | 10267 | 0.011 | 0.24 | NO
50 | MAPK1 | MAPK1 | MAPK1 | 10305 | 0.011 | 0.23 | NO
51 | INSRR | INSRR | INSRR | 10609 | 0.007 | 0.22 | NO
52 | CDKN1B | CDKN1B | CDKN1B | 10668 | 0.0064 | 0.21 | NO
53 | MAP2K2 | MAP2K2 | MAP2K2 | 10714 | 0.0058 | 0.21 | NO
54 | HSP90AA1 | HSP90AA1 | HSP90AA1 | 10748 | 0.0052 | 0.21 | NO
55 | AKT2 | AKT2 | AKT2 | 11099 | 0.0008 | 0.19 | NO
56 | NKX3-1 | NKX3-1 | NKX3-1 | 11234 | -0.001 | 0.18 | NO
57 | PIK3CD | PIK3CD | PIK3CD | 11292 | -0.0018 | 0.18 | NO
58 | RAF1 | RAF1 | RAF1 | 11328 | -0.0022 | 0.18 | NO
59 | PDPK1 | PDPK1 | PDPK1 | 11511 | -0.0048 | 0.17 | NO
60 | KRAS | KRAS | KRAS | 11523 | -0.0049 | 0.17 | NO
61 | CHUK | CHUK | CHUK | 11693 | -0.0075 | 0.16 | NO
62 | TP53 | TP53 | TP53 | 11867 | -0.0098 | 0.15 | NO
63 | RELA | RELA | RELA | 12337 | -0.017 | 0.12 | NO
64 | SOS2 | SOS2 | SOS2 | 12356 | -0.017 | 0.12 | NO
65 | CTNNB1 | CTNNB1 | CTNNB1 | 12367 | -0.018 | 0.12 | NO
66 | TGFA | TGFA | TGFA | 12532 | -0.02 | 0.12 | NO
67 | MAPK3 | MAPK3 | MAPK3 | 12736 | -0.023 | 0.11 | NO
68 | ARAF | ARAF | ARAF | 12866 | -0.026 | 0.1 | NO
69 | PIK3R2 | PIK3R2 | PIK3R2 | 12876 | -0.026 | 0.1 | NO
70 | TCF7L1 | TCF7L1 | TCF7L1 | 13041 | -0.028 | 0.098 | NO
71 | NFKB1 | NFKB1 | NFKB1 | 13189 | -0.031 | 0.092 | NO
72 | CREB3 | CREB3 | CREB3 | 13260 | -0.033 | 0.091 | NO
73 | GSTP1 | GSTP1 | GSTP1 | 13655 | -0.041 | 0.072 | NO
74 | IKBKG | IKBKG | IKBKG | 13709 | -0.042 | 0.073 | NO
75 | NFKBIA | NFKBIA | NFKBIA | 13967 | -0.048 | 0.063 | NO
76 | HRAS | HRAS | HRAS | 14457 | -0.061 | 0.04 | NO
77 | BAD | BAD | BAD | 14488 | -0.062 | 0.044 | NO
78 | PIK3CB | PIK3CB | PIK3CB | 14720 | -0.069 | 0.038 | NO
79 | AKT1 | AKT1 | AKT1 | 14735 | -0.07 | 0.044 | NO
80 | PIK3R5 | PIK3R5 | PIK3R5 | 14762 | -0.07 | 0.049 | NO
81 | GRB2 | GRB2 | GRB2 | 14763 | -0.07 | 0.056 | NO
82 | MAP2K1 | MAP2K1 | MAP2K1 | 14788 | -0.071 | 0.061 | NO
83 | CASP9 | CASP9 | CASP9 | 14790 | -0.072 | 0.068 | NO
84 | MDM2 | MDM2 | MDM2 | 15207 | -0.086 | 0.052 | NO
85 | PDGFD | PDGFD | PDGFD | 16598 | -0.2 | -0.0091 | NO
86 | CREB5 | CREB5 | CREB5 | 16768 | -0.24 | 0.004 | NO
87 | CDKN1A | CDKN1A | CDKN1A | 16840 | -0.25 | 0.024 | 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 ENDOMETRIAL CANCER.

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

genes ES table in pathway: KEGG PROSTATE CANCER

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 | HEY2 | HEY2 | HEY2 | 99 | 0.58 | 0.14 | YES
2 | MAMLD1 | MAMLD1 | MAMLD1 | 278 | 0.5 | 0.24 | YES
3 | HES1 | HES1 | HES1 | 617 | 0.42 | 0.33 | YES
4 | HES5 | HES5 | HES5 | 1048 | 0.36 | 0.39 | YES
5 | TLE2 | TLE2 | TLE2 | 1503 | 0.31 | 0.44 | YES
6 | MAML2 | MAML2 | MAML2 | 1689 | 0.29 | 0.5 | YES
7 | HEY1 | HEY1 | HEY1 | 2862 | 0.2 | 0.48 | NO
8 | CDK8 | CDK8 | CDK8 | 5176 | 0.098 | 0.36 | NO
9 | MYC | MYC | MYC | 5427 | 0.09 | 0.37 | NO
10 | HDAC7 | HDAC7 | HDAC7 | 5712 | 0.083 | 0.38 | NO
11 | HIF1A | HIF1A | HIF1A | 6016 | 0.076 | 0.38 | NO
12 | CUL1 | CUL1 | CUL1 | 6296 | 0.07 | 0.38 | NO
13 | FBXW7 | FBXW7 | FBXW7 | 6399 | 0.067 | 0.39 | NO
14 | TBL1XR1 | TBL1XR1 | TBL1XR1 | 6863 | 0.058 | 0.37 | NO
15 | CCNC | CCNC | CCNC | 7382 | 0.049 | 0.36 | NO
16 | HDAC2 | HDAC2 | HDAC2 | 7479 | 0.048 | 0.36 | NO
17 | CREBBP | CREBBP | CREBBP | 8220 | 0.037 | 0.33 | NO
18 | HDAC6 | HDAC6 | HDAC6 | 8295 | 0.036 | 0.33 | NO
19 | HDAC1 | HDAC1 | HDAC1 | 8625 | 0.032 | 0.32 | NO
20 | KAT2B | KAT2B | KAT2B | 9079 | 0.026 | 0.3 | NO
21 | HDAC8 | HDAC8 | HDAC8 | 9460 | 0.021 | 0.28 | NO
22 | EP300 | EP300 | EP300 | 9530 | 0.02 | 0.28 | NO
23 | RPS27A | RPS27A | RPS27A | 9596 | 0.019 | 0.29 | NO
24 | TLE3 | TLE3 | TLE3 | 10001 | 0.015 | 0.27 | NO
25 | MAML3 | MAML3 | MAML3 | 10014 | 0.014 | 0.27 | NO
26 | KAT2A | KAT2A | KAT2A | 10048 | 0.014 | 0.27 | NO
27 | RBX1 | RBX1 | RBX1 | 10054 | 0.014 | 0.27 | NO
28 | HEYL | HEYL | HEYL | 10070 | 0.014 | 0.28 | NO
29 | HDAC9 | HDAC9 | HDAC9 | 10240 | 0.012 | 0.27 | NO
30 | MAML1 | MAML1 | MAML1 | 10694 | 0.006 | 0.24 | NO
31 | SNW1 | SNW1 | SNW1 | 11150 | 0.0002 | 0.22 | NO
32 | NCOR1 | NCOR1 | NCOR1 | 11391 | -0.0031 | 0.2 | NO
33 | HDAC5 | HDAC5 | HDAC5 | 11489 | -0.0044 | 0.2 | NO
34 | NCOR2 | NCOR2 | NCOR2 | 11644 | -0.0067 | 0.19 | NO
35 | UBA52 | UBA52 | UBA52 | 11762 | -0.0084 | 0.19 | NO
36 | RBPJ | RBPJ | RBPJ | 12492 | -0.02 | 0.15 | NO
37 | SKP1 | SKP1 | SKP1 | 13004 | -0.028 | 0.13 | NO
38 | HDAC3 | HDAC3 | HDAC3 | 13428 | -0.036 | 0.11 | NO
39 | TLE4 | TLE4 | TLE4 | 13532 | -0.038 | 0.11 | NO
40 | HDAC10 | HDAC10 | HDAC10 | 14187 | -0.053 | 0.089 | NO
41 | TBL1X | TBL1X | TBL1X | 14360 | -0.058 | 0.093 | NO
42 | HDAC11 | HDAC11 | HDAC11 | 14921 | -0.075 | 0.078 | NO
43 | HDAC4 | HDAC4 | HDAC4 | 15729 | -0.11 | 0.059 | NO
44 | TLE1 | TLE1 | TLE1 | 15915 | -0.13 | 0.078 | 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 PROSTATE CANCER.

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

genes ES table in pathway: KEGG THYROID CANCER

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 | SORBS1 | SORBS1 | SORBS1 | 50 | 0.63 | 0.058 | YES
2 | CDH1 | CDH1 | CDH1 | 140 | 0.56 | 0.11 | YES
3 | EGFR | EGFR | EGFR | 177 | 0.54 | 0.16 | YES
4 | SNAI2 | SNAI2 | SNAI2 | 409 | 0.46 | 0.19 | YES
5 | TJP1 | TJP1 | TJP1 | 475 | 0.45 | 0.23 | YES
6 | LEF1 | LEF1 | LEF1 | 642 | 0.42 | 0.26 | YES
7 | MET | MET | MET | 676 | 0.41 | 0.3 | YES
8 | FGFR1 | FGFR1 | FGFR1 | 776 | 0.4 | 0.33 | YES
9 | WASF1 | WASF1 | WASF1 | 894 | 0.38 | 0.36 | YES
10 | PTPRB | PTPRB | PTPRB | 941 | 0.37 | 0.39 | YES
11 | WASF3 | WASF3 | WASF3 | 980 | 0.36 | 0.42 | YES
12 | PVRL3 | PVRL3 | PVRL3 | 1224 | 0.34 | 0.44 | YES
13 | PTPRM | PTPRM | PTPRM | 1299 | 0.33 | 0.47 | YES
14 | IGF1R | IGF1R | IGF1R | 1338 | 0.32 | 0.5 | YES
15 | PARD3 | PARD3 | PARD3 | 1378 | 0.32 | 0.53 | YES
16 | MLLT4 | MLLT4 | MLLT4 | 1552 | 0.3 | 0.55 | YES
17 | TCF7 | TCF7 | TCF7 | 1589 | 0.3 | 0.57 | YES
18 | RAC3 | RAC3 | RAC3 | 2504 | 0.22 | 0.54 | NO
19 | ERBB2 | ERBB2 | ERBB2 | 2526 | 0.22 | 0.56 | NO
20 | LMO7 | LMO7 | LMO7 | 3470 | 0.17 | 0.52 | NO
21 | SNAI1 | SNAI1 | SNAI1 | 3820 | 0.15 | 0.52 | NO
22 | CTNNA3 | CTNNA3 | CTNNA3 | 3921 | 0.14 | 0.52 | NO
23 | YES1 | YES1 | YES1 | 4089 | 0.14 | 0.53 | NO
24 | PVRL2 | PVRL2 | PVRL2 | 5898 | 0.078 | 0.43 | NO
25 | TCF7L2 | TCF7L2 | TCF7L2 | 6035 | 0.075 | 0.43 | NO
26 | CSNK2A1 | CSNK2A1 | CSNK2A1 | 6943 | 0.056 | 0.38 | NO
27 | CSNK2A2 | CSNK2A2 | CSNK2A2 | 7040 | 0.055 | 0.38 | NO
28 | ACP1 | ACP1 | ACP1 | 7085 | 0.054 | 0.38 | NO
29 | MAP3K7 | MAP3K7 | MAP3K7 | 7290 | 0.051 | 0.38 | NO
30 | SMAD4 | SMAD4 | SMAD4 | 7333 | 0.05 | 0.38 | NO
31 | TGFBR1 | TGFBR1 | TGFBR1 | 7542 | 0.047 | 0.37 | NO
32 | SMAD3 | SMAD3 | SMAD3 | 7609 | 0.046 | 0.37 | NO
33 | PVRL1 | PVRL1 | PVRL1 | 7704 | 0.045 | 0.37 | NO
34 | VCL | VCL | VCL | 7723 | 0.044 | 0.38 | NO
35 | CREBBP | CREBBP | CREBBP | 8220 | 0.037 | 0.35 | NO
36 | SMAD2 | SMAD2 | SMAD2 | 8772 | 0.03 | 0.32 | NO
37 | WASL | WASL | WASL | 8782 | 0.03 | 0.32 | NO
38 | FYN | FYN | FYN | 8850 | 0.029 | 0.32 | NO
39 | NLK | NLK | NLK | 8852 | 0.029 | 0.32 | NO
40 | WASF2 | WASF2 | WASF2 | 9261 | 0.024 | 0.3 | NO
41 | ACTN3 | ACTN3 | ACTN3 | 9390 | 0.022 | 0.3 | NO
42 | FARP2 | FARP2 | FARP2 | 9413 | 0.022 | 0.3 | NO
43 | TGFBR2 | TGFBR2 | TGFBR2 | 9510 | 0.02 | 0.3 | NO
44 | PTPRF | PTPRF | PTPRF | 9520 | 0.02 | 0.3 | NO
45 | EP300 | EP300 | EP300 | 9530 | 0.02 | 0.3 | NO
46 | BAIAP2 | BAIAP2 | BAIAP2 | 9676 | 0.019 | 0.29 | NO
47 | MAPK1 | MAPK1 | MAPK1 | 10305 | 0.011 | 0.26 | NO
48 | ACTN2 | ACTN2 | ACTN2 | 11532 | -0.005 | 0.18 | NO
49 | CTNND1 | CTNND1 | CTNND1 | 11596 | -0.0059 | 0.18 | NO
50 | FER | FER | FER | 11748 | -0.0081 | 0.17 | NO
51 | ACTN1 | ACTN1 | ACTN1 | 12073 | -0.013 | 0.16 | NO
52 | CTNNB1 | CTNNB1 | CTNNB1 | 12367 | -0.018 | 0.14 | NO
53 | PTPN1 | PTPN1 | PTPN1 | 12373 | -0.018 | 0.14 | NO
54 | CSNK2B | CSNK2B | CSNK2B | 12513 | -0.02 | 0.14 | NO
55 | MAPK3 | MAPK3 | MAPK3 | 12736 | -0.023 | 0.12 | NO
56 | TCF7L1 | TCF7L1 | TCF7L1 | 13041 | -0.028 | 0.11 | NO
57 | RAC2 | RAC2 | RAC2 | 13438 | -0.036 | 0.091 | NO
58 | ACTB | ACTB | ACTB | 13587 | -0.039 | 0.086 | NO
59 | ACTG1 | ACTG1 | ACTG1 | 13649 | -0.041 | 0.086 | NO
60 | ACTN4 | ACTN4 | ACTN4 | 13712 | -0.042 | 0.087 | NO
61 | CDC42 | CDC42 | CDC42 | 14018 | -0.049 | 0.074 | NO
62 | INSR | INSR | INSR | 14031 | -0.049 | 0.078 | NO
63 | RHOA | RHOA | RHOA | 14076 | -0.05 | 0.08 | NO
64 | IQGAP1 | IQGAP1 | IQGAP1 | 14182 | -0.053 | 0.079 | NO
65 | SSX2IP | SSX2IP | SSX2IP | 14210 | -0.054 | 0.082 | NO
66 | RAC1 | RAC1 | RAC1 | 14572 | -0.064 | 0.068 | NO
67 | SRC | SRC | SRC | 15443 | -0.096 | 0.026 | NO
68 | WAS | WAS | WAS | 15453 | -0.097 | 0.035 | NO
69 | PTPRJ | PTPRJ | PTPRJ | 15756 | -0.12 | 0.029 | NO
70 | CTNNA1 | CTNNA1 | CTNNA1 | 15811 | -0.12 | 0.037 | NO
71 | PTPN6 | PTPN6 | PTPN6 | 16139 | -0.14 | 0.032 | NO
72 | PVRL4 | PVRL4 | PVRL4 | 17081 | -0.35 | 0.01 | 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 THYROID CANCER.

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

genes ES table in pathway: KEGG MELANOMA

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 | CCND1 | CCND1 | CCND1 | 63 | 0.61 | 0.12 | YES
2 | EGFR | EGFR | EGFR | 177 | 0.54 | 0.22 | YES
3 | EGF | EGF | EGF | 253 | 0.51 | 0.32 | YES
4 | PLCG1 | PLCG1 | PLCG1 | 686 | 0.41 | 0.37 | YES
5 | FHIT | FHIT | FHIT | 2256 | 0.24 | 0.33 | YES
6 | AKT3 | AKT3 | AKT3 | 2347 | 0.24 | 0.37 | YES
7 | PIK3R3 | PIK3R3 | PIK3R3 | 2395 | 0.23 | 0.42 | YES
8 | ERBB2 | ERBB2 | ERBB2 | 2526 | 0.22 | 0.45 | YES
9 | CDK6 | CDK6 | CDK6 | 3866 | 0.15 | 0.4 | NO
10 | PIK3CA | PIK3CA | PIK3CA | 5255 | 0.095 | 0.34 | NO
11 | E2F2 | E2F2 | E2F2 | 5441 | 0.09 | 0.35 | NO
12 | FOXO3 | FOXO3 | FOXO3 | 5514 | 0.088 | 0.36 | NO
13 | SOS1 | SOS1 | SOS1 | 5782 | 0.081 | 0.36 | NO
14 | BRAF | BRAF | BRAF | 6025 | 0.075 | 0.36 | NO
15 | PIK3R1 | PIK3R1 | PIK3R1 | 6522 | 0.065 | 0.35 | NO
16 | PRKCB | PRKCB | PRKCB | 7241 | 0.052 | 0.32 | NO
17 | RARB | RARB | RARB | 7281 | 0.051 | 0.32 | NO
18 | RB1 | RB1 | RB1 | 7562 | 0.047 | 0.32 | NO
19 | CDK4 | CDK4 | CDK4 | 7826 | 0.043 | 0.31 | NO
20 | E2F1 | E2F1 | E2F1 | 8092 | 0.039 | 0.3 | NO
21 | NRAS | NRAS | NRAS | 8475 | 0.034 | 0.29 | NO
22 | PLCG2 | PLCG2 | PLCG2 | 8675 | 0.032 | 0.28 | NO
23 | E2F3 | E2F3 | E2F3 | 9827 | 0.017 | 0.22 | NO
24 | PIK3CG | PIK3CG | PIK3CG | 9829 | 0.017 | 0.22 | NO
25 | MAPK1 | MAPK1 | MAPK1 | 10305 | 0.011 | 0.2 | NO
26 | RXRB | RXRB | RXRB | 10507 | 0.0082 | 0.19 | NO
27 | MAP2K2 | MAP2K2 | MAP2K2 | 10714 | 0.0058 | 0.18 | NO
28 | RASSF1 | RASSF1 | RASSF1 | 11085 | 0.001 | 0.15 | NO
29 | AKT2 | AKT2 | AKT2 | 11099 | 0.0008 | 0.15 | NO
30 | PIK3CD | PIK3CD | PIK3CD | 11292 | -0.0018 | 0.14 | NO
31 | RAF1 | RAF1 | RAF1 | 11328 | -0.0022 | 0.14 | NO
32 | PDPK1 | PDPK1 | PDPK1 | 11511 | -0.0048 | 0.13 | NO
33 | KRAS | KRAS | KRAS | 11523 | -0.0049 | 0.13 | NO
34 | PRKCA | PRKCA | PRKCA | 11637 | -0.0066 | 0.13 | NO
35 | TP53 | TP53 | TP53 | 11867 | -0.0098 | 0.12 | NO
36 | PRKCG | PRKCG | PRKCG | 12322 | -0.017 | 0.092 | NO
37 | STK4 | STK4 | STK4 | 12335 | -0.017 | 0.095 | NO
38 | SOS2 | SOS2 | SOS2 | 12356 | -0.017 | 0.097 | NO
39 | TGFA | TGFA | TGFA | 12532 | -0.02 | 0.091 | NO
40 | MAPK3 | MAPK3 | MAPK3 | 12736 | -0.023 | 0.084 | NO
41 | ARAF | ARAF | ARAF | 12866 | -0.026 | 0.082 | NO
42 | PIK3R2 | PIK3R2 | PIK3R2 | 12876 | -0.026 | 0.086 | NO
43 | RASSF5 | RASSF5 | RASSF5 | 13131 | -0.03 | 0.078 | NO
44 | HRAS | HRAS | HRAS | 14457 | -0.061 | 0.013 | NO
45 | BAD | BAD | BAD | 14488 | -0.062 | 0.023 | NO
46 | PIK3CB | PIK3CB | PIK3CB | 14720 | -0.069 | 0.024 | NO
47 | AKT1 | AKT1 | AKT1 | 14735 | -0.07 | 0.037 | NO
48 | PIK3R5 | PIK3R5 | PIK3R5 | 14762 | -0.07 | 0.049 | NO
49 | GRB2 | GRB2 | GRB2 | 14763 | -0.07 | 0.063 | NO
50 | MAP2K1 | MAP2K1 | MAP2K1 | 14788 | -0.071 | 0.076 | NO
51 | CASP9 | CASP9 | CASP9 | 14790 | -0.072 | 0.09 | NO
52 | CDKN2A | CDKN2A | CDKN2A | 15760 | -0.12 | 0.057 | NO
53 | RXRA | RXRA | RXRA | 16210 | -0.15 | 0.061 | 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 MELANOMA.

Figure S18. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG MELANOMA, 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 NON SMALL CELL LUNG CANCER

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 | CCND1 | CCND1 | CCND1 | 63 | 0.61 | 0.084 | YES
2 | EGFR | EGFR | EGFR | 177 | 0.54 | 0.16 | YES
3 | EGF | EGF | EGF | 253 | 0.51 | 0.22 | YES
4 | PGF | PGF | PGF | 920 | 0.37 | 0.24 | YES
5 | TGFB2 | TGFB2 | TGFB2 | 1632 | 0.3 | 0.24 | YES
6 | VEGFA | VEGFA | VEGFA | 1915 | 0.27 | 0.26 | YES
7 | VEGFC | VEGFC | VEGFC | 2162 | 0.25 | 0.28 | YES
8 | FIGF | FIGF | FIGF | 2170 | 0.25 | 0.32 | YES
9 | AKT3 | AKT3 | AKT3 | 2347 | 0.24 | 0.34 | YES
10 | PIK3R3 | PIK3R3 | PIK3R3 | 2395 | 0.23 | 0.37 | YES
11 | RAC3 | RAC3 | RAC3 | 2504 | 0.22 | 0.4 | YES
12 | ERBB2 | ERBB2 | ERBB2 | 2526 | 0.22 | 0.43 | YES
13 | TGFB3 | TGFB3 | TGFB3 | 3038 | 0.19 | 0.42 | NO
14 | BCL2L1 | BCL2L1 | BCL2L1 | 3673 | 0.16 | 0.41 | NO
15 | CDK6 | CDK6 | CDK6 | 3866 | 0.15 | 0.42 | NO
16 | STAT1 | STAT1 | STAT1 | 5119 | 0.099 | 0.36 | NO
17 | MAPK8 | MAPK8 | MAPK8 | 5228 | 0.096 | 0.37 | NO
18 | PIK3CA | PIK3CA | PIK3CA | 5255 | 0.095 | 0.38 | NO
19 | E2F2 | E2F2 | E2F2 | 5441 | 0.09 | 0.38 | NO
20 | JAK1 | JAK1 | JAK1 | 5494 | 0.089 | 0.39 | NO
21 | MAPK10 | MAPK10 | MAPK10 | 6004 | 0.076 | 0.37 | NO
22 | BRAF | BRAF | BRAF | 6025 | 0.075 | 0.38 | NO
23 | ARHGEF6 | ARHGEF6 | ARHGEF6 | 6032 | 0.075 | 0.39 | NO
24 | PIK3R1 | PIK3R1 | PIK3R1 | 6522 | 0.065 | 0.37 | NO
25 | SMAD4 | SMAD4 | SMAD4 | 7333 | 0.05 | 0.33 | NO
26 | TGFBR1 | TGFBR1 | TGFBR1 | 7542 | 0.047 | 0.33 | NO
27 | RB1 | RB1 | RB1 | 7562 | 0.047 | 0.33 | NO
28 | SMAD3 | SMAD3 | SMAD3 | 7609 | 0.046 | 0.34 | NO
29 | BRCA2 | BRCA2 | BRCA2 | 7761 | 0.044 | 0.34 | NO
30 | CDK4 | CDK4 | CDK4 | 7826 | 0.043 | 0.34 | NO
31 | E2F1 | E2F1 | E2F1 | 8092 | 0.039 | 0.33 | NO
32 | VEGFB | VEGFB | VEGFB | 8280 | 0.036 | 0.32 | NO
33 | RALA | RALA | RALA | 8314 | 0.036 | 0.33 | NO
34 | RALBP1 | RALBP1 | RALBP1 | 8502 | 0.034 | 0.32 | NO
35 | RALGDS | RALGDS | RALGDS | 8570 | 0.033 | 0.32 | NO
36 | SMAD2 | SMAD2 | SMAD2 | 8772 | 0.03 | 0.31 | NO
37 | TGFBR2 | TGFBR2 | TGFBR2 | 9510 | 0.02 | 0.27 | NO
38 | E2F3 | E2F3 | E2F3 | 9827 | 0.017 | 0.26 | NO
39 | PIK3CG | PIK3CG | PIK3CG | 9829 | 0.017 | 0.26 | NO
40 | STAT3 | STAT3 | STAT3 | 9858 | 0.016 | 0.26 | NO
41 | IKBKB | IKBKB | IKBKB | 9869 | 0.016 | 0.26 | NO
42 | MAPK1 | MAPK1 | MAPK1 | 10305 | 0.011 | 0.24 | NO
43 | AKT2 | AKT2 | AKT2 | 11099 | 0.0008 | 0.19 | NO
44 | PIK3CD | PIK3CD | PIK3CD | 11292 | -0.0018 | 0.18 | NO
45 | RAF1 | RAF1 | RAF1 | 11328 | -0.0022 | 0.18 | NO
46 | KRAS | KRAS | KRAS | 11523 | -0.0049 | 0.17 | NO
47 | CHUK | CHUK | CHUK | 11693 | -0.0075 | 0.16 | NO
48 | TP53 | TP53 | TP53 | 11867 | -0.0098 | 0.15 | NO
49 | RAD51 | RAD51 | RAD51 | 12001 | -0.012 | 0.14 | NO
50 | RELA | RELA | RELA | 12337 | -0.017 | 0.13 | NO
51 | TGFA | TGFA | TGFA | 12532 | -0.02 | 0.12 | NO
52 | MAPK9 | MAPK9 | MAPK9 | 12618 | -0.022 | 0.12 | NO
53 | MAPK3 | MAPK3 | MAPK3 | 12736 | -0.023 | 0.11 | NO
54 | ARAF | ARAF | ARAF | 12866 | -0.026 | 0.11 | NO
55 | PIK3R2 | PIK3R2 | PIK3R2 | 12876 | -0.026 | 0.11 | NO
56 | NFKB1 | NFKB1 | NFKB1 | 13189 | -0.031 | 0.1 | NO
57 | RAC2 | RAC2 | RAC2 | 13438 | -0.036 | 0.091 | NO
58 | IKBKG | IKBKG | IKBKG | 13709 | -0.042 | 0.081 | NO
59 | CDC42 | CDC42 | CDC42 | 14018 | -0.049 | 0.07 | NO
60 | PLD1 | PLD1 | PLD1 | 14316 | -0.057 | 0.061 | NO
61 | BAD | BAD | BAD | 14488 | -0.062 | 0.06 | NO
62 | TGFB1 | TGFB1 | TGFB1 | 14565 | -0.064 | 0.065 | NO
63 | RAC1 | RAC1 | RAC1 | 14572 | -0.064 | 0.073 | NO
64 | PIK3CB | PIK3CB | PIK3CB | 14720 | -0.069 | 0.075 | NO
65 | AKT1 | AKT1 | AKT1 | 14735 | -0.07 | 0.084 | NO
66 | PIK3R5 | PIK3R5 | PIK3R5 | 14762 | -0.07 | 0.092 | NO
67 | MAP2K1 | MAP2K1 | MAP2K1 | 14788 | -0.071 | 0.1 | NO
68 | CASP9 | CASP9 | CASP9 | 14790 | -0.072 | 0.11 | NO
69 | RALB | RALB | RALB | 15693 | -0.11 | 0.075 | NO
70 | CDKN2A | CDKN2A | CDKN2A | 15760 | -0.12 | 0.087 | 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 NON SMALL CELL LUNG CANCER.

Figure S20. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG NON SMALL CELL LUNG CANCER, 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

- up-regulated, please check the list of up-regulated genes

- down-regulated, please check the list of down-regulated genes

Expression level

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

- highly expressed genes, please check the list of high (top 30%) expressed genes

- low expressed genes, please check the list of low (bottom 30%) expressed genes

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

- significantly differently expressed genes by eBayes lm fit, please check the list of significant genes

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 LYSOSOME | 118 | genes.ES.table | 0.55 | 1.8 | 0.002 | 0.39 | 0.46 | 0.45 | 0.14 | 0.39 | 0 | 0.093
KEGG FC GAMMA R MEDIATED PHAGOCYTOSIS | 92 | genes.ES.table | 0.54 | 1.8 | 0 | 0.32 | 0.59 | 0.42 | 0.16 | 0.36 | 0.1 | 0.079
BIOCARTA HIVNEF PATHWAY | 58 | genes.ES.table | 0.42 | 1.8 | 0.0099 | 0.37 | 0.5 | 0.41 | 0.19 | 0.34 | 0 | 0.091
BIOCARTA PYK2 PATHWAY | 28 | genes.ES.table | 0.54 | 1.7 | 0.016 | 0.32 | 0.63 | 0.64 | 0.23 | 0.5 | 0.12 | 0.086
BIOCARTA TOLL PATHWAY | 37 | genes.ES.table | 0.62 | 1.8 | 0.0096 | 0.38 | 0.53 | 0.49 | 0.18 | 0.4 | 0.097 | 0.097
ST TUMOR NECROSIS FACTOR PATHWAY | 28 | genes.ES.table | 0.54 | 1.7 | 0.029 | 0.32 | 0.7 | 0.5 | 0.22 | 0.39 | 0.12 | 0.084
PID IL1PATHWAY | 34 | genes.ES.table | 0.57 | 1.8 | 0.0098 | 0.35 | 0.57 | 0.38 | 0.17 | 0.32 | 0.098 | 0.087
PID IFNGPATHWAY | 40 | genes.ES.table | 0.53 | 1.7 | 0.02 | 0.32 | 0.66 | 0.55 | 0.25 | 0.41 | 0.12 | 0.086
PID IL8CXCR2 PATHWAY | 34 | genes.ES.table | 0.6 | 1.7 | 0.01 | 0.31 | 0.67 | 0.59 | 0.2 | 0.47 | 0.12 | 0.08
PID MAPKTRKPATHWAY | 32 | genes.ES.table | 0.6 | 2 | 0 | 0.39 | 0.1 | 0.59 | 0.23 | 0.46 | 0 | 0.075

genes ES table in pathway: KEGG LYSOSOME

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 | EHD4 | EHD4 | EHD4 | 492 | 0.4 | 0.098 | YES
2 | PRKCD | PRKCD | PRKCD | 906 | 0.27 | 0.16 | YES
3 | MAPK7 | MAPK7 | MAPK7 | 925 | 0.26 | 0.24 | YES
4 | MAP2K6 | MAP2K6 | MAP2K6 | 1062 | 0.24 | 0.31 | YES
5 | MAP2K1 | MAP2K1 | MAP2K1 | 1187 | 0.22 | 0.37 | YES
6 | FOS | FOS | FOS | 1620 | 0.16 | 0.4 | YES
7 | CDK5 | CDK5 | CDK5 | 1630 | 0.16 | 0.45 | YES
8 | MEF2C | MEF2C | MEF2C | 1850 | 0.14 | 0.48 | YES
9 | RAP1A | RAP1A | RAP1A | 1908 | 0.14 | 0.52 | YES
10 | MAP2K3 | MAP2K3 | MAP2K3 | 2376 | 0.1 | 0.53 | YES
11 | EGR1 | EGR1 | EGR1 | 2873 | 0.079 | 0.52 | YES
12 | MAPK3 | MAPK3 | MAPK3 | 2933 | 0.076 | 0.54 | YES
13 | RPS6KA1 | RPS6KA1 | RPS6KA1 | 3013 | 0.072 | 0.56 | YES
14 | RIT1 | RIT1 | RIT1 | 3192 | 0.066 | 0.57 | YES
15 | MAPKAPK2 | MAPKAPK2 | MAPKAPK2 | 3527 | 0.054 | 0.57 | YES
16 | MAP3K2 | MAP3K2 | MAP3K2 | 3598 | 0.051 | 0.58 | YES
17 | MAPK14 | MAPK14 | MAPK14 | 3883 | 0.043 | 0.58 | YES
18 | RAP1B | RAP1B | RAP1B | 3933 | 0.042 | 0.59 | YES
19 | MAPK1 | MAPK1 | MAPK1 | 3962 | 0.041 | 0.6 | YES
20 | RUSC1 | RUSC1 | RUSC1 | 4236 | 0.034 | 0.6 | NO
21 | RAF1 | RAF1 | RAF1 | 4606 | 0.025 | 0.58 | NO
22 | RPS6KA5 | RPS6KA5 | RPS6KA5 | 5244 | 0.012 | 0.55 | NO
23 | KRAS | KRAS | KRAS | 5734 | 0.0021 | 0.52 | NO
24 | SRF | SRF | SRF | 5822 | 0.00036 | 0.52 | NO
25 | NRAS | NRAS | NRAS | 6219 | -0.0071 | 0.5 | NO
26 | CDK5R1 | CDK5R1 | CDK5R1 | 7384 | -0.028 | 0.44 | NO
27 | CREB1 | CREB1 | CREB1 | 7723 | -0.033 | 0.43 | NO
28 | HRAS | HRAS | HRAS | 7785 | -0.034 | 0.44 | NO
29 | ELK1 | ELK1 | ELK1 | 7912 | -0.036 | 0.44 | NO
30 | MAP2K5 | MAP2K5 | MAP2K5 | 8859 | -0.052 | 0.4 | NO
31 | BRAF | BRAF | BRAF | 10291 | -0.079 | 0.34 | NO
32 | TRPV1 | TRPV1 | TRPV1 | 13783 | -0.19 | 0.2 | 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 LYSOSOME.

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

genes ES table in pathway: KEGG FC GAMMA R MEDIATED PHAGOCYTOSIS

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 | TLR8 | TLR8 | TLR8 | 15 | 0.92 | 0.048 | YES
2 | TLR5 | TLR5 | TLR5 | 16 | 0.92 | 0.097 | YES
3 | CD14 | CD14 | CD14 | 36 | 0.84 | 0.14 | YES
4 | S100A12 | S100A12 | S100A12 | 55 | 0.8 | 0.18 | YES
5 | TLR7 | TLR7 | TLR7 | 60 | 0.79 | 0.22 | YES
6 | LY86 | LY86 | LY86 | 112 | 0.7 | 0.26 | YES
7 | TICAM2 | TICAM2 | TICAM2 | 118 | 0.69 | 0.29 | YES
8 | LY96 | LY96 | LY96 | 135 | 0.67 | 0.33 | YES
9 | NOD2 | NOD2 | NOD2 | 166 | 0.63 | 0.36 | YES
10 | CTSL1 | CTSL1 | CTSL1 | 205 | 0.59 | 0.39 | YES
11 | TLR4 | TLR4 | TLR4 | 270 | 0.54 | 0.41 | YES
12 | CD180 | CD180 | CD180 | 286 | 0.52 | 0.44 | YES
13 | CTSS | CTSS | CTSS | 499 | 0.4 | 0.45 | YES
14 | PELI3 | PELI3 | PELI3 | 518 | 0.39 | 0.47 | YES
15 | TLR6 | TLR6 | TLR6 | 584 | 0.37 | 0.48 | YES
16 | TLR2 | TLR2 | TLR2 | 656 | 0.34 | 0.5 | YES
17 | TLR1 | TLR1 | TLR1 | 700 | 0.33 | 0.51 | YES
18 | DUSP6 | DUSP6 | DUSP6 | 702 | 0.33 | 0.53 | YES
19 | UNC93B1 | UNC93B1 | UNC93B1 | 807 | 0.3 | 0.54 | YES
20 | CTSB | CTSB | CTSB | 911 | 0.27 | 0.55 | YES
21 | MAPK7 | MAPK7 | MAPK7 | 925 | 0.26 | 0.56 | YES
22 | PELI1 | PELI1 | PELI1 | 1031 | 0.24 | 0.57 | YES
23 | MAP2K6 | MAP2K6 | MAP2K6 | 1062 | 0.24 | 0.58 | YES
24 | MAP2K1 | MAP2K1 | MAP2K1 | 1187 | 0.22 | 0.58 | YES
25 | MYD88 | MYD88 | MYD88 | 1291 | 0.2 | 0.59 | YES
26 | FOS | FOS | FOS | 1620 | 0.16 | 0.58 | YES
27 | NFKB2 | NFKB2 | NFKB2 | 1695 | 0.15 | 0.58 | YES
28 | MEF2C | MEF2C | MEF2C | 1850 | 0.14 | 0.58 | YES
29 | TIRAP | TIRAP | TIRAP | 1963 | 0.13 | 0.58 | YES
30 | TICAM1 | TICAM1 | TICAM1 | 1992 | 0.13 | 0.58 | YES
31 | IRAK3 | IRAK3 | IRAK3 | 2010 | 0.13 | 0.59 | YES
32 | EEA1 | EEA1 | EEA1 | 2117 | 0.12 | 0.59 | YES
33 | MAP2K3 | MAP2K3 | MAP2K3 | 2376 | 0.1 | 0.58 | NO
34 | CTSK | CTSK | CTSK | 2442 | 0.1 | 0.58 | NO
35 | DUSP7 | DUSP7 | DUSP7 | 2585 | 0.093 | 0.58 | NO
36 | NFKBIA | NFKBIA | NFKBIA | 2653 | 0.09 | 0.58 | NO
37 | CNPY3 | CNPY3 | CNPY3 | 2691 | 0.088 | 0.58 | NO
38 | CHUK | CHUK | CHUK | 2910 | 0.078 | 0.57 | NO
39 | TLR10 | TLR10 | TLR10 | 2919 | 0.077 | 0.58 | NO
40 | MAPK3 | MAPK3 | MAPK3 | 2933 | 0.076 | 0.58 | NO
41 | IKBKG | IKBKG | IKBKG | 2970 | 0.074 | 0.58 | NO
42 | RPS6KA1 | RPS6KA1 | RPS6KA1 | 3013 | 0.072 | 0.58 | NO
43 | TBK1 | TBK1 | TBK1 | 3306 | 0.062 | 0.57 | NO
44 | IRAK4 | IRAK4 | IRAK4 | 3430 | 0.058 | 0.57 | NO
45 | TMEM189-UBE2V1 | TMEM189-UBE2V1 | TMEM189-UBE2V1 | 3481 | 0.056 | 0.57 | NO
46 | MAPKAPK2 | MAPKAPK2 | MAPKAPK2 | 3527 | 0.054 | 0.57 | NO
47 | PPP2CA | PPP2CA | PPP2CA | 3533 | 0.054 | 0.57 | NO
48 | MAP3K1 | MAP3K1 | MAP3K1 | 3562 | 0.052 | 0.57 | NO
49 | TRAF3 | TRAF3 | TRAF3 | 3575 | 0.052 | 0.57 | NO
50 | IRAK1 | IRAK1 | IRAK1 | 3643 | 0.05 | 0.57 | NO
51 | JUN | JUN | JUN | 3719 | 0.048 | 0.57 | NO
52 | IRF7 | IRF7 | IRF7 | 3829 | 0.045 | 0.56 | NO
53 | MAPK14 | MAPK14 | MAPK14 | 3883 | 0.043 | 0.56 | NO
54 | MAPK1 | MAPK1 | MAPK1 | 3962 | 0.041 | 0.56 | NO
55 | ATF1 | ATF1 | ATF1 | 3964 | 0.041 | 0.56 | NO
56 | DUSP3 | DUSP3 | DUSP3 | 4256 | 0.033 | 0.55 | NO
57 | UBE2N | UBE2N | UBE2N | 4444 | 0.028 | 0.54 | NO
58 | RPS6KA3 | RPS6KA3 | RPS6KA3 | 4467 | 0.028 | 0.54 | NO
59 | MAP2K4 | MAP2K4 | MAP2K4 | 4595 | 0.025 | 0.53 | NO
60 | RIPK2 | RIPK2 | RIPK2 | 4619 | 0.025 | 0.53 | NO
61 | BTK | BTK | BTK | 4725 | 0.022 | 0.53 | NO
62 | NFKBIB | NFKBIB | NFKBIB | 4784 | 0.021 | 0.53 | NO
63 | MAPK9 | MAPK9 | MAPK9 | 5022 | 0.016 | 0.51 | NO
64 | MAPKAPK3 | MAPKAPK3 | MAPKAPK3 | 5165 | 0.013 | 0.51 | NO
65 | DNM2 | DNM2 | DNM2 | 5193 | 0.013 | 0.5 | NO
66 | RPS6KA5 | RPS6KA5 | RPS6KA5 | 5244 | 0.012 | 0.5 | NO
67 | PPP2CB | PPP2CB | PPP2CB | 5384 | 0.0088 | 0.5 | NO
68 | IKBKE | IKBKE | IKBKE | 5516 | 0.0063 | 0.49 | NO
69 | MAP2K2 | MAP2K2 | MAP2K2 | 5602 | 0.0045 | 0.48 | NO
70 | HSP90B1 | HSP90B1 | HSP90B1 | 5658 | 0.0033 | 0.48 | NO
71 | CDK1 | CDK1 | CDK1 | 5829 | 0.00029 | 0.47 | NO
72 | MEF2A | MEF2A | MEF2A | 5888 | -0.0011 | 0.47 | NO
73 | PLCG2 | PLCG2 | PLCG2 | 5915 | -0.0015 | 0.46 | NO
74 | RELA | RELA | RELA | 6026 | -0.0035 | 0.46 | NO
75 | PPP2R1A | PPP2R1A | PPP2R1A | 6098 | -0.0048 | 0.46 | NO
76 | UBA52 | UBA52 | UBA52 | 6462 | -0.012 | 0.43 | NO
77 | PPP2R1B | PPP2R1B | PPP2R1B | 6548 | -0.013 | 0.43 | NO
78 | PIK3R4 | PIK3R4 | PIK3R4 | 6617 | -0.014 | 0.43 | NO
79 | MAPK10 | MAPK10 | MAPK10 | 6625 | -0.014 | 0.43 | NO
80 | RIPK1 | RIPK1 | RIPK1 | 6771 | -0.017 | 0.42 | NO
81 | IRF3 | IRF3 | IRF3 | 7002 | -0.021 | 0.41 | NO
82 | PPP2R5D | PPP2R5D | PPP2R5D | 7028 | -0.022 | 0.41 | NO
83 | TAB2 | TAB2 | TAB2 | 7098 | -0.023 | 0.4 | NO
84 | IKBKB | IKBKB | IKBKB | 7288 | -0.026 | 0.39 | NO
85 | ECSIT | ECSIT | ECSIT | 7296 | -0.026 | 0.4 | NO
86 | MAP3K7 | MAP3K7 | MAP3K7 | 7426 | -0.028 | 0.39 | NO
87 | CREB1 | CREB1 | CREB1 | 7723 | -0.033 | 0.37 | NO
88 | MAP2K7 | MAP2K7 | MAP2K7 | 7853 | -0.035 | 0.37 | NO
89 | ELK1 | ELK1 | ELK1 | 7912 | -0.036 | 0.37 | NO
90 | HMGB1 | HMGB1 | HMGB1 | 8037 | -0.039 | 0.36 | NO
91 | S100B | S100B | S100B | 8093 | -0.04 | 0.36 | NO
92 | AGER | AGER | AGER | 8162 | -0.041 | 0.36 | NO
93 | ZFYVE20 | ZFYVE20 | ZFYVE20 | 8501 | -0.046 | 0.34 | NO
94 | TRAF6 | TRAF6 | TRAF6 | 8541 | -0.047 | 0.34 | NO
95 | TAB1 | TAB1 | TAB1 | 8543 | -0.047 | 0.34 | NO
96 | NOD1 | NOD1 | NOD1 | 8872 | -0.053 | 0.33 | NO
97 | SIGIRR | SIGIRR | SIGIRR | 8907 | -0.053 | 0.33 | NO
98 | TAB3 | TAB3 | TAB3 | 8990 | -0.054 | 0.33 | NO
99 | RPS27A | RPS27A | RPS27A | 9037 | -0.055 | 0.33 | NO
100 | PELI2 | PELI2 | PELI2 | 9054 | -0.056 | 0.33 | NO
101 | ATF2 | ATF2 | ATF2 | 9567 | -0.066 | 0.3 | NO
102 | PIK3C3 | PIK3C3 | PIK3C3 | 9661 | -0.068 | 0.3 | NO
103 | LGMN | LGMN | LGMN | 10111 | -0.076 | 0.28 | NO
104 | IRAK2 | IRAK2 | IRAK2 | 10996 | -0.095 | 0.23 | NO
105 | TLR9 | TLR9 | TLR9 | 11686 | -0.11 | 0.2 | NO
106 | DUSP4 | DUSP4 | DUSP4 | 12626 | -0.14 | 0.15 | NO
107 | MAPK8 | MAPK8 | MAPK8 | 12703 | -0.15 | 0.15 | NO
108 | RPS6KA2 | RPS6KA2 | RPS6KA2 | 13091 | -0.16 | 0.14 | NO
109 | APP | APP | APP | 15575 | -0.29 | 0.011 | NO
110 | LBP | LBP | LBP | 16040 | -0.33 | 0.0014 | NO
111 | DNM1 | DNM1 | DNM1 | 16384 | -0.37 | 0.001 | NO
112 | TLR3 | TLR3 | TLR3 | 16390 | -0.37 | 0.02 | NO
113 | MAPK11 | MAPK11 | MAPK11 | 17156 | -0.57 | 0.006 | 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 FC GAMMA R MEDIATED PHAGOCYTOSIS.

Figure S24. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG FC GAMMA R MEDIATED PHAGOCYTOSIS, 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 HIVNEF PATHWAY

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 | CD14 | CD14 | CD14 | 36 | 0.84 | 0.067 | YES
2 | S100A12 | S100A12 | S100A12 | 55 | 0.8 | 0.13 | YES
3 | TICAM2 | TICAM2 | TICAM2 | 118 | 0.69 | 0.19 | YES
4 | LY96 | LY96 | LY96 | 135 | 0.67 | 0.24 | YES
5 | NOD2 | NOD2 | NOD2 | 166 | 0.63 | 0.29 | YES
6 | TLR4 | TLR4 | TLR4 | 270 | 0.54 | 0.33 | YES
7 | PELI3 | PELI3 | PELI3 | 518 | 0.39 | 0.35 | YES
8 | TLR6 | TLR6 | TLR6 | 584 | 0.37 | 0.37 | YES
9 | TLR2 | TLR2 | TLR2 | 656 | 0.34 | 0.4 | YES
10 | TLR1 | TLR1 | TLR1 | 700 | 0.33 | 0.42 | YES
11 | DUSP6 | DUSP6 | DUSP6 | 702 | 0.33 | 0.45 | YES
12 | MAPK7 | MAPK7 | MAPK7 | 925 | 0.26 | 0.46 | YES
13 | PELI1 | PELI1 | PELI1 | 1031 | 0.24 | 0.47 | YES
14 | MAP2K6 | MAP2K6 | MAP2K6 | 1062 | 0.24 | 0.49 | YES
15 | MAP2K1 | MAP2K1 | MAP2K1 | 1187 | 0.22 | 0.5 | YES
16 | MYD88 | MYD88 | MYD88 | 1291 | 0.2 | 0.51 | YES
17 | FOS | FOS | FOS | 1620 | 0.16 | 0.51 | YES
18 | NFKB2 | NFKB2 | NFKB2 | 1695 | 0.15 | 0.52 | YES
19 | MEF2C | MEF2C | MEF2C | 1850 | 0.14 | 0.52 | YES
20 | TIRAP | TIRAP | TIRAP | 1963 | 0.13 | 0.52 | YES
21 | TICAM1 | TICAM1 | TICAM1 | 1992 | 0.13 | 0.53 | YES
22 | IRAK3 | IRAK3 | IRAK3 | 2010 | 0.13 | 0.54 | YES
23 | MAP2K3 | MAP2K3 | MAP2K3 | 2376 | 0.1 | 0.53 | NO
24 | DUSP7 | DUSP7 | DUSP7 | 2585 | 0.093 | 0.52 | NO
25 | NFKBIA | NFKBIA | NFKBIA | 2653 | 0.09 | 0.53 | NO
26 | CHUK | CHUK | CHUK | 2910 | 0.078 | 0.52 | NO
27 | MAPK3 | MAPK3 | MAPK3 | 2933 | 0.076 | 0.52 | NO
28 | IKBKG | IKBKG | IKBKG | 2970 | 0.074 | 0.53 | NO
29 | RPS6KA1 | RPS6KA1 | RPS6KA1 | 3013 | 0.072 | 0.53 | NO
30 | TBK1 | TBK1 | TBK1 | 3306 | 0.062 | 0.52 | NO
31 | IRAK4 | IRAK4 | IRAK4 | 3430 | 0.058 | 0.52 | NO
32 | TMEM189-UBE2V1 | TMEM189-UBE2V1 | TMEM189-UBE2V1 | 3481 | 0.056 | 0.52 | NO
33 | MAPKAPK2 | MAPKAPK2 | MAPKAPK2 | 3527 | 0.054 | 0.52 | NO
34 | PPP2CA | PPP2CA | PPP2CA | 3533 | 0.054 | 0.52 | NO
35 | MAP3K1 | MAP3K1 | MAP3K1 | 3562 | 0.052 | 0.53 | NO
36 | TRAF3 | TRAF3 | TRAF3 | 3575 | 0.052 | 0.53 | NO
37 | IRAK1 | IRAK1 | IRAK1 | 3643 | 0.05 | 0.53 | NO
38 | JUN | JUN | JUN | 3719 | 0.048 | 0.53 | NO
39 | IRF7 | IRF7 | IRF7 | 3829 | 0.045 | 0.53 | NO
40 | MAPK14 | MAPK14 | MAPK14 | 3883 | 0.043 | 0.53 | NO
41 | MAPK1 | MAPK1 | MAPK1 | 3962 | 0.041 | 0.53 | NO
42 | ATF1 | ATF1 | ATF1 | 3964 | 0.041 | 0.53 | NO
43 | DUSP3 | DUSP3 | DUSP3 | 4256 | 0.033 | 0.52 | NO
44 | UBE2N | UBE2N | UBE2N | 4444 | 0.028 | 0.51 | NO
45 | RPS6KA3 | RPS6KA3 | RPS6KA3 | 4467 | 0.028 | 0.51 | NO
46 | MAP2K4 | MAP2K4 | MAP2K4 | 4595 | 0.025 | 0.5 | NO
47 | RIPK2 | RIPK2 | RIPK2 | 4619 | 0.025 | 0.5 | NO
48 | BTK | BTK | BTK | 4725 | 0.022 | 0.5 | NO
49 | NFKBIB | NFKBIB | NFKBIB | 4784 | 0.021 | 0.5 | NO
50 | MAPK9 | MAPK9 | MAPK9 | 5022 | 0.016 | 0.49 | NO
51 | MAPKAPK3 | MAPKAPK3 | MAPKAPK3 | 5165 | 0.013 | 0.48 | NO
52 | RPS6KA5 | RPS6KA5 | RPS6KA5 | 5244 | 0.012 | 0.48 | NO
53 | PPP2CB | PPP2CB | PPP2CB | 5384 | 0.0088 | 0.47 | NO
54 | IKBKE | IKBKE | IKBKE | 5516 | 0.0063 | 0.46 | NO
55 | MAP2K2 | MAP2K2 | MAP2K2 | 5602 | 0.0045 | 0.46 | NO
56 | CDK1 | CDK1 | CDK1 | 5829 | 0.00029 | 0.44 | NO
57 | MEF2A | MEF2A | MEF2A | 5888 | -0.0011 | 0.44 | NO
58 | RELA | RELA | RELA | 6026 | -0.0035 | 0.43 | NO
59 | PPP2R1A | PPP2R1A | PPP2R1A | 6098 | -0.0048 | 0.43 | NO
60 | UBA52 | UBA52 | UBA52 | 6462 | -0.012 | 0.41 | NO
61 | PPP2R1B | PPP2R1B | PPP2R1B | 6548 | -0.013 | 0.4 | NO
62 | MAPK10 | MAPK10 | MAPK10 | 6625 | -0.014 | 0.4 | NO
63 | RIPK1 | RIPK1 | RIPK1 | 6771 | -0.017 | 0.4 | NO
64 | IRF3 | IRF3 | IRF3 | 7002 | -0.021 | 0.38 | NO
65 | PPP2R5D | PPP2R5D | PPP2R5D | 7028 | -0.022 | 0.38 | NO
66 | TAB2 | TAB2 | TAB2 | 7098 | -0.023 | 0.38 | NO
67 | IKBKB | IKBKB | IKBKB | 7288 | -0.026 | 0.37 | NO
68 | ECSIT | ECSIT | ECSIT | 7296 | -0.026 | 0.37 | NO
69 | MAP3K7 | MAP3K7 | MAP3K7 | 7426 | -0.028 | 0.37 | NO
70 | CREB1 | CREB1 | CREB1 | 7723 | -0.033 | 0.36 | NO
71 | MAP2K7 | MAP2K7 | MAP2K7 | 7853 | -0.035 | 0.35 | NO
72 | ELK1 | ELK1 | ELK1 | 7912 | -0.036 | 0.35 | NO
73 | HMGB1 | HMGB1 | HMGB1 | 8037 | -0.039 | 0.35 | NO
74 | S100B | S100B | S100B | 8093 | -0.04 | 0.35 | NO
75 | AGER | AGER | AGER | 8162 | -0.041 | 0.34 | NO
76 | TRAF6 | TRAF6 | TRAF6 | 8541 | -0.047 | 0.33 | NO
77 | TAB1 | TAB1 | TAB1 | 8543 | -0.047 | 0.33 | NO
78 | NOD1 | NOD1 | NOD1 | 8872 | -0.053 | 0.32 | NO
79 | SIGIRR | SIGIRR | SIGIRR | 8907 | -0.053 | 0.32 | NO
80 | TAB3 | TAB3 | TAB3 | 8990 | -0.054 | 0.32 | NO
81 | RPS27A | RPS27A | RPS27A | 9037 | -0.055 | 0.32 | NO
82 | PELI2 | PELI2 | PELI2 | 9054 | -0.056 | 0.32 | NO
83 | ATF2 | ATF2 | ATF2 | 9567 | -0.066 | 0.3 | NO
84 | IRAK2 | IRAK2 | IRAK2 | 10996 | -0.095 | 0.22 | NO
85 | DUSP4 | DUSP4 | DUSP4 | 12626 | -0.14 | 0.14 | NO
86 | MAPK8 | MAPK8 | MAPK8 | 12703 | -0.15 | 0.15 | NO
87 | RPS6KA2 | RPS6KA2 | RPS6KA2 | 13091 | -0.16 | 0.14 | NO
88 | APP | APP | APP | 15575 | -0.29 | 0.02 | NO
89 | TLR3 | TLR3 | TLR3 | 16390 | -0.37 | 0.0033 | NO
90 | MAPK11 | MAPK11 | MAPK11 | 17156 | -0.57 | 0.006 | 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: BIOCARTA HIVNEF PATHWAY.

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

genes ES table in pathway: BIOCARTA PYK2 PATHWAY

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 | S100A12 | S100A12 | S100A12 | 55 | 0.8 | 0.078 | YES
2 | LY96 | LY96 | LY96 | 135 | 0.67 | 0.14 | YES
3 | NOD2 | NOD2 | NOD2 | 166 | 0.63 | 0.2 | YES
4 | TLR4 | TLR4 | TLR4 | 270 | 0.54 | 0.25 | YES
5 | PELI3 | PELI3 | PELI3 | 518 | 0.39 | 0.28 | YES
6 | TLR6 | TLR6 | TLR6 | 584 | 0.37 | 0.31 | YES
7 | TLR2 | TLR2 | TLR2 | 656 | 0.34 | 0.34 | YES
8 | TLR1 | TLR1 | TLR1 | 700 | 0.33 | 0.37 | YES
9 | DUSP6 | DUSP6 | DUSP6 | 702 | 0.33 | 0.41 | YES
10 | MAPK7 | MAPK7 | MAPK7 | 925 | 0.26 | 0.42 | YES
11 | PELI1 | PELI1 | PELI1 | 1031 | 0.24 | 0.44 | YES
12 | MAP2K6 | MAP2K6 | MAP2K6 | 1062 | 0.24 | 0.46 | YES
13 | MAP2K1 | MAP2K1 | MAP2K1 | 1187 | 0.22 | 0.48 | YES
14 | MYD88 | MYD88 | MYD88 | 1291 | 0.2 | 0.49 | YES
15 | FOS | FOS | FOS | 1620 | 0.16 | 0.49 | YES
16 | NFKB2 | NFKB2 | NFKB2 | 1695 | 0.15 | 0.5 | YES
17 | MEF2C | MEF2C | MEF2C | 1850 | 0.14 | 0.5 | YES
18 | TIRAP | TIRAP | TIRAP | 1963 | 0.13 | 0.51 | YES
19 | IRAK3 | IRAK3 | IRAK3 | 2010 | 0.13 | 0.52 | YES
20 | MAP2K3 | MAP2K3 | MAP2K3 | 2376 | 0.1 | 0.51 | YES
21 | DUSP7 | DUSP7 | DUSP7 | 2585 | 0.093 | 0.51 | YES
22 | NFKBIA | NFKBIA | NFKBIA | 2653 | 0.09 | 0.51 | YES
23 | CHUK | CHUK | CHUK | 2910 | 0.078 | 0.51 | YES
24 | MAPK3 | MAPK3 | MAPK3 | 2933 | 0.076 | 0.51 | YES
25 | IKBKG | IKBKG | IKBKG | 2970 | 0.074 | 0.52 | YES
26 | RPS6KA1 | RPS6KA1 | RPS6KA1 | 3013 | 0.072 | 0.52 | YES
27 | IRAK4 | IRAK4 | IRAK4 | 3430 | 0.058 | 0.5 | NO
28 | TMEM189-UBE2V1 | TMEM189-UBE2V1 | TMEM189-UBE2V1 | 3481 | 0.056 | 0.51 | NO
29 | MAPKAPK2 | MAPKAPK2 | MAPKAPK2 | 3527 | 0.054 | 0.51 | NO
30 | PPP2CA | PPP2CA | PPP2CA | 3533 | 0.054 | 0.52 | NO
31 | MAP3K1 | MAP3K1 | MAP3K1 | 3562 | 0.052 | 0.52 | NO
32 | IRAK1 | IRAK1 | IRAK1 | 3643 | 0.05 | 0.52 | NO
33 | JUN | JUN | JUN | 3719 | 0.048 | 0.52 | NO
34 | MAPK14 | MAPK14 | MAPK14 | 3883 | 0.043 | 0.52 | NO
35 | MAPK1 | MAPK1 | MAPK1 | 3962 | 0.041 | 0.52 | NO
36 | ATF1 | ATF1 | ATF1 | 3964 | 0.041 | 0.52 | NO
37 | DUSP3 | DUSP3 | DUSP3 | 4256 | 0.033 | 0.51 | NO
38 | UBE2N | UBE2N | UBE2N | 4444 | 0.028 | 0.5 | NO
39 | RPS6KA3 | RPS6KA3 | RPS6KA3 | 4467 | 0.028 | 0.5 | NO
40 | MAP2K4 | MAP2K4 | MAP2K4 | 4595 | 0.025 | 0.49 | NO
41 | RIPK2 | RIPK2 | RIPK2 | 4619 | 0.025 | 0.5 | NO
42 | BTK | BTK | BTK | 4725 | 0.022 | 0.49 | NO
43 | NFKBIB | NFKBIB | NFKBIB | 4784 | 0.021 | 0.49 | NO
44 | MAPK9 | MAPK9 | MAPK9 | 5022 | 0.016 | 0.48 | NO
45 | MAPKAPK3 | MAPKAPK3 | MAPKAPK3 | 5165 | 0.013 | 0.47 | NO
46 | RPS6KA5 | RPS6KA5 | RPS6KA5 | 5244 | 0.012 | 0.47 | NO
47 | PPP2CB | PPP2CB | PPP2CB | 5384 | 0.0088 | 0.46 | NO
48 | MAP2K2 | MAP2K2 | MAP2K2 | 5602 | 0.0045 | 0.45 | NO
49 | CDK1 | CDK1 | CDK1 | 5829 | 0.00029 | 0.44 | NO
50 | MEF2A | MEF2A | MEF2A | 5888 | -0.0011 | 0.43 | NO
51 | RELA | RELA | RELA | 6026 | -0.0035 | 0.42 | NO
52 | PPP2R1A | PPP2R1A | PPP2R1A | 6098 | -0.0048 | 0.42 | NO
53 | UBA52 | UBA52 | UBA52 | 6462 | -0.012 | 0.4 | NO
54 | PPP2R1B | PPP2R1B | PPP2R1B | 6548 | -0.013 | 0.4 | NO
55 | MAPK10 | MAPK10 | MAPK10 | 6625 | -0.014 | 0.4 | NO
56 | PPP2R5D | PPP2R5D | PPP2R5D | 7028 | -0.022 | 0.37 | NO
57 | TAB2 | TAB2 | TAB2 | 7098 | -0.023 | 0.37 | NO
58 | IKBKB | IKBKB | IKBKB | 7288 | -0.026 | 0.36 | NO
59 | ECSIT | ECSIT | ECSIT | 7296 | -0.026 | 0.37 | NO
60 | MAP3K7 | MAP3K7 | MAP3K7 | 7426 | -0.028 | 0.36 | NO
61 | CREB1 | CREB1 | CREB1 | 7723 | -0.033 | 0.35 | NO
62 | MAP2K7 | MAP2K7 | MAP2K7 | 7853 | -0.035 | 0.34 | NO
63 | ELK1 | ELK1 | ELK1 | 7912 | -0.036 | 0.34 | NO
64 | HMGB1 | HMGB1 | HMGB1 | 8037 | -0.039 | 0.34 | NO
65 | S100B | S100B | S100B | 8093 | -0.04 | 0.34 | NO
66 | AGER | AGER | AGER | 8162 | -0.041 | 0.34 | NO
67 | TRAF6 | TRAF6 | TRAF6 | 8541 | -0.047 | 0.32 | NO
68 | TAB1 | TAB1 | TAB1 | 8543 | -0.047 | 0.33 | NO
69 | NOD1 | NOD1 | NOD1 | 8872 | -0.053 | 0.32 | NO
70 | SIGIRR | SIGIRR | SIGIRR | 8907 | -0.053 | 0.32 | NO
71 | TAB3 | TAB3 | TAB3 | 8990 | -0.054 | 0.32 | NO
72 | RPS27A | RPS27A | RPS27A | 9037 | -0.055 | 0.32 | NO
73 | PELI2 | PELI2 | PELI2 | 9054 | -0.056 | 0.33 | NO
74 | ATF2 | ATF2 | ATF2 | 9567 | -0.066 | 0.3 | NO
75 | IRAK2 | IRAK2 | IRAK2 | 10996 | -0.095 | 0.23 | NO
76 | DUSP4 | DUSP4 | DUSP4 | 12626 | -0.14 | 0.15 | NO
77 | MAPK8 | MAPK8 | MAPK8 | 12703 | -0.15 | 0.16 | NO
78 | RPS6KA2 | RPS6KA2 | RPS6KA2 | 13091 | -0.16 | 0.16 | NO
79 | APP | APP | APP | 15575 | -0.29 | 0.04 | NO
80 | MAPK11 | MAPK11 | MAPK11 | 17156 | -0.57 | 0.006 | 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: BIOCARTA PYK2 PATHWAY.

Figure S28. Get High-res Image For the top 5 core enriched genes in the pathway: BIOCARTA PYK2 PATHWAY, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: BIOCARTA TOLL PATHWAY

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

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | MEFV | MEFV | MEFV | 12 | 0.93 | 0.026 | YES
2 | TLR8 | TLR8 | TLR8 | 15 | 0.92 | 0.053 | YES
3 | TLR5 | TLR5 | TLR5 | 16 | 0.92 | 0.08 | YES
4 | CD14 | CD14 | CD14 | 36 | 0.84 | 0.1 | YES
5 | S100A12 | S100A12 | S100A12 | 55 | 0.8 | 0.12 | YES
6 | TLR7 | TLR7 | TLR7 | 60 | 0.79 | 0.15 | YES
7 | NLRC4 | NLRC4 | NLRC4 | 66 | 0.78 | 0.17 | YES
8 | CCR2 | CCR2 | CCR2 | 98 | 0.72 | 0.19 | YES
9 | LGALS3 | LGALS3 | LGALS3 | 110 | 0.7 | 0.21 | YES
10 | LY86 | LY86 | LY86 | 112 | 0.7 | 0.23 | YES
11 | TICAM2 | TICAM2 | TICAM2 | 118 | 0.69 | 0.25 | YES
12 | LY96 | LY96 | LY96 | 135 | 0.67 | 0.27 | YES
13 | NOD2 | NOD2 | NOD2 | 166 | 0.63 | 0.28 | YES
14 | CTSL1 | CTSL1 | CTSL1 | 205 | 0.59 | 0.3 | YES
15 | CR1 | CR1 | CR1 | 246 | 0.56 | 0.31 | YES
16 | C3 | C3 | C3 | 257 | 0.55 | 0.33 | YES
17 | AIM2 | AIM2 | AIM2 | 263 | 0.54 | 0.34 | YES
18 | C2 | C2 | C2 | 266 | 0.54 | 0.36 | YES
19 | TLR4 | TLR4 | TLR4 | 270 | 0.54 | 0.37 | YES
20 | CD180 | CD180 | CD180 | 286 | 0.52 | 0.39 | YES
21 | CD4 | CD4 | CD4 | 353 | 0.48 | 0.4 | YES
22 | P2RX7 | P2RX7 | P2RX7 | 475 | 0.41 | 0.4 | YES
23 | CTSS | CTSS | CTSS | 499 | 0.4 | 0.41 | YES
24 | PELI3 | PELI3 | PELI3 | 518 | 0.39 | 0.42 | YES
25 | CASP1 | CASP1 | CASP1 | 578 | 0.37 | 0.43 | YES
26 | NLRP3 | NLRP3 | NLRP3 | 580 | 0.37 | 0.44 | YES
27 | TLR6 | TLR6 | TLR6 | 584 | 0.37 | 0.45 | YES
28 | TLR2 | TLR2 | TLR2 | 656 | 0.34 | 0.46 | YES
29 | CFB | CFB | CFB | 697 | 0.33 | 0.46 | YES
30 | TLR1 | TLR1 | TLR1 | 700 | 0.33 | 0.47 | YES
31 | DUSP6 | DUSP6 | DUSP6 | 702 | 0.33 | 0.48 | YES
32 | CARD9 | CARD9 | CARD9 | 735 | 0.32 | 0.49 | YES
33 | UNC93B1 | UNC93B1 | UNC93B1 | 807 | 0.3 | 0.49 | YES
34 | NLRP1 | NLRP1 | NLRP1 | 845 | 0.29 | 0.5 | YES
35 | C1QA | C1QA | C1QA | 851 | 0.29 | 0.51 | YES
36 | UBE2D1 | UBE2D1 | UBE2D1 | 904 | 0.27 | 0.51 | YES
37 | CTSB | CTSB | CTSB | 911 | 0.27 | 0.52 | YES
38 | PSTPIP1 | PSTPIP1 | PSTPIP1 | 912 | 0.27 | 0.53 | YES
39 | MAPK7 | MAPK7 | MAPK7 | 925 | 0.26 | 0.54 | YES
40 | PELI1 | PELI1 | PELI1 | 1031 | 0.24 | 0.54 | YES
41 | MAP2K6 | MAP2K6 | MAP2K6 | 1062 | 0.24 | 0.54 | YES
42 | DEFB1 | DEFB1 | DEFB1 | 1065 | 0.24 | 0.55 | YES
43 | CFD | CFD | CFD | 1128 | 0.23 | 0.55 | YES
44 | PYCARD | PYCARD | PYCARD | 1182 | 0.22 | 0.55 | YES
45 | MAP2K1 | MAP2K1 | MAP2K1 | 1187 | 0.22 | 0.56 | YES
46 | MYD88 | MYD88 | MYD88 | 1291 | 0.2 | 0.56 | YES
47 | RNF135 | RNF135 | RNF135 | 1337 | 0.2 | 0.56 | YES
48 | FOS | FOS | FOS | 1620 | 0.16 | 0.55 | YES
49 | C4BPA | C4BPA | C4BPA | 1646 | 0.16 | 0.56 | YES
50 | NFKB2 | NFKB2 | NFKB2 | 1695 | 0.15 | 0.56 | YES
51 | CAPZA2 | CAPZA2 | CAPZA2 | 1716 | 0.15 | 0.56 | YES
52 | MEF2C | MEF2C | MEF2C | 1850 | 0.14 | 0.56 | YES
53 | RIPK3 | RIPK3 | RIPK3 | 1910 | 0.14 | 0.56 | YES
54 | TIRAP | TIRAP | TIRAP | 1963 | 0.13 | 0.56 | YES
55 | TICAM1 | TICAM1 | TICAM1 | 1992 | 0.13 | 0.56 | YES
56 | IRAK3 | IRAK3 | IRAK3 | 2010 | 0.13 | 0.56 | YES
57 | EEA1 | EEA1 | EEA1 | 2117 | 0.12 | 0.56 | YES
58 | C1QC | C1QC | C1QC | 2168 | 0.12 | 0.56 | YES
59 | C5 | C5 | C5 | 2285 | 0.11 | 0.56 | YES
60 | IRF2 | IRF2 | IRF2 | 2345 | 0.11 | 0.56 | YES
61 | CD55 | CD55 | CD55 | 2370 | 0.1 | 0.56 | YES
62 | MAP2K3 | MAP2K3 | MAP2K3 | 2376 | 0.1 | 0.56 | YES
63 | CAPZA1 | CAPZA1 | CAPZA1 | 2385 | 0.1 | 0.56 | YES
64 | CTSK | CTSK | CTSK | 2442 | 0.1 | 0.56 | YES
65 | C1QB | C1QB | C1QB | 2455 | 0.1 | 0.56 | YES
66 | TANK | TANK | TANK | 2539 | 0.096 | 0.56 | YES
67 | DUSP7 | DUSP7 | DUSP7 | 2585 | 0.093 | 0.56 | YES
68 | MAPK13 | MAPK13 | MAPK13 | 2590 | 0.093 | 0.56 | YES
69 | NFKBIA | NFKBIA | NFKBIA | 2653 | 0.09 | 0.56 | NO
70 | CNPY3 | CNPY3 | CNPY3 | 2691 | 0.088 | 0.56 | NO
71 | BIRC3 | BIRC3 | BIRC3 | 2767 | 0.084 | 0.56 | NO
72 | DEFA4 | DEFA4 | DEFA4 | 2782 | 0.083 | 0.56 | NO
73 | TXNIP | TXNIP | TXNIP | 2867 | 0.079 | 0.56 | NO
74 | CHUK | CHUK | CHUK | 2910 | 0.078 | 0.56 | NO
75 | TLR10 | TLR10 | TLR10 | 2919 | 0.077 | 0.56 | NO
76 | MAPK3 | MAPK3 | MAPK3 | 2933 | 0.076 | 0.56 | NO
77 | IKBKG | IKBKG | IKBKG | 2970 | 0.074 | 0.56 | NO
78 | RPS6KA1 | RPS6KA1 | RPS6KA1 | 3013 | 0.072 | 0.56 | NO
79 | ZBP1 | ZBP1 | ZBP1 | 3067 | 0.071 | 0.56 | NO
80 | PANX1 | PANX1 | PANX1 | 3089 | 0.07 | 0.56 | NO
81 | TNFAIP3 | TNFAIP3 | TNFAIP3 | 3174 | 0.066 | 0.56 | NO
82 | FADD | FADD | FADD | 3265 | 0.063 | 0.56 | NO
83 | TBK1 | TBK1 | TBK1 | 3306 | 0.062 | 0.56 | NO
84 | IRAK4 | IRAK4 | IRAK4 | 3430 | 0.058 | 0.55 | NO
85 | TMEM189-UBE2V1 | TMEM189-UBE2V1 | TMEM189-UBE2V1 | 3481 | 0.056 | 0.55 | NO
86 | MAPKAPK2 | MAPKAPK2 | MAPKAPK2 | 3527 | 0.054 | 0.55 | NO
87 | PPP2CA | PPP2CA | PPP2CA | 3533 | 0.054 | 0.55 | NO
88 | MAP3K1 | MAP3K1 | MAP3K1 | 3562 | 0.052 | 0.55 | NO
89 | TRAF3 | TRAF3 | TRAF3 | 3575 | 0.052 | 0.55 | NO
90 | IRAK1 | IRAK1 | IRAK1 | 3643 | 0.05 | 0.55 | NO
91 | JUN | JUN | JUN | 3719 | 0.048 | 0.55 | NO
92 | IRF7 | IRF7 | IRF7 | 3829 | 0.045 | 0.54 | NO
93 | TRIM25 | TRIM25 | TRIM25 | 3872 | 0.043 | 0.54 | NO
94 | MAPK14 | MAPK14 | MAPK14 | 3883 | 0.043 | 0.54 | NO
95 | MAPK1 | MAPK1 | MAPK1 | 3962 | 0.041 | 0.54 | NO
96 | ATF1 | ATF1 | ATF1 | 3964 | 0.041 | 0.54 | NO
97 | HERC5 | HERC5 | HERC5 | 4120 | 0.037 | 0.53 | NO
98 | DUSP3 | DUSP3 | DUSP3 | 4256 | 0.033 | 0.52 | NO
99 | ISG15 | ISG15 | ISG15 | 4259 | 0.033 | 0.52 | NO
100 | IRF1 | IRF1 | IRF1 | 4276 | 0.033 | 0.52 | NO
101 | CD46 | CD46 | CD46 | 4286 | 0.032 | 0.52 | NO
102 | TAX1BP1 | TAX1BP1 | TAX1BP1 | 4399 | 0.03 | 0.52 | NO
103 | UBE2N | UBE2N | UBE2N | 4444 | 0.028 | 0.52 | NO
104 | RPS6KA3 | RPS6KA3 | RPS6KA3 | 4467 | 0.028 | 0.52 | NO
105 | ATG5 | ATG5 | ATG5 | 4561 | 0.026 | 0.51 | NO
106 | MAP2K4 | MAP2K4 | MAP2K4 | 4595 | 0.025 | 0.51 | NO
107 | RIPK2 | RIPK2 | RIPK2 | 4619 | 0.025 | 0.51 | NO
108 | CASP10 | CASP10 | CASP10 | 4628 | 0.025 | 0.51 | NO
109 | DAK | DAK | DAK | 4650 | 0.024 | 0.51 | NO
110 | BIRC2 | BIRC2 | BIRC2 | 4666 | 0.024 | 0.51 | NO
111 | BTK | BTK | BTK | 4725 | 0.022 | 0.51 | NO
112 | NFKBIB | NFKBIB | NFKBIB | 4784 | 0.021 | 0.5 | NO
113 | UBE2D3 | UBE2D3 | UBE2D3 | 4844 | 0.02 | 0.5 | NO
114 | CREBBP | CREBBP | CREBBP | 4926 | 0.018 | 0.5 | NO
115 | MAPK9 | MAPK9 | MAPK9 | 5022 | 0.016 | 0.49 | NO
116 | EP300 | EP300 | EP300 | 5126 | 0.014 | 0.48 | NO
117 | CASP9 | CASP9 | CASP9 | 5131 | 0.014 | 0.48 | NO
118 | MAPKAPK3 | MAPKAPK3 | MAPKAPK3 | 5165 | 0.013 | 0.48 | NO
119 | NLRC5 | NLRC5 | NLRC5 | 5188 | 0.013 | 0.48 | NO
120 | DNM2 | DNM2 | DNM2 | 5193 | 0.013 | 0.48 | NO
121 | RPS6KA5 | RPS6KA5 | RPS6KA5 | 5244 | 0.012 | 0.48 | NO
122 | PPP2CB | PPP2CB | PPP2CB | 5384 | 0.0088 | 0.47 | NO
123 | DDOST | DDOST | DDOST | 5391 | 0.0087 | 0.47 | NO
124 | ATG12 | ATG12 | ATG12 | 5452 | 0.0076 | 0.47 | NO
125 | DEFA1B | DEFA1B | DEFA1B | 5496 | 0.0067 | 0.47 | NO
126 | IKBKE | IKBKE | IKBKE | 5516 | 0.0063 | 0.47 | NO
127 | UBE2D2 | UBE2D2 | UBE2D2 | 5579 | 0.0049 | 0.46 | NO
128 | MAP2K2 | MAP2K2 | MAP2K2 | 5602 | 0.0045 | 0.46 | NO
129 | HSP90B1 | HSP90B1 | HSP90B1 | 5658 | 0.0033 | 0.46 | NO
130 | DDX58 | DDX58 | DDX58 | 5685 | 0.0028 | 0.46 | NO
131 | CASP4 | CASP4 | CASP4 | 5765 | 0.0015 | 0.45 | NO
132 | CDK1 | CDK1 | CDK1 | 5829 | 0.00029 | 0.45 | NO
133 | MEF2A | MEF2A | MEF2A | 5888 | -0.0011 | 0.44 | NO
134 | PLCG2 | PLCG2 | PLCG2 | 5915 | -0.0015 | 0.44 | NO
135 | NLRX1 | NLRX1 | NLRX1 | 5958 | -0.0022 | 0.44 | NO
136 | RELA | RELA | RELA | 6026 | -0.0035 | 0.44 | NO
137 | PPP2R1A | PPP2R1A | PPP2R1A | 6098 | -0.0048 | 0.43 | NO
138 | C4BPB | C4BPB | C4BPB | 6283 | -0.0079 | 0.42 | NO
139 | UBE2K | UBE2K | UBE2K | 6422 | -0.011 | 0.42 | NO
140 | UBA52 | UBA52 | UBA52 | 6462 | -0.012 | 0.41 | NO
141 | DHX58 | DHX58 | DHX58 | 6490 | -0.012 | 0.41 | NO
142 | PPP2R1B | PPP2R1B | PPP2R1B | 6548 | -0.013 | 0.41 | NO
143 | PIK3R4 | PIK3R4 | PIK3R4 | 6617 | -0.014 | 0.4 | NO
144 | PCBP2 | PCBP2 | PCBP2 | 6622 | -0.014 | 0.4 | NO
145 | MAPK10 | MAPK10 | MAPK10 | 6625 | -0.014 | 0.4 | NO
146 | RIPK1 | RIPK1 | RIPK1 | 6771 | -0.017 | 0.4 | NO
147 | IRF3 | IRF3 | IRF3 | 7002 | -0.021 | 0.38 | NO
148 | PPP2R5D | PPP2R5D | PPP2R5D | 7028 | -0.022 | 0.38 | NO
149 | TAB2 | TAB2 | TAB2 | 7098 | -0.023 | 0.38 | NO
150 | CASP8 | CASP8 | CASP8 | 7222 | -0.025 | 0.37 | NO
151 | IKBKB | IKBKB | IKBKB | 7288 | -0.026 | 0.37 | NO
152 | ECSIT | ECSIT | ECSIT | 7296 | -0.026 | 0.37 | NO
153 | MAP3K7 | MAP3K7 | MAP3K7 | 7426 | -0.028 | 0.36 | NO
154 | CYLD | CYLD | CYLD | 7531 | -0.03 | 0.36 | NO
155 | CREB1 | CREB1 | CREB1 | 7723 | -0.033 | 0.35 | NO
156 | UBA7 | UBA7 | UBA7 | 7772 | -0.034 | 0.35 | NO
157 | PRKCSH | PRKCSH | PRKCSH | 7822 | -0.035 | 0.34 | NO
158 | MAP2K7 | MAP2K7 | MAP2K7 | 7853 | -0.035 | 0.34 | NO
159 | ELK1 | ELK1 | ELK1 | 7912 | -0.036 | 0.34 | NO
160 | MAVS | MAVS | MAVS | 7974 | -0.038 | 0.34 | NO
161 | HMGB1 | HMGB1 | HMGB1 | 8037 | -0.039 | 0.34 | NO
162 | OTUD5 | OTUD5 | OTUD5 | 8088 | -0.04 | 0.34 | NO
163 | S100B | S100B | S100B | 8093 | -0.04 | 0.34 | NO
164 | CASP2 | CASP2 | CASP2 | 8112 | -0.04 | 0.34 | NO
165 | PIN1 | PIN1 | PIN1 | 8117 | -0.04 | 0.34 | NO
166 | AGER | AGER | AGER | 8162 | -0.041 | 0.34 | NO
167 | IFIH1 | IFIH1 | IFIH1 | 8214 | -0.042 | 0.33 | NO
168 | UBE2L6 | UBE2L6 | UBE2L6 | 8337 | -0.044 | 0.33 | NO
169 | SIKE1 | SIKE1 | SIKE1 | 8391 | -0.045 | 0.33 | NO
170 | ZFYVE20 | ZFYVE20 | ZFYVE20 | 8501 | -0.046 | 0.32 | NO
171 | TRAF6 | TRAF6 | TRAF6 | 8541 | -0.047 | 0.32 | NO
172 | TAB1 | TAB1 | TAB1 | 8543 | -0.047 | 0.32 | NO
173 | TXN | TXN | TXN | 8768 | -0.051 | 0.31 | NO
174 | NOD1 | NOD1 | NOD1 | 8872 | -0.053 | 0.3 | NO
175 | SIGIRR | SIGIRR | SIGIRR | 8907 | -0.053 | 0.3 | NO
176 | TAB3 | TAB3 | TAB3 | 8990 | -0.054 | 0.3 | NO
177 | RPS27A | RPS27A | RPS27A | 9037 | -0.055 | 0.3 | NO
178 | PELI2 | PELI2 | PELI2 | 9054 | -0.056 | 0.3 | NO
179 | ATF2 | ATF2 | ATF2 | 9567 | -0.066 | 0.27 | NO
180 | PIK3C3 | PIK3C3 | PIK3C3 | 9661 | -0.068 | 0.27 | NO
181 | LGMN | LGMN | LGMN | 10111 | -0.076 | 0.25 | NO
182 | HSP90AB1 | HSP90AB1 | HSP90AB1 | 10218 | -0.078 | 0.24 | NO
183 | IRAK2 | IRAK2 | IRAK2 | 10996 | -0.095 | 0.2 | NO
184 | ART1 | ART1 | ART1 | 11130 | -0.099 | 0.19 | NO
185 | C4A | C4A | C4A | 11397 | -0.11 | 0.18 | NO
186 | TLR9 | TLR9 | TLR9 | 11686 | -0.11 | 0.17 | NO
187 | TRAF2 | TRAF2 | TRAF2 | 11789 | -0.12 | 0.16 | NO
188 | CCR6 | CCR6 | CCR6 | 11935 | -0.12 | 0.16 | NO
189 | PROS1 | PROS1 | PROS1 | 12123 | -0.13 | 0.15 | NO
190 | MASP2 | MASP2 | MASP2 | 12471 | -0.14 | 0.14 | NO
191 | C7 | C7 | C7 | 12599 | -0.14 | 0.13 | NO
192 | DUSP4 | DUSP4 | DUSP4 | 12626 | -0.14 | 0.14 | NO
193 | MAPK8 | MAPK8 | MAPK8 | 12703 | -0.15 | 0.14 | NO
194 | RNF125 | RNF125 | RNF125 | 12704 | -0.15 | 0.14 | NO
195 | RPS6KA2 | RPS6KA2 | RPS6KA2 | 13091 | -0.16 | 0.12 | NO
196 | C8G | C8G | C8G | 13288 | -0.17 | 0.12 | NO
197 | BCL2L1 | BCL2L1 | BCL2L1 | 13818 | -0.19 | 0.09 | NO
198 | BCL2 | BCL2 | BCL2 | 14661 | -0.23 | 0.047 | NO
199 | CFI | CFI | CFI | 14719 | -0.24 | 0.051 | NO
200 | IFNA21 | IFNA21 | IFNA21 | 15133 | -0.26 | 0.034 | NO
201 | CFH | CFH | CFH | 15423 | -0.28 | 0.025 | NO
202 | MAPK12 | MAPK12 | MAPK12 | 15521 | -0.29 | 0.028 | NO
203 | APP | APP | APP | 15575 | -0.29 | 0.033 | NO
204 | C1S | C1S | C1S | 15615 | -0.3 | 0.04 | NO
205 | IFNB1 | IFNB1 | IFNB1 | 15680 | -0.3 | 0.045 | NO
206 | LBP | LBP | LBP | 16040 | -0.33 | 0.033 | NO
207 | DNM1 | DNM1 | DNM1 | 16384 | -0.37 | 0.024 | NO
208 | TLR3 | TLR3 | TLR3 | 16390 | -0.37 | 0.034 | NO
209 | MAPK11 | MAPK11 | MAPK11 | 17156 | -0.57 | 0.006 | NO

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

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

genes ES table in pathway: ST TUMOR NECROSIS FACTOR PATHWAY

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

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | TLR8 | TLR8 | TLR8 | 15 | 0.92 | 0.1 | YES
2 | S100A12 | S100A12 | S100A12 | 55 | 0.8 | 0.19 | YES
3 | TLR7 | TLR7 | TLR7 | 60 | 0.79 | 0.27 | YES
4 | NOD2 | NOD2 | NOD2 | 166 | 0.63 | 0.34 | YES
5 | PELI3 | PELI3 | PELI3 | 518 | 0.39 | 0.36 | YES
6 | DUSP6 | DUSP6 | DUSP6 | 702 | 0.33 | 0.38 | YES
7 | MAPK7 | MAPK7 | MAPK7 | 925 | 0.26 | 0.4 | YES
8 | PELI1 | PELI1 | PELI1 | 1031 | 0.24 | 0.42 | YES
9 | MAP2K6 | MAP2K6 | MAP2K6 | 1062 | 0.24 | 0.45 | YES
10 | MAP2K1 | MAP2K1 | MAP2K1 | 1187 | 0.22 | 0.46 | YES
11 | MYD88 | MYD88 | MYD88 | 1291 | 0.2 | 0.48 | YES
12 | FOS | FOS | FOS | 1620 | 0.16 | 0.48 | YES
13 | NFKB2 | NFKB2 | NFKB2 | 1695 | 0.15 | 0.49 | YES
14 | MEF2C | MEF2C | MEF2C | 1850 | 0.14 | 0.5 | YES
15 | MAP2K3 | MAP2K3 | MAP2K3 | 2376 | 0.1 | 0.48 | NO
16 | DUSP7 | DUSP7 | DUSP7 | 2585 | 0.093 | 0.48 | NO
17 | NFKBIA | NFKBIA | NFKBIA | 2653 | 0.09 | 0.48 | NO
18 | CHUK | CHUK | CHUK | 2910 | 0.078 | 0.48 | NO
19 | MAPK3 | MAPK3 | MAPK3 | 2933 | 0.076 | 0.48 | NO
20 | IKBKG | IKBKG | IKBKG | 2970 | 0.074 | 0.49 | NO
21 | RPS6KA1 | RPS6KA1 | RPS6KA1 | 3013 | 0.072 | 0.49 | NO
22 | IRAK4 | IRAK4 | IRAK4 | 3430 | 0.058 | 0.48 | NO
23 | TMEM189-UBE2V1 | TMEM189-UBE2V1 | TMEM189-UBE2V1 | 3481 | 0.056 | 0.48 | NO
24 | MAPKAPK2 | MAPKAPK2 | MAPKAPK2 | 3527 | 0.054 | 0.48 | NO
25 | PPP2CA | PPP2CA | PPP2CA | 3533 | 0.054 | 0.49 | NO
26 | MAP3K1 | MAP3K1 | MAP3K1 | 3562 | 0.052 | 0.49 | NO
27 | IRAK1 | IRAK1 | IRAK1 | 3643 | 0.05 | 0.49 | NO
28 | JUN | JUN | JUN | 3719 | 0.048 | 0.49 | NO
29 | MAPK14 | MAPK14 | MAPK14 | 3883 | 0.043 | 0.49 | NO
30 | MAPK1 | MAPK1 | MAPK1 | 3962 | 0.041 | 0.49 | NO
31 | ATF1 | ATF1 | ATF1 | 3964 | 0.041 | 0.49 | NO
32 | DUSP3 | DUSP3 | DUSP3 | 4256 | 0.033 | 0.48 | NO
33 | UBE2N | UBE2N | UBE2N | 4444 | 0.028 | 0.47 | NO
34 | RPS6KA3 | RPS6KA3 | RPS6KA3 | 4467 | 0.028 | 0.48 | NO
35 | MAP2K4 | MAP2K4 | MAP2K4 | 4595 | 0.025 | 0.47 | NO
36 | RIPK2 | RIPK2 | RIPK2 | 4619 | 0.025 | 0.47 | NO
37 | NFKBIB | NFKBIB | NFKBIB | 4784 | 0.021 | 0.46 | NO
38 | MAPK9 | MAPK9 | MAPK9 | 5022 | 0.016 | 0.45 | NO
39 | MAPKAPK3 | MAPKAPK3 | MAPKAPK3 | 5165 | 0.013 | 0.45 | NO
40 | RPS6KA5 | RPS6KA5 | RPS6KA5 | 5244 | 0.012 | 0.44 | NO
41 | PPP2CB | PPP2CB | PPP2CB | 5384 | 0.0088 | 0.44 | NO
42 | MAP2K2 | MAP2K2 | MAP2K2 | 5602 | 0.0045 | 0.42 | NO
43 | CDK1 | CDK1 | CDK1 | 5829 | 0.00029 | 0.41 | NO
44 | MEF2A | MEF2A | MEF2A | 5888 | -0.0011 | 0.41 | NO
45 | RELA | RELA | RELA | 6026 | -0.0035 | 0.4 | NO
46 | PPP2R1A | PPP2R1A | PPP2R1A | 6098 | -0.0048 | 0.4 | NO
47 | UBA52 | UBA52 | UBA52 | 6462 | -0.012 | 0.38 | NO
48 | PPP2R1B | PPP2R1B | PPP2R1B | 6548 | -0.013 | 0.37 | NO
49 | MAPK10 | MAPK10 | MAPK10 | 6625 | -0.014 | 0.37 | NO
50 | PPP2R5D | PPP2R5D | PPP2R5D | 7028 | -0.022 | 0.35 | NO
51 | TAB2 | TAB2 | TAB2 | 7098 | -0.023 | 0.35 | NO
52 | IKBKB | IKBKB | IKBKB | 7288 | -0.026 | 0.34 | NO
53 | ECSIT | ECSIT | ECSIT | 7296 | -0.026 | 0.34 | NO
54 | MAP3K7 | MAP3K7 | MAP3K7 | 7426 | -0.028 | 0.34 | NO
55 | CREB1 | CREB1 | CREB1 | 7723 | -0.033 | 0.32 | NO
56 | MAP2K7 | MAP2K7 | MAP2K7 | 7853 | -0.035 | 0.32 | NO
57 | ELK1 | ELK1 | ELK1 | 7912 | -0.036 | 0.32 | NO
58 | HMGB1 | HMGB1 | HMGB1 | 8037 | -0.039 | 0.32 | NO
59 | S100B | S100B | S100B | 8093 | -0.04 | 0.32 | NO
60 | AGER | AGER | AGER | 8162 | -0.041 | 0.32 | NO
61 | TRAF6 | TRAF6 | TRAF6 | 8541 | -0.047 | 0.3 | NO
62 | TAB1 | TAB1 | TAB1 | 8543 | -0.047 | 0.31 | NO
63 | NOD1 | NOD1 | NOD1 | 8872 | -0.053 | 0.29 | NO
64 | TAB3 | TAB3 | TAB3 | 8990 | -0.054 | 0.29 | NO
65 | RPS27A | RPS27A | RPS27A | 9037 | -0.055 | 0.3 | NO
66 | PELI2 | PELI2 | PELI2 | 9054 | -0.056 | 0.3 | NO
67 | ATF2 | ATF2 | ATF2 | 9567 | -0.066 | 0.28 | NO
68 | IRAK2 | IRAK2 | IRAK2 | 10996 | -0.095 | 0.21 | NO
69 | TLR9 | TLR9 | TLR9 | 11686 | -0.11 | 0.18 | NO
70 | DUSP4 | DUSP4 | DUSP4 | 12626 | -0.14 | 0.14 | NO
71 | MAPK8 | MAPK8 | MAPK8 | 12703 | -0.15 | 0.15 | NO
72 | RPS6KA2 | RPS6KA2 | RPS6KA2 | 13091 | -0.16 | 0.15 | NO
73 | APP | APP | APP | 15575 | -0.29 | 0.035 | NO
74 | MAPK11 | MAPK11 | MAPK11 | 17156 | -0.57 | 0.006 | 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: ST TUMOR NECROSIS FACTOR PATHWAY.

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

genes ES table in pathway: PID IL1PATHWAY

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 | SLC11A1 | SLC11A1 | SLC11A1 | 32 | 0.85 | 0.041 | YES
2 | SORT1 | SORT1 | SORT1 | 131 | 0.67 | 0.069 | YES
3 | CTSL1 | CTSL1 | CTSL1 | 205 | 0.59 | 0.095 | YES
4 | CTSH | CTSH | CTSH | 207 | 0.59 | 0.12 | YES
5 | SGSH | SGSH | SGSH | 239 | 0.56 | 0.15 | YES
6 | CTSL2 | CTSL2 | CTSL2 | 291 | 0.52 | 0.18 | YES
7 | CD68 | CD68 | CD68 | 321 | 0.5 | 0.2 | YES
8 | AP1S2 | AP1S2 | AP1S2 | 462 | 0.42 | 0.21 | YES
9 | CTSS | CTSS | CTSS | 499 | 0.4 | 0.23 | YES
10 | IGF2R | IGF2R | IGF2R | 506 | 0.4 | 0.25 | YES
11 | AP1S3 | AP1S3 | AP1S3 | 531 | 0.39 | 0.27 | YES
12 | CTSZ | CTSZ | CTSZ | 601 | 0.36 | 0.28 | YES
13 | ARSG | ARSG | ARSG | 616 | 0.36 | 0.3 | YES
14 | NAGA | NAGA | NAGA | 689 | 0.33 | 0.31 | YES
15 | GAA | GAA | GAA | 731 | 0.32 | 0.32 | YES
16 | HEXB | HEXB | HEXB | 742 | 0.32 | 0.34 | YES
17 | CLTCL1 | CLTCL1 | CLTCL1 | 802 | 0.3 | 0.35 | YES
18 | PSAP | PSAP | PSAP | 894 | 0.28 | 0.36 | YES
19 | CTSB | CTSB | CTSB | 911 | 0.27 | 0.37 | YES
20 | GNS | GNS | GNS | 940 | 0.26 | 0.38 | YES
21 | FUCA1 | FUCA1 | FUCA1 | 969 | 0.25 | 0.4 | YES
22 | ATP6V0D1 | ATP6V0D1 | ATP6V0D1 | 1024 | 0.24 | 0.4 | YES
23 | CTSD | CTSD | CTSD | 1140 | 0.23 | 0.41 | YES
24 | TCIRG1 | TCIRG1 | TCIRG1 | 1181 | 0.22 | 0.42 | YES
25 | NPC2 | NPC2 | NPC2 | 1190 | 0.22 | 0.43 | YES
26 | GM2A | GM2A | GM2A | 1216 | 0.21 | 0.44 | YES
27 | ATP6V0A1 | ATP6V0A1 | ATP6V0A1 | 1327 | 0.2 | 0.44 | YES
28 | MCOLN1 | MCOLN1 | MCOLN1 | 1368 | 0.19 | 0.45 | YES
29 | LIPA | LIPA | LIPA | 1481 | 0.18 | 0.45 | YES
30 | PPT1 | PPT1 | PPT1 | 1586 | 0.17 | 0.45 | YES
31 | LAPTM5 | LAPTM5 | LAPTM5 | 1680 | 0.16 | 0.46 | YES
32 | PLA2G15 | PLA2G15 | PLA2G15 | 1682 | 0.16 | 0.46 | YES
33 | AP1S1 | AP1S1 | AP1S1 | 1782 | 0.15 | 0.46 | YES
34 | SLC17A5 | SLC17A5 | SLC17A5 | 1844 | 0.14 | 0.47 | YES
35 | GBA | GBA | GBA | 1859 | 0.14 | 0.48 | YES
36 | MAN2B1 | MAN2B1 | MAN2B1 | 1861 | 0.14 | 0.48 | YES
37 | ASAH1 | ASAH1 | ASAH1 | 1918 | 0.14 | 0.48 | YES
38 | ARSB | ARSB | ARSB | 1947 | 0.13 | 0.49 | YES
39 | TPP1 | TPP1 | TPP1 | 1955 | 0.13 | 0.5 | YES
40 | GUSB | GUSB | GUSB | 1998 | 0.13 | 0.5 | YES
41 | CD63 | CD63 | CD63 | 2027 | 0.13 | 0.5 | YES
42 | ACP2 | ACP2 | ACP2 | 2049 | 0.13 | 0.51 | YES
43 | GGA2 | GGA2 | GGA2 | 2071 | 0.12 | 0.52 | YES
44 | SMPD1 | SMPD1 | SMPD1 | 2116 | 0.12 | 0.52 | YES
45 | GLB1 | GLB1 | GLB1 | 2122 | 0.12 | 0.52 | YES
46 | ATP6V0B | ATP6V0B | ATP6V0B | 2147 | 0.12 | 0.53 | YES
47 | NAGPA | NAGPA | NAGPA | 2167 | 0.12 | 0.54 | YES
48 | NEU1 | NEU1 | NEU1 | 2189 | 0.12 | 0.54 | YES
49 | ATP6V0C | ATP6V0C | ATP6V0C | 2193 | 0.12 | 0.55 | YES
50 | CTSA | CTSA | CTSA | 2197 | 0.12 | 0.55 | YES
51 | CLTB | CLTB | CLTB | 2355 | 0.11 | 0.55 | YES
52 | CTSO | CTSO | CTSO | 2427 | 0.1 | 0.55 | YES
53 | CTSK | CTSK | CTSK | 2442 | 0.1 | 0.55 | YES
54 | SUMF1 | SUMF1 | SUMF1 | 2744 | 0.086 | 0.54 | NO
55 | CLTA | CLTA | CLTA | 2809 | 0.082 | 0.54 | NO
56 | HYAL1 | HYAL1 | HYAL1 | 2831 | 0.081 | 0.54 | NO
57 | ARSA | ARSA | ARSA | 2837 | 0.081 | 0.55 | NO
58 | GLA | GLA | GLA | 2866 | 0.079 | 0.55 | NO
59 | GALC | GALC | GALC | 2966 | 0.075 | 0.55 | NO
60 | AP1M1 | AP1M1 | AP1M1 | 3119 | 0.068 | 0.54 | NO
61 | AGA | AGA | AGA | 3153 | 0.067 | 0.54 | NO
62 | AP3B1 | AP3B1 | AP3B1 | 3215 | 0.065 | 0.54 | NO
63 | AP3S1 | AP3S1 | AP3S1 | 3317 | 0.061 | 0.54 | NO
64 | M6PR | M6PR | M6PR | 3338 | 0.061 | 0.54 | NO
65 | LAMP1 | LAMP1 | LAMP1 | 3356 | 0.06 | 0.54 | NO
66 | ACP5 | ACP5 | ACP5 | 3402 | 0.059 | 0.54 | NO
67 | CTSG | CTSG | CTSG | 3416 | 0.058 | 0.55 | NO
68 | SCARB2 | SCARB2 | SCARB2 | 3417 | 0.058 | 0.55 | NO
69 | CLN3 | CLN3 | CLN3 | 3458 | 0.056 | 0.55 | NO
70 | GALNS | GALNS | GALNS | 3791 | 0.046 | 0.53 | NO
71 | CLTC | CLTC | CLTC | 3792 | 0.046 | 0.53 | NO
72 | HEXA | HEXA | HEXA | 3817 | 0.045 | 0.54 | NO
73 | MANBA | MANBA | MANBA | 3942 | 0.042 | 0.53 | NO
74 | AP3S2 | AP3S2 | AP3S2 | 3952 | 0.041 | 0.53 | NO
75 | CLN5 | CLN5 | CLN5 | 4050 | 0.039 | 0.53 | NO
76 | NPC1 | NPC1 | NPC1 | 4261 | 0.033 | 0.52 | NO
77 | ATP6AP1 | ATP6AP1 | ATP6AP1 | 4396 | 0.03 | 0.51 | NO
78 | AP3D1 | AP3D1 | AP3D1 | 4411 | 0.029 | 0.51 | NO
79 | GNPTG | GNPTG | GNPTG | 4460 | 0.028 | 0.51 | NO
80 | LAMP2 | LAMP2 | LAMP2 | 4617 | 0.025 | 0.5 | NO
81 | AP4E1 | AP4E1 | AP4E1 | 4770 | 0.022 | 0.5 | NO
82 | AP3M1 | AP3M1 | AP3M1 | 5038 | 0.016 | 0.48 | NO
83 | ATP6V1H | ATP6V1H | ATP6V1H | 5073 | 0.015 | 0.48 | NO
84 | AP1B1 | AP1B1 | AP1B1 | 5152 | 0.014 | 0.48 | NO
85 | ENTPD4 | ENTPD4 | ENTPD4 | 5303 | 0.01 | 0.47 | NO
86 | CTSC | CTSC | CTSC | 5497 | 0.0067 | 0.46 | NO
87 | NAGLU | NAGLU | NAGLU | 5761 | 0.0016 | 0.44 | NO
88 | CTNS | CTNS | CTNS | 5812 | 0.0005 | 0.44 | NO
89 | AP1G1 | AP1G1 | AP1G1 | 5914 | -0.0015 | 0.43 | NO
90 | LAPTM4A | LAPTM4A | LAPTM4A | 6061 | -0.0041 | 0.42 | NO
91 | GGA3 | GGA3 | GGA3 | 6083 | -0.0046 | 0.42 | NO
92 | GGA1 | GGA1 | GGA1 | 6561 | -0.013 | 0.4 | NO
93 | HGSNAT | HGSNAT | HGSNAT | 7469 | -0.029 | 0.34 | NO
94 | AP4M1 | AP4M1 | AP4M1 | 7668 | -0.032 | 0.33 | NO
95 | SLC11A2 | SLC11A2 | SLC11A2 | 7679 | -0.032 | 0.34 | NO
96 | AP4B1 | AP4B1 | AP4B1 | 7819 | -0.035 | 0.33 | NO
97 | GNPTAB | GNPTAB | GNPTAB | 8818 | -0.052 | 0.27 | NO
98 | IDS | IDS | IDS | 9595 | -0.066 | 0.23 | NO
99 | DNASE2 | DNASE2 | DNASE2 | 9617 | -0.067 | 0.23 | NO
100 | CD164 | CD164 | CD164 | 9758 | -0.069 | 0.23 | NO
101 | LGMN | LGMN | LGMN | 10111 | -0.076 | 0.21 | NO
102 | ATP6V0D2 | ATP6V0D2 | ATP6V0D2 | 10596 | -0.086 | 0.19 | NO
103 | AP3B2 | AP3B2 | AP3B2 | 11149 | -0.1 | 0.16 | NO
104 | IDUA | IDUA | IDUA | 11557 | -0.11 | 0.14 | NO
105 | ATP6V0A2 | ATP6V0A2 | ATP6V0A2 | 11852 | -0.12 | 0.13 | NO
106 | AP1M2 | AP1M2 | AP1M2 | 12231 | -0.13 | 0.12 | NO
107 | MFSD8 | MFSD8 | MFSD8 | 12569 | -0.14 | 0.1 | NO
108 | AP4S1 | AP4S1 | AP4S1 | 13620 | -0.18 | 0.051 | NO
109 | AP3M2 | AP3M2 | AP3M2 | 13748 | -0.19 | 0.054 | NO
110 | NAPSA | NAPSA | NAPSA | 14485 | -0.22 | 0.022 | NO
111 | LAMP3 | LAMP3 | LAMP3 | 14832 | -0.24 | 0.014 | NO
112 | CTSW | CTSW | CTSW | 15259 | -0.27 | 0.0027 | NO
113 | ABCA2 | ABCA2 | ABCA2 | 15517 | -0.29 | 0.0023 | NO
114 | ABCB9 | ABCB9 | ABCB9 | 15752 | -0.31 | 0.0041 | NO
115 | PPT2 | PPT2 | PPT2 | 15999 | -0.33 | 0.0064 | NO
116 | CTSE | CTSE | CTSE | 16315 | -0.36 | 0.0063 | NO
117 | LAPTM4B | LAPTM4B | LAPTM4B | 16911 | -0.47 | -0.0048 | NO
118 | CTSF | CTSF | CTSF | 17000 | -0.5 | 0.015 | 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: PID IL1PATHWAY.

Figure S34. Get High-res Image For the top 5 core enriched genes in the pathway: PID IL1PATHWAY, 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 IFNGPATHWAY

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 | TNFRSF1B | TNFRSF1B | TNFRSF1B | 282 | 0.53 | 0.08 | YES
2 | LMNA | LMNA | LMNA | 850 | 0.29 | 0.1 | YES
3 | PRKCD | PRKCD | PRKCD | 906 | 0.27 | 0.15 | YES
4 | TNF | TNF | TNF | 927 | 0.26 | 0.19 | YES
5 | APAF1 | APAF1 | APAF1 | 1530 | 0.17 | 0.19 | YES
6 | GSN | GSN | GSN | 1765 | 0.15 | 0.2 | YES
7 | PTK2 | PTK2 | PTK2 | 1791 | 0.14 | 0.23 | YES
8 | FAS | FAS | FAS | 1961 | 0.13 | 0.24 | YES
9 | MDM2 | MDM2 | MDM2 | 2078 | 0.12 | 0.26 | YES
10 | PSEN2 | PSEN2 | PSEN2 | 2175 | 0.12 | 0.28 | YES
11 | BID | BID | BID | 2320 | 0.11 | 0.29 | YES
12 | PSEN1 | PSEN1 | PSEN1 | 2415 | 0.1 | 0.3 | YES
13 | LMNB1 | LMNB1 | LMNB1 | 2466 | 0.099 | 0.32 | YES
14 | NFKB1 | NFKB1 | NFKB1 | 2508 | 0.097 | 0.33 | YES
15 | NFKBIA | NFKBIA | NFKBIA | 2653 | 0.09 | 0.34 | YES
16 | BIRC3 | BIRC3 | BIRC3 | 2767 | 0.084 | 0.35 | YES
17 | CHUK | CHUK | CHUK | 2910 | 0.078 | 0.35 | YES
18 | ARHGDIB | ARHGDIB | ARHGDIB | 2939 | 0.076 | 0.37 | YES
19 | CFLAR | CFLAR | CFLAR | 2998 | 0.073 | 0.38 | YES
20 | MAP3K14 | MAP3K14 | MAP3K14 | 3070 | 0.07 | 0.38 | YES
21 | RB1 | RB1 | RB1 | 3166 | 0.067 | 0.39 | YES
22 | CYCS | CYCS | CYCS | 3233 | 0.064 | 0.4 | YES
23 | FADD | FADD | FADD | 3265 | 0.063 | 0.41 | YES
24 | PAK2 | PAK2 | PAK2 | 3332 | 0.061 | 0.42 | YES
25 | MAP3K1 | MAP3K1 | MAP3K1 | 3562 | 0.052 | 0.41 | NO
26 | BAG4 | BAG4 | BAG4 | 3667 | 0.049 | 0.42 | NO
27 | ACTG1 | ACTG1 | ACTG1 | 4331 | 0.032 | 0.38 | NO
28 | TRADD | TRADD | TRADD | 4575 | 0.026 | 0.37 | NO
29 | BIRC2 | BIRC2 | BIRC2 | 4666 | 0.024 | 0.37 | NO
30 | CDK11B | CDK11B | CDK11B | 4722 | 0.023 | 0.37 | NO
31 | MAP3K5 | MAP3K5 | MAP3K5 | 4872 | 0.019 | 0.37 | NO
32 | TNFRSF1A | TNFRSF1A | TNFRSF1A | 4873 | 0.019 | 0.37 | NO
33 | CASP7 | CASP7 | CASP7 | 4882 | 0.019 | 0.38 | NO
34 | CASP9 | CASP9 | CASP9 | 5131 | 0.014 | 0.36 | NO
35 | CDK11A | CDK11A | CDK11A | 5140 | 0.014 | 0.37 | NO
36 | XIAP | XIAP | XIAP | 5226 | 0.012 | 0.36 | NO
37 | RASA1 | RASA1 | RASA1 | 5295 | 0.011 | 0.36 | NO
38 | RELA | RELA | RELA | 6026 | -0.0035 | 0.32 | NO
39 | TRAF1 | TRAF1 | TRAF1 | 6461 | -0.011 | 0.3 | NO
40 | DAXX | DAXX | DAXX | 6685 | -0.015 | 0.29 | NO
41 | RIPK1 | RIPK1 | RIPK1 | 6771 | -0.017 | 0.28 | NO
42 | CASP8 | CASP8 | CASP8 | 7222 | -0.025 | 0.26 | NO
43 | MAP2K7 | MAP2K7 | MAP2K7 | 7853 | -0.035 | 0.23 | NO
44 | CASP2 | CASP2 | CASP2 | 8112 | -0.04 | 0.22 | NO
45 | PRKDC | PRKDC | PRKDC | 8621 | -0.049 | 0.2 | NO
46 | LMNB2 | LMNB2 | LMNB2 | 8760 | -0.051 | 0.2 | NO
47 | SPTAN1 | SPTAN1 | SPTAN1 | 9110 | -0.057 | 0.2 | NO
48 | NUMA1 | NUMA1 | NUMA1 | 9665 | -0.068 | 0.18 | NO
49 | PARP1 | PARP1 | PARP1 | 10406 | -0.082 | 0.15 | NO
50 | DFFA | DFFA | DFFA | 10744 | -0.09 | 0.14 | NO
51 | TRAF2 | TRAF2 | TRAF2 | 11789 | -0.12 | 0.1 | NO
52 | CRADD | CRADD | CRADD | 12040 | -0.12 | 0.11 | NO
53 | DFFB | DFFB | DFFB | 12097 | -0.13 | 0.13 | NO
54 | CASP3 | CASP3 | CASP3 | 12426 | -0.14 | 0.14 | NO
55 | MAPK8 | MAPK8 | MAPK8 | 12703 | -0.15 | 0.15 | NO
56 | FASLG | FASLG | FASLG | 12758 | -0.15 | 0.17 | NO
57 | BCL2 | BCL2 | BCL2 | 14661 | -0.23 | 0.11 | NO
58 | CASP6 | CASP6 | CASP6 | 14885 | -0.24 | 0.14 | 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: PID IFNGPATHWAY.

Figure S36. Get High-res Image For the top 5 core enriched genes in the pathway: PID IFNGPATHWAY, 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 IL8CXCR2 PATHWAY

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

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | CD14 | CD14 | CD14 | 36 | 0.84 | 0.13 | YES
2 | TLR7 | TLR7 | TLR7 | 60 | 0.79 | 0.26 | YES
3 | LY96 | LY96 | LY96 | 135 | 0.67 | 0.36 | YES
4 | TLR4 | TLR4 | TLR4 | 270 | 0.54 | 0.43 | YES
5 | TLR6 | TLR6 | TLR6 | 584 | 0.37 | 0.47 | YES
6 | TLR2 | TLR2 | TLR2 | 656 | 0.34 | 0.52 | YES
7 | MAP2K6 | MAP2K6 | MAP2K6 | 1062 | 0.24 | 0.54 | YES
8 | MYD88 | MYD88 | MYD88 | 1291 | 0.2 | 0.56 | YES
9 | FOS | FOS | FOS | 1620 | 0.16 | 0.56 | YES
10 | TIRAP | TIRAP | TIRAP | 1963 | 0.13 | 0.56 | YES
11 | TOLLIP | TOLLIP | TOLLIP | 1982 | 0.13 | 0.58 | YES
12 | MAP2K3 | MAP2K3 | MAP2K3 | 2376 | 0.1 | 0.58 | YES
13 | NFKB1 | NFKB1 | NFKB1 | 2508 | 0.097 | 0.59 | YES
14 | NFKBIA | NFKBIA | NFKBIA | 2653 | 0.09 | 0.59 | YES
15 | CHUK | CHUK | CHUK | 2910 | 0.078 | 0.59 | YES
16 | TLR10 | TLR10 | TLR10 | 2919 | 0.077 | 0.6 | YES
17 | IKBKG | IKBKG | IKBKG | 2970 | 0.074 | 0.61 | YES
18 | MAP3K14 | MAP3K14 | MAP3K14 | 3070 | 0.07 | 0.62 | YES
19 | MAP3K1 | MAP3K1 | MAP3K1 | 3562 | 0.052 | 0.6 | NO
20 | IRAK1 | IRAK1 | IRAK1 | 3643 | 0.05 | 0.6 | NO
21 | JUN | JUN | JUN | 3719 | 0.048 | 0.6 | NO
22 | MAPK14 | MAPK14 | MAPK14 | 3883 | 0.043 | 0.6 | NO
23 | MAP2K4 | MAP2K4 | MAP2K4 | 4595 | 0.025 | 0.56 | NO
24 | RELA | RELA | RELA | 6026 | -0.0035 | 0.48 | NO
25 | TAB2 | TAB2 | TAB2 | 7098 | -0.023 | 0.42 | NO
26 | PGLYRP1 | PGLYRP1 | PGLYRP1 | 7198 | -0.024 | 0.42 | NO
27 | IKBKB | IKBKB | IKBKB | 7288 | -0.026 | 0.42 | NO
28 | ECSIT | ECSIT | ECSIT | 7296 | -0.026 | 0.42 | NO
29 | MAP3K7 | MAP3K7 | MAP3K7 | 7426 | -0.028 | 0.42 | NO
30 | ELK1 | ELK1 | ELK1 | 7912 | -0.036 | 0.4 | NO
31 | TRAF6 | TRAF6 | TRAF6 | 8541 | -0.047 | 0.37 | NO
32 | TAB1 | TAB1 | TAB1 | 8543 | -0.047 | 0.38 | NO
33 | EIF2AK2 | EIF2AK2 | EIF2AK2 | 10813 | -0.091 | 0.26 | NO
34 | PPARA | PPARA | PPARA | 11097 | -0.098 | 0.26 | NO
35 | TLR9 | TLR9 | TLR9 | 11686 | -0.11 | 0.24 | NO
36 | MAPK8 | MAPK8 | MAPK8 | 12703 | -0.15 | 0.2 | NO
37 | TLR3 | TLR3 | TLR3 | 16390 | -0.37 | 0.05 | NO

Figure S37. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: PID IL8CXCR2 PATHWAY.

Figure S38. Get High-res Image For the top 5 core enriched genes in the pathway: PID IL8CXCR2 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 MAPKTRKPATHWAY

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 | IL1RN | IL1RN | IL1RN | 56 | 0.8 | 0.16 | YES
2 | NOD2 | NOD2 | NOD2 | 166 | 0.63 | 0.28 | YES
3 | PELI3 | PELI3 | PELI3 | 518 | 0.39 | 0.34 | YES
4 | IL1R2 | IL1R2 | IL1R2 | 695 | 0.33 | 0.4 | YES
5 | PELI1 | PELI1 | PELI1 | 1031 | 0.24 | 0.42 | YES
6 | MAP2K6 | MAP2K6 | MAP2K6 | 1062 | 0.24 | 0.47 | YES
7 | MAP2K1 | MAP2K1 | MAP2K1 | 1187 | 0.22 | 0.51 | YES
8 | MYD88 | MYD88 | MYD88 | 1291 | 0.2 | 0.54 | YES
9 | MAP3K3 | MAP3K3 | MAP3K3 | 1307 | 0.2 | 0.58 | YES
10 | TOLLIP | TOLLIP | TOLLIP | 1982 | 0.13 | 0.57 | YES
11 | IRAK3 | IRAK3 | IRAK3 | 2010 | 0.13 | 0.59 | YES
12 | IL1A | IL1A | IL1A | 2498 | 0.098 | 0.58 | YES
13 | CHUK | CHUK | CHUK | 2910 | 0.078 | 0.58 | YES
14 | IKBKG | IKBKG | IKBKG | 2970 | 0.074 | 0.59 | YES
15 | IRAK4 | IRAK4 | IRAK4 | 3430 | 0.058 | 0.57 | YES
16 | TMEM189-UBE2V1 | TMEM189-UBE2V1 | TMEM189-UBE2V1 | 3481 | 0.056 | 0.58 | YES
17 | TNIP2 | TNIP2 | TNIP2 | 3516 | 0.054 | 0.59 | YES
18 | IRAK1 | IRAK1 | IRAK1 | 3643 | 0.05 | 0.59 | YES
19 | SQSTM1 | SQSTM1 | SQSTM1 | 3828 | 0.045 | 0.59 | NO
20 | UBE2N | UBE2N | UBE2N | 4444 | 0.028 | 0.56 | NO
21 | MAP2K4 | MAP2K4 | MAP2K4 | 4595 | 0.025 | 0.56 | NO
22 | RIPK2 | RIPK2 | RIPK2 | 4619 | 0.025 | 0.56 | NO
23 | CUL1 | CUL1 | CUL1 | 5409 | 0.0083 | 0.52 | NO
24 | RBX1 | RBX1 | RBX1 | 5641 | 0.0035 | 0.51 | NO
25 | IL1RAP | IL1RAP | IL1RAP | 5654 | 0.0033 | 0.51 | NO
26 | MAP3K8 | MAP3K8 | MAP3K8 | 6162 | -0.006 | 0.48 | NO
27 | SKP1 | SKP1 | SKP1 | 6594 | -0.013 | 0.46 | NO
28 | TAB2 | TAB2 | TAB2 | 7098 | -0.023 | 0.43 | NO
29 | IKBKB | IKBKB | IKBKB | 7288 | -0.026 | 0.42 | NO
30 | MAP3K7 | MAP3K7 | MAP3K7 | 7426 | -0.028 | 0.42 | NO
31 | TRAF6 | TRAF6 | TRAF6 | 8541 | -0.047 | 0.37 | NO
32 | TAB1 | TAB1 | TAB1 | 8543 | -0.047 | 0.38 | NO
33 | NOD1 | NOD1 | NOD1 | 8872 | -0.053 | 0.37 | NO
34 | TAB3 | TAB3 | TAB3 | 8990 | -0.054 | 0.37 | NO
35 | PELI2 | PELI2 | PELI2 | 9054 | -0.056 | 0.38 | NO
36 | IL1R1 | IL1R1 | IL1R1 | 10985 | -0.095 | 0.29 | NO
37 | IRAK2 | IRAK2 | IRAK2 | 10996 | -0.095 | 0.31 | NO
38 | BTRC | BTRC | BTRC | 11931 | -0.12 | 0.28 | NO
39 | IL1B | IL1B | IL1B | 13055 | -0.16 | 0.24 | NO

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

Figure S40. Get High-res Image For the top 5 core enriched genes in the pathway: PID MAPKTRKPATHWAY, 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

- up-regulated, please check the list of up-regulated genes

- down-regulated, please check the list of down-regulated genes

Expression level

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

- highly expressed genes, please check the list of high (top 30%) expressed genes

- low expressed genes, please check the list of low (bottom 30%) expressed genes

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

- significantly differently expressed genes by eBayes lm fit, please check the list of significant genes

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 GLYCOSYLPHOSPHATIDYLINOSITOL GPI ANCHOR BIOSYNTHESIS | 25 | genes.ES.table | 0.54 | 1.8 | 0.0076 | 0.3 | 0.47 | 0.64 | 0.37 | 0.4 | 0 | 0.068
KEGG AMINOACYL TRNA BIOSYNTHESIS | 41 | genes.ES.table | 0.36 | 1.2 | 0.26 | 1 | 1 | 0.51 | 0.36 | 0.33 | 0.89 | 0.43
KEGG RIBOSOME | 85 | genes.ES.table | 0.54 | 1.4 | 0.21 | 1 | 0.98 | 0.89 | 0.4 | 0.54 | 0.89 | 0.44
KEGG RNA POLYMERASE | 29 | genes.ES.table | 0.5 | 1.7 | 0.035 | 0.6 | 0.77 | 0.69 | 0.41 | 0.41 | 0.25 | 0.17
PID MYC PATHWAY | 25 | genes.ES.table | 0.5 | 1.9 | 0.0019 | 0.36 | 0.33 | 0.48 | 0.31 | 0.33 | 0 | 0.075
REACTOME TRANSLATION | 146 | genes.ES.table | 0.41 | 1.4 | 0.25 | 1 | 0.98 | 0.62 | 0.39 | 0.38 | 0.82 | 0.4
REACTOME FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX | 49 | genes.ES.table | 0.4 | 1.2 | 0.34 | 1 | 1 | 0.71 | 0.41 | 0.42 | 0.99 | 0.49
REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE | 109 | genes.ES.table | 0.44 | 1.3 | 0.27 | 1 | 0.99 | 0.73 | 0.39 | 0.45 | 0.79 | 0.38
REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S | 57 | genes.ES.table | 0.4 | 1.2 | 0.32 | 0.99 | 1 | 0.67 | 0.41 | 0.4 | 0.84 | 0.39
REACTOME PEPTIDE CHAIN ELONGATION | 85 | genes.ES.table | 0.49 | 1.3 | 0.26 | 0.97 | 0.99 | 0.88 | 0.39 | 0.54 | 0.76 | 0.36

genes ES table in pathway: KEGG GLYCOSYLPHOSPHATIDYLINOSITOL GPI ANCHOR BIOSYNTHESIS

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 | KAT2A | KAT2A | KAT2A | 1829 | 0.14 | 0.02 | YES
2 | SUPT3H | SUPT3H | SUPT3H | 2229 | 0.12 | 0.1 | YES
3 | MYC | MYC | MYC | 2347 | 0.12 | 0.2 | YES
4 | RUVBL2 | RUVBL2 | RUVBL2 | 3226 | 0.085 | 0.23 | YES
5 | RUVBL1 | RUVBL1 | RUVBL1 | 3821 | 0.07 | 0.25 | YES
6 | CDKN2A | CDKN2A | CDKN2A | 3831 | 0.07 | 0.31 | YES
7 | PIN1 | PIN1 | PIN1 | 3923 | 0.067 | 0.37 | YES
8 | PML | PML | PML | 4520 | 0.055 | 0.38 | YES
9 | SUPT7L | SUPT7L | SUPT7L | 4705 | 0.052 | 0.42 | YES
10 | ZBTB17 | ZBTB17 | ZBTB17 | 4717 | 0.052 | 0.46 | YES
11 | MAX | MAX | MAX | 5246 | 0.043 | 0.47 | YES
12 | TAF9 | TAF9 | TAF9 | 5330 | 0.041 | 0.5 | YES
13 | TAF12 | TAF12 | TAF12 | 7198 | 0.018 | 0.41 | NO
14 | AXIN1 | AXIN1 | AXIN1 | 7426 | 0.014 | 0.41 | NO
15 | ACTL6A | ACTL6A | ACTL6A | 8467 | 0.002 | 0.35 | NO
16 | PPP2CA | PPP2CA | PPP2CA | 8501 | 0.0016 | 0.35 | NO
17 | SKP2 | SKP2 | SKP2 | 8715 | -0.0011 | 0.34 | NO
18 | TAF10 | TAF10 | TAF10 | 8824 | -0.0024 | 0.34 | NO
19 | KAT5 | KAT5 | KAT5 | 8891 | -0.0031 | 0.33 | NO
20 | HBP1 | HBP1 | HBP1 | 9076 | -0.0053 | 0.33 | NO
21 | GSK3B | GSK3B | GSK3B | 9919 | -0.016 | 0.29 | NO
22 | TRRAP | TRRAP | TRRAP | 10202 | -0.02 | 0.3 | NO
23 | PAK2 | PAK2 | PAK2 | 11101 | -0.034 | 0.27 | NO
24 | PPP2R5A | PPP2R5A | PPP2R5A | 11244 | -0.036 | 0.3 | NO
25 | FBXW7 | FBXW7 | FBXW7 | 12239 | -0.059 | 0.29 | 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 GLYCOSYLPHOSPHATIDYLINOSITOL GPI ANCHOR BIOSYNTHESIS.

Figure S42. 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 AMINOACYL TRNA BIOSYNTHESIS

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 | PIGZ | PIGZ | PIGZ | 860 | 0.22 | 0.16 | YES
2 | PIGU | PIGU | PIGU | 2351 | 0.12 | 0.18 | YES
3 | PIGV | PIGV | PIGV | 3255 | 0.084 | 0.2 | YES
4 | PIGM | PIGM | PIGM | 3948 | 0.067 | 0.22 | YES
5 | PIGG | PIGG | PIGG | 4486 | 0.056 | 0.24 | YES
6 | PIGT | PIGT | PIGT | 4681 | 0.052 | 0.28 | YES
7 | PIGF | PIGF | PIGF | 4726 | 0.052 | 0.32 | YES
8 | DPM2 | DPM2 | DPM2 | 4798 | 0.05 | 0.36 | YES
9 | PIGX | PIGX | PIGX | 5027 | 0.046 | 0.39 | YES
10 | PIGQ | PIGQ | PIGQ | 5088 | 0.045 | 0.43 | YES
11 | GPAA1 | GPAA1 | GPAA1 | 5200 | 0.043 | 0.46 | YES
12 | PIGO | PIGO | PIGO | 5510 | 0.039 | 0.48 | YES
13 | PIGW | PIGW | PIGW | 6018 | 0.032 | 0.48 | YES
14 | PIGC | PIGC | PIGC | 6109 | 0.031 | 0.5 | YES
15 | PIGS | PIGS | PIGS | 6309 | 0.028 | 0.52 | YES
16 | PIGH | PIGH | PIGH | 6414 | 0.027 | 0.54 | YES
17 | PIGA | PIGA | PIGA | 7540 | 0.013 | 0.48 | NO
18 | PIGL | PIGL | PIGL | 7544 | 0.013 | 0.5 | NO
19 | PIGN | PIGN | PIGN | 7696 | 0.011 | 0.5 | NO
20 | PIGY | PIGY | PIGY | 7860 | 0.0093 | 0.5 | NO
21 | PIGB | PIGB | PIGB | 8676 | -0.00063 | 0.45 | NO
22 | PIGK | PIGK | PIGK | 9363 | -0.0088 | 0.42 | NO
23 | PGAP1 | PGAP1 | PGAP1 | 9704 | -0.013 | 0.41 | NO
24 | PIGP | PIGP | PIGP | 9863 | -0.015 | 0.42 | NO
25 | GPLD1 | GPLD1 | GPLD1 | 9865 | -0.015 | 0.43 | 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 AMINOACYL TRNA BIOSYNTHESIS.

Figure S44. Get High-res Image For the top 5 core enriched genes in the pathway: KEGG AMINOACYL TRNA 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 RIBOSOME

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 | POLR3G | POLR3G | POLR3G | 1925 | 0.14 | -0.01 | YES
2 | POLR2H | POLR2H | POLR2H | 1990 | 0.13 | 0.086 | YES
3 | POLR1C | POLR1C | POLR1C | 2057 | 0.13 | 0.18 | YES
4 | POLR2I | POLR2I | POLR2I | 2124 | 0.13 | 0.27 | YES
5 | ZNRD1 | ZNRD1 | ZNRD1 | 2336 | 0.12 | 0.34 | YES
6 | POLR2F | POLR2F | POLR2F | 3781 | 0.071 | 0.31 | YES
7 | POLR2J3 | POLR2J3 | POLR2J3 | 3790 | 0.07 | 0.37 | YES
8 | POLR2J2 | POLR2J2 | POLR2J2 | 4082 | 0.064 | 0.4 | YES
9 | POLR3H | POLR3H | POLR3H | 4835 | 0.049 | 0.39 | YES
10 | POLR3B | POLR3B | POLR3B | 5158 | 0.044 | 0.4 | YES
11 | POLR3D | POLR3D | POLR3D | 5235 | 0.043 | 0.43 | YES
12 | POLR2L | POLR2L | POLR2L | 5300 | 0.042 | 0.46 | YES
13 | POLR1D | POLR1D | POLR1D | 5685 | 0.036 | 0.46 | YES
14 | POLR2A | POLR2A | POLR2A | 5779 | 0.035 | 0.48 | YES
15 | POLR3K | POLR3K | POLR3K | 6559 | 0.025 | 0.46 | YES
16 | POLR2D | POLR2D | POLR2D | 6756 | 0.023 | 0.46 | YES
17 | POLR2J | POLR2J | POLR2J | 6798 | 0.022 | 0.48 | YES
18 | POLR1B | POLR1B | POLR1B | 7004 | 0.02 | 0.48 | YES
19 | POLR3F | POLR3F | POLR3F | 7023 | 0.02 | 0.5 | YES
20 | POLR1E | POLR1E | POLR1E | 7128 | 0.018 | 0.5 | YES
21 | POLR2C | POLR2C | POLR2C | 7765 | 0.01 | 0.47 | NO
22 | POLR2G | POLR2G | POLR2G | 7844 | 0.0095 | 0.48 | NO
23 | POLR1A | POLR1A | POLR1A | 8227 | 0.0048 | 0.46 | NO
24 | POLR3GL | POLR3GL | POLR3GL | 8621 | 0.00018 | 0.44 | NO
25 | POLR2E | POLR2E | POLR2E | 9135 | -0.0061 | 0.41 | NO
26 | POLR3A | POLR3A | POLR3A | 10138 | -0.019 | 0.37 | NO
27 | POLR3C | POLR3C | POLR3C | 10249 | -0.02 | 0.38 | NO
28 | POLR2B | POLR2B | POLR2B | 10287 | -0.021 | 0.39 | NO
29 | POLR2K | POLR2K | POLR2K | 10313 | -0.021 | 0.4 | 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 RIBOSOME.

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

genes ES table in pathway: KEGG RNA POLYMERASE

Table 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 | LZTS1 | LZTS1 | LZTS1 | 1965 | 0.14 | -0.0096 | YES
2 | POLR2H | POLR2H | POLR2H | 1990 | 0.13 | 0.092 | YES
3 | POLR1C | POLR1C | POLR1C | 2057 | 0.13 | 0.19 | YES
4 | SNAPC4 | SNAPC4 | SNAPC4 | 2736 | 0.1 | 0.23 | YES
5 | POLR3E | POLR3E | POLR3E | 3755 | 0.071 | 0.22 | YES
6 | POLR2F | POLR2F | POLR2F | 3781 | 0.071 | 0.28 | YES
7 | SNAPC1 | SNAPC1 | SNAPC1 | 4359 | 0.058 | 0.29 | YES
8 | POLR3H | POLR3H | POLR3H | 4835 | 0.049 | 0.3 | YES
9 | POLR3B | POLR3B | POLR3B | 5158 | 0.044 | 0.32 | YES
10 | POLR3D | POLR3D | POLR3D | 5235 | 0.043 | 0.34 | YES
11 | SNAPC2 | SNAPC2 | SNAPC2 | 5269 | 0.042 | 0.38 | YES
12 | POLR2L | POLR2L | POLR2L | 5300 | 0.042 | 0.41 | YES
13 | POLR1D | POLR1D | POLR1D | 5685 | 0.036 | 0.41 | YES
14 | POLR3K | POLR3K | POLR3K | 6559 | 0.025 | 0.38 | YES
15 | BRF2 | BRF2 | BRF2 | 6586 | 0.025 | 0.4 | YES
16 | POU2F1 | POU2F1 | POU2F1 | 6597 | 0.025 | 0.42 | YES
17 | POLR3F | POLR3F | POLR3F | 7023 | 0.02 | 0.41 | NO
18 | TBP | TBP | TBP | 8175 | 0.0056 | 0.35 | NO
19 | POLR3GL | POLR3GL | POLR3GL | 8621 | 0.00018 | 0.32 | NO
20 | POLR2E | POLR2E | POLR2E | 9135 | -0.0061 | 0.3 | NO
21 | POLR3A | POLR3A | POLR3A | 10138 | -0.019 | 0.25 | NO
22 | POLR3C | POLR3C | POLR3C | 10249 | -0.02 | 0.26 | NO
23 | POLR2K | POLR2K | POLR2K | 10313 | -0.021 | 0.27 | NO
24 | SNAPC5 | SNAPC5 | SNAPC5 | 11477 | -0.041 | 0.24 | NO
25 | SNAPC3 | SNAPC3 | SNAPC3 | 11727 | -0.046 | 0.26 | NO
26 | ZNF143 | ZNF143 | ZNF143 | 12863 | -0.079 | 0.26 | 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 RNA POLYMERASE.

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

genes ES table in pathway: PID MYC PATHWAY

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

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | RPSAP9 | RPSAP9 | RPSAP9 | 981 | 0.21 | -0.017 | YES
2 | RPS26 | RPS26 | RPS26 | 1570 | 0.16 | -0.02 | YES
3 | RPL9 | RPL9 | RPL9 | 1646 | 0.15 | 0.0049 | YES
4 | RPL36A | RPL36A | RPL36A | 2319 | 0.12 | -0.011 | YES
5 | RPL21 | RPL21 | RPL21 | 2469 | 0.11 | 0.0017 | YES
6 | RPL37 | RPL37 | RPL37 | 2989 | 0.092 | -0.011 | YES
7 | GSPT2 | GSPT2 | GSPT2 | 3108 | 0.088 | -0.00035 | YES
8 | RPL36 | RPL36 | RPL36 | 3302 | 0.083 | 0.0044 | YES
9 | RPL12 | RPL12 | RPL12 | 3427 | 0.079 | 0.013 | YES
10 | RPS15 | RPS15 | RPS15 | 3447 | 0.079 | 0.027 | YES
11 | RPL35A | RPL35A | RPL35A | 3459 | 0.079 | 0.042 | YES
12 | RPL39 | RPL39 | RPL39 | 3594 | 0.075 | 0.048 | YES
13 | UPF3A | UPF3A | UPF3A | 3665 | 0.073 | 0.058 | YES
14 | RPL31 | RPL31 | RPL31 | 3739 | 0.072 | 0.068 | YES
15 | RPS17 | RPS17 | RPS17 | 3843 | 0.069 | 0.076 | YES
16 | RPL29 | RPL29 | RPL29 | 3854 | 0.069 | 0.088 | YES
17 | RPL10A | RPL10A | RPL10A | 3899 | 0.068 | 0.099 | YES
18 | RPL23 | RPL23 | RPL23 | 3936 | 0.067 | 0.11 | YES
19 | RPS28 | RPS28 | RPS28 | 4069 | 0.064 | 0.12 | YES
20 | NCBP2 | NCBP2 | NCBP2 | 4102 | 0.064 | 0.12 | YES
21 | RPL28 | RPL28 | RPL28 | 4148 | 0.063 | 0.14 | YES
22 | RPL26 | RPL26 | RPL26 | 4178 | 0.062 | 0.14 | YES
23 | RPL13 | RPL13 | RPL13 | 4188 | 0.062 | 0.16 | YES
24 | RPS4X | RPS4X | RPS4X | 4284 | 0.06 | 0.16 | YES
25 | RPL18 | RPL18 | RPL18 | 4314 | 0.059 | 0.17 | YES
26 | RPS10 | RPS10 | RPS10 | 4324 | 0.059 | 0.18 | YES
27 | RPL41 | RPL41 | RPL41 | 4385 | 0.058 | 0.19 | YES
28 | RPL17 | RPL17 | RPL17 | 4475 | 0.056 | 0.2 | YES
29 | RPS15A | RPS15A | RPS15A | 4511 | 0.055 | 0.2 | YES
30 | RPL34 | RPL34 | RPL34 | 4515 | 0.055 | 0.22 | YES
31 | RPL32 | RPL32 | RPL32 | 4525 | 0.055 | 0.23 | YES
32 | RPL38 | RPL38 | RPL38 | 4542 | 0.055 | 0.24 | YES
33 | UPF3B | UPF3B | UPF3B | 4602 | 0.054 | 0.24 | YES
34 | RPL22 | RPL22 | RPL22 | 4610 | 0.053 | 0.25 | YES
35 | RPL37A | RPL37A | RPL37A | 4626 | 0.053 | 0.26 | YES
36 | RPL18A | RPL18A | RPL18A | 4743 | 0.051 | 0.26 | YES
37 | RPS14 | RPS14 | RPS14 | 4763 | 0.051 | 0.27 | YES
38 | RPS24 | RPS24 | RPS24 | 4772 | 0.051 | 0.28 | YES
39 | RPS20 | RPS20 | RPS20 | 4802 | 0.05 | 0.29 | YES
40 | RPL35 | RPL35 | RPL35 | 4891 | 0.048 | 0.3 | YES
41 | RPL27 | RPL27 | RPL27 | 4987 | 0.047 | 0.3 | YES
42 | RPLP2 | RPLP2 | RPLP2 | 4996 | 0.047 | 0.31 | YES
43 | RPS2 | RPS2 | RPS2 | 5025 | 0.046 | 0.32 | YES
44 | RPSA | RPSA | RPSA | 5045 | 0.046 | 0.32 | YES
45 | RPS23 | RPS23 | RPS23 | 5068 | 0.045 | 0.33 | YES
46 | RPS18 | RPS18 | RPS18 | 5225 | 0.043 | 0.33 | YES
47 | RPL23A | RPL23A | RPL23A | 5256 | 0.043 | 0.34 | YES
48 | RPS5 | RPS5 | RPS5 | 5278 | 0.042 | 0.34 | YES
49 | RPL14 | RPL14 | RPL14 | 5284 | 0.042 | 0.35 | YES
50 | RPS9 | RPS9 | RPS9 | 5288 | 0.042 | 0.36 | YES
51 | RPLP1 | RPLP1 | RPLP1 | 5334 | 0.041 | 0.36 | YES
52 | RPS7 | RPS7 | RPS7 | 5348 | 0.041 | 0.37 | YES
53 | RNPS1 | RNPS1 | RNPS1 | 5407 | 0.04 | 0.38 | YES
54 | RPL10 | RPL10 | RPL10 | 5428 | 0.04 | 0.38 | YES
55 | RPL24 | RPL24 | RPL24 | 5429 | 0.04 | 0.39 | YES
56 | RPS13 | RPS13 | RPS13 | 5577 | 0.038 | 0.39 | YES
57 | RPS11 | RPS11 | RPS11 | 5664 | 0.037 | 0.39 | YES
58 | RPL11 | RPL11 | RPL11 | 5717 | 0.036 | 0.4 | YES
59 | RPS21 | RPS21 | RPS21 | 5720 | 0.036 | 0.4 | YES
60 | RPL30 | RPL30 | RPL30 | 5769 | 0.035 | 0.41 | YES
61 | RPS16 | RPS16 | RPS16 | 5783 | 0.035 | 0.41 | YES
62 | RPS27A | RPS27A | RPS27A | 5809 | 0.035 | 0.42 | YES
63 | RPL27A | RPL27A | RPL27A | 5854 | 0.034 | 0.42 | YES
64 | RPS3 | RPS3 | RPS3 | 5858 | 0.034 | 0.43 | YES
65 | RPS6 | RPS6 | RPS6 | 5872 | 0.034 | 0.44 | YES
66 | RPS19 | RPS19 | RPS19 | 5890 | 0.034 | 0.44 | YES
67 | RPL15 | RPL15 | RPL15 | 5903 | 0.034 | 0.45 | YES
68 | FAU | FAU | FAU | 5975 | 0.033 | 0.45 | YES
69 | RPLP0 | RPLP0 | RPLP0 | 5994 | 0.033 | 0.45 | YES
70 | RPS29 | RPS29 | RPS29 | 6231 | 0.03 | 0.45 | YES
71 | RPL3 | RPL3 | RPL3 | 6266 | 0.029 | 0.45 | YES
72 | RPL6 | RPL6 | RPL6 | 6307 | 0.028 | 0.45 | YES
73 | RPL8 | RPL8 | RPL8 | 6322 | 0.028 | 0.46 | YES
74 | RPS8 | RPS8 | RPS8 | 6342 | 0.028 | 0.46 | YES
75 | PPP2R2A | PPP2R2A | PPP2R2A | 6399 | 0.027 | 0.46 | YES
76 | ETF1 | ETF1 | ETF1 | 6410 | 0.027 | 0.47 | YES
77 | RPS12 | RPS12 | RPS12 | 6519 | 0.026 | 0.47 | YES
78 | SMG6 | SMG6 | SMG6 | 6621 | 0.025 | 0.47 | YES
79 | RPL13A | RPL13A | RPL13A | 6646 | 0.024 | 0.47 | YES
80 | UBA52 | UBA52 | UBA52 | 6773 | 0.023 | 0.47 | YES
81 | RPL5 | RPL5 | RPL5 | 6803 | 0.022 | 0.47 | YES
82 | RPS3A | RPS3A | RPS3A | 6807 | 0.022 | 0.47 | YES
83 | MAGOH | MAGOH | MAGOH | 6858 | 0.022 | 0.47 | YES
84 | CASC3 | CASC3 | CASC3 | 7461 | 0.014 | 0.44 | NO
85 | RBM8A | RBM8A | RBM8A | 7521 | 0.013 | 0.44 | NO
86 | RPL7A | RPL7A | RPL7A | 7555 | 0.013 | 0.44 | NO
87 | SMG5 | SMG5 | SMG5 | 7595 | 0.012 | 0.44 | NO
88 | RPS25 | RPS25 | RPS25 | 7786 | 0.01 | 0.43 | NO
89 | RPL4 | RPL4 | RPL4 | 7983 | 0.0078 | 0.42 | NO
90 | RPL19 | RPL19 | RPL19 | 8017 | 0.0073 | 0.42 | NO
91 | RPL26L1 | RPL26L1 | RPL26L1 | 8488 | 0.0017 | 0.4 | NO
92 | PPP2CA | PPP2CA | PPP2CA | 8501 | 0.0016 | 0.4 | NO
93 | PPP2R1A | PPP2R1A | PPP2R1A | 9151 | -0.0063 | 0.36 | NO
94 | SMG1 | SMG1 | SMG1 | 9390 | -0.0092 | 0.35 | NO
95 | PABPC1 | PABPC1 | PABPC1 | 9502 | -0.011 | 0.34 | NO
96 | EIF4A3 | EIF4A3 | EIF4A3 | 9572 | -0.012 | 0.34 | NO
97 | SMG7 | SMG7 | SMG7 | 9673 | -0.013 | 0.34 | NO
98 | EIF4G1 | EIF4G1 | EIF4G1 | 9722 | -0.014 | 0.34 | NO
99 | RPL7 | RPL7 | RPL7 | 9782 | -0.014 | 0.34 | NO
100 | UPF2 | UPF2 | UPF2 | 10331 | -0.022 | 0.31 | NO
101 | NCBP1 | NCBP1 | NCBP1 | 10966 | -0.032 | 0.28 | NO
102 | RPS27 | RPS27 | RPS27 | 13088 | -0.088 | 0.17 | NO
103 | RPS4Y1 | RPS4Y1 | RPS4Y1 | 14512 | -0.16 | 0.12 | NO
104 | FAM153A | FAM153A | FAM153A | 15115 | -0.21 | 0.12 | NO

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

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

genes ES table in pathway: REACTOME TRANSLATION

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

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | RPSAP9 | RPSAP9 | RPSAP9 | 981 | 0.21 | -0.017 | YES
2 | RPS26 | RPS26 | RPS26 | 1570 | 0.16 | -0.021 | YES
3 | RPL9 | RPL9 | RPL9 | 1646 | 0.15 | 0.0037 | YES
4 | POLR2H | POLR2H | POLR2H | 1990 | 0.13 | 0.0093 | YES
5 | POLR2I | POLR2I | POLR2I | 2124 | 0.13 | 0.026 | YES
6 | RPL36A | RPL36A | RPL36A | 2319 | 0.12 | 0.037 | YES
7 | RPL21 | RPL21 | RPL21 | 2469 | 0.11 | 0.05 | YES
8 | RPL37 | RPL37 | RPL37 | 2989 | 0.092 | 0.037 | YES
9 | RPL36 | RPL36 | RPL36 | 3302 | 0.083 | 0.035 | YES
10 | RPL12 | RPL12 | RPL12 | 3427 | 0.079 | 0.043 | YES
11 | RPS15 | RPS15 | RPS15 | 3447 | 0.079 | 0.057 | YES
12 | RPL35A | RPL35A | RPL35A | 3459 | 0.079 | 0.071 | YES
13 | RPL39 | RPL39 | RPL39 | 3594 | 0.075 | 0.078 | YES
14 | RPL31 | RPL31 | RPL31 | 3739 | 0.072 | 0.083 | YES
15 | POLR2F | POLR2F | POLR2F | 3781 | 0.071 | 0.094 | YES
16 | RPS17 | RPS17 | RPS17 | 3843 | 0.069 | 0.1 | YES
17 | RPL29 | RPL29 | RPL29 | 3854 | 0.069 | 0.12 | YES
18 | RPL10A | RPL10A | RPL10A | 3899 | 0.068 | 0.13 | YES
19 | RPL23 | RPL23 | RPL23 | 3936 | 0.067 | 0.14 | YES
20 | RPS28 | RPS28 | RPS28 | 4069 | 0.064 | 0.14 | YES
21 | RPL28 | RPL28 | RPL28 | 4148 | 0.063 | 0.15 | YES
22 | RPL26 | RPL26 | RPL26 | 4178 | 0.062 | 0.16 | YES
23 | RPL13 | RPL13 | RPL13 | 4188 | 0.062 | 0.17 | YES
24 | RPS4X | RPS4X | RPS4X | 4284 | 0.06 | 0.18 | YES
25 | RPL18 | RPL18 | RPL18 | 4314 | 0.059 | 0.19 | YES
26 | RPS10 | RPS10 | RPS10 | 4324 | 0.059 | 0.2 | YES
27 | RPL41 | RPL41 | RPL41 | 4385 | 0.058 | 0.21 | YES
28 | RPL17 | RPL17 | RPL17 | 4475 | 0.056 | 0.21 | YES
29 | RPS15A | RPS15A | RPS15A | 4511 | 0.055 | 0.22 | YES
30 | RPL34 | RPL34 | RPL34 | 4515 | 0.055 | 0.23 | YES
31 | RPL32 | RPL32 | RPL32 | 4525 | 0.055 | 0.24 | YES
32 | RPL38 | RPL38 | RPL38 | 4542 | 0.055 | 0.25 | YES
33 | RPL22 | RPL22 | RPL22 | 4610 | 0.053 | 0.26 | YES
34 | RPL37A | RPL37A | RPL37A | 4626 | 0.053 | 0.26 | YES
35 | GTF2F1 | GTF2F1 | GTF2F1 | 4704 | 0.052 | 0.27 | YES
36 | RPL18A | RPL18A | RPL18A | 4743 | 0.051 | 0.28 | YES
37 | RPS14 | RPS14 | RPS14 | 4763 | 0.051 | 0.29 | YES
38 | RPS24 | RPS24 | RPS24 | 4772 | 0.051 | 0.3 | YES
39 | RPS20 | RPS20 | RPS20 | 4802 | 0.05 | 0.3 | YES
40 | RPL35 | RPL35 | RPL35 | 4891 | 0.048 | 0.31 | YES
41 | RPL27 | RPL27 | RPL27 | 4987 | 0.047 | 0.31 | YES
42 | RPLP2 | RPLP2 | RPLP2 | 4996 | 0.047 | 0.32 | YES
43 | RPS2 | RPS2 | RPS2 | 5025 | 0.046 | 0.33 | YES
44 | RPSA | RPSA | RPSA | 5045 | 0.046 | 0.34 | YES
45 | RPS23 | RPS23 | RPS23 | 5068 | 0.045 | 0.34 | YES
46 | RPS18 | RPS18 | RPS18 | 5225 | 0.043 | 0.34 | YES
47 | RPL23A | RPL23A | RPL23A | 5256 | 0.043 | 0.35 | YES
48 | RPS5 | RPS5 | RPS5 | 5278 | 0.042 | 0.36 | YES
49 | RPL14 | RPL14 | RPL14 | 5284 | 0.042 | 0.36 | YES
50 | RPS9 | RPS9 | RPS9 | 5288 | 0.042 | 0.37 | YES
51 | POLR2L | POLR2L | POLR2L | 5300 | 0.042 | 0.38 | YES
52 | RPLP1 | RPLP1 | RPLP1 | 5334 | 0.041 | 0.38 | YES
53 | RPS7 | RPS7 | RPS7 | 5348 | 0.041 | 0.39 | YES
54 | RPL10 | RPL10 | RPL10 | 5428 | 0.04 | 0.4 | YES
55 | RPL24 | RPL24 | RPL24 | 5429 | 0.04 | 0.4 | YES
56 | RPS13 | RPS13 | RPS13 | 5577 | 0.038 | 0.4 | YES
57 | RPS11 | RPS11 | RPS11 | 5664 | 0.037 | 0.4 | YES
58 | RPL11 | RPL11 | RPL11 | 5717 | 0.036 | 0.41 | YES
59 | RPS21 | RPS21 | RPS21 | 5720 | 0.036 | 0.41 | YES
60 | RPL30 | RPL30 | RPL30 | 5769 | 0.035 | 0.42 | YES
61 | POLR2A | POLR2A | POLR2A | 5779 | 0.035 | 0.42 | YES
62 | RPS16 | RPS16 | RPS16 | 5783 | 0.035 | 0.43 | YES
63 | RPS27A | RPS27A | RPS27A | 5809 | 0.035 | 0.44 | YES
64 | RPL27A | RPL27A | RPL27A | 5854 | 0.034 | 0.44 | YES
65 | RPS3 | RPS3 | RPS3 | 5858 | 0.034 | 0.45 | YES
66 | RPS6 | RPS6 | RPS6 | 5872 | 0.034 | 0.45 | YES
67 | RPS19 | RPS19 | RPS19 | 5890 | 0.034 | 0.46 | YES
68 | RPL15 | RPL15 | RPL15 | 5903 | 0.034 | 0.46 | YES
69 | FAU | FAU | FAU | 5975 | 0.033 | 0.46 | YES
70 | RPLP0 | RPLP0 | RPLP0 | 5994 | 0.033 | 0.47 | YES
71 | RPS29 | RPS29 | RPS29 | 6231 | 0.03 | 0.46 | YES
72 | RPL3 | RPL3 | RPL3 | 6266 | 0.029 | 0.47 | YES
73 | RPL6 | RPL6 | RPL6 | 6307 | 0.028 | 0.47 | YES
74 | RPL8 | RPL8 | RPL8 | 6322 | 0.028 | 0.47 | YES
75 | RPS8 | RPS8 | RPS8 | 6342 | 0.028 | 0.48 | YES
76 | RPS12 | RPS12 | RPS12 | 6519 | 0.026 | 0.47 | YES
77 | RPL13A | RPL13A | RPL13A | 6646 | 0.024 | 0.47 | YES
78 | POLR2D | POLR2D | POLR2D | 6756 | 0.023 | 0.47 | YES
79 | UBA52 | UBA52 | UBA52 | 6773 | 0.023 | 0.47 | YES
80 | POLR2J | POLR2J | POLR2J | 6798 | 0.022 | 0.47 | YES
81 | RPL5 | RPL5 | RPL5 | 6803 | 0.022 | 0.48 | YES
82 | RPS3A | RPS3A | RPS3A | 6807 | 0.022 | 0.48 | YES
83 | HSP90AA1 | HSP90AA1 | HSP90AA1 | 7134 | 0.018 | 0.47 | NO
84 | RPL7A | RPL7A | RPL7A | 7555 | 0.013 | 0.44 | NO
85 | POLR2C | POLR2C | POLR2C | 7765 | 0.01 | 0.44 | NO
86 | RPS25 | RPS25 | RPS25 | 7786 | 0.01 | 0.44 | NO
87 | POLR2G | POLR2G | POLR2G | 7844 | 0.0095 | 0.43 | NO
88 | RPL4 | RPL4 | RPL4 | 7983 | 0.0078 | 0.43 | NO
89 | RPL19 | RPL19 | RPL19 | 8017 | 0.0073 | 0.43 | NO
90 | GRSF1 | GRSF1 | GRSF1 | 8480 | 0.0018 | 0.4 | NO
91 | RPL26L1 | RPL26L1 | RPL26L1 | 8488 | 0.0017 | 0.4 | NO
92 | IPO5 | IPO5 | IPO5 | 8737 | -0.0013 | 0.39 | NO
93 | POLR2E | POLR2E | POLR2E | 9135 | -0.0061 | 0.36 | NO
94 | RPL7 | RPL7 | RPL7 | 9782 | -0.014 | 0.33 | NO
95 | GTF2F2 | GTF2F2 | GTF2F2 | 9819 | -0.015 | 0.33 | NO
96 | POLR2B | POLR2B | POLR2B | 10287 | -0.021 | 0.31 | NO
97 | POLR2K | POLR2K | POLR2K | 10313 | -0.021 | 0.31 | NO
98 | DNAJC3 | DNAJC3 | DNAJC3 | 11174 | -0.035 | 0.27 | NO
99 | RPS27 | RPS27 | RPS27 | 13088 | -0.088 | 0.17 | NO
100 | RPS4Y1 | RPS4Y1 | RPS4Y1 | 14512 | -0.16 | 0.12 | NO
101 | FAM153A | FAM153A | FAM153A | 15115 | -0.21 | 0.12 | NO

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

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

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

Table 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 | RPS26 | RPS26 | RPS26 | 1570 | 0.16 | -0.054 | YES
2 | RPL9 | RPL9 | RPL9 | 1646 | 0.15 | -0.023 | YES
3 | RPL36A | RPL36A | RPL36A | 2319 | 0.12 | -0.035 | YES
4 | RPL21 | RPL21 | RPL21 | 2469 | 0.11 | -0.017 | YES
5 | RPL22L1 | RPL22L1 | RPL22L1 | 2763 | 0.1 | -0.011 | YES
6 | RPL37 | RPL37 | RPL37 | 2989 | 0.092 | -0.0024 | YES
7 | RPL36 | RPL36 | RPL36 | 3302 | 0.083 | -0.0013 | YES
8 | RPL12 | RPL12 | RPL12 | 3427 | 0.079 | 0.01 | YES
9 | RPS15 | RPS15 | RPS15 | 3447 | 0.079 | 0.027 | YES
10 | RPL35A | RPL35A | RPL35A | 3459 | 0.079 | 0.045 | YES
11 | RPL39 | RPL39 | RPL39 | 3594 | 0.075 | 0.055 | YES
12 | RPL31 | RPL31 | RPL31 | 3739 | 0.072 | 0.063 | YES
13 | RPS17 | RPS17 | RPS17 | 3843 | 0.069 | 0.073 | YES
14 | RPL29 | RPL29 | RPL29 | 3854 | 0.069 | 0.089 | YES
15 | RPL10A | RPL10A | RPL10A | 3899 | 0.068 | 0.1 | YES
16 | RPL23 | RPL23 | RPL23 | 3936 | 0.067 | 0.12 | YES
17 | RPS28 | RPS28 | RPS28 | 4069 | 0.064 | 0.12 | YES
18 | RPL28 | RPL28 | RPL28 | 4148 | 0.063 | 0.13 | YES
19 | RPL26 | RPL26 | RPL26 | 4178 | 0.062 | 0.15 | YES
20 | RPL13 | RPL13 | RPL13 | 4188 | 0.062 | 0.16 | YES
21 | RPS4X | RPS4X | RPS4X | 4284 | 0.06 | 0.17 | YES
22 | RPL18 | RPL18 | RPL18 | 4314 | 0.059 | 0.18 | YES
23 | RPS10 | RPS10 | RPS10 | 4324 | 0.059 | 0.19 | YES
24 | RPL41 | RPL41 | RPL41 | 4385 | 0.058 | 0.2 | YES
25 | RPL17 | RPL17 | RPL17 | 4475 | 0.056 | 0.21 | YES
26 | RPS15A | RPS15A | RPS15A | 4511 | 0.055 | 0.22 | YES
27 | RPL34 | RPL34 | RPL34 | 4515 | 0.055 | 0.24 | YES
28 | RPL32 | RPL32 | RPL32 | 4525 | 0.055 | 0.25 | YES
29 | RPL38 | RPL38 | RPL38 | 4542 | 0.055 | 0.26 | YES
30 | RPL22 | RPL22 | RPL22 | 4610 | 0.053 | 0.27 | YES
31 | RPL37A | RPL37A | RPL37A | 4626 | 0.053 | 0.28 | YES
32 | RPL18A | RPL18A | RPL18A | 4743 | 0.051 | 0.28 | YES
33 | RPS24 | RPS24 | RPS24 | 4772 | 0.051 | 0.3 | YES
34 | RPS20 | RPS20 | RPS20 | 4802 | 0.05 | 0.3 | YES
35 | RPL35 | RPL35 | RPL35 | 4891 | 0.048 | 0.31 | YES
36 | RPL27 | RPL27 | RPL27 | 4987 | 0.047 | 0.32 | YES
37 | RPLP2 | RPLP2 | RPLP2 | 4996 | 0.047 | 0.33 | YES
38 | RPS2 | RPS2 | RPS2 | 5025 | 0.046 | 0.34 | YES
39 | RPSA | RPSA | RPSA | 5045 | 0.046 | 0.35 | YES
40 | RPS23 | RPS23 | RPS23 | 5068 | 0.045 | 0.36 | YES
41 | RPS18 | RPS18 | RPS18 | 5225 | 0.043 | 0.36 | YES
42 | RPL23A | RPL23A | RPL23A | 5256 | 0.043 | 0.36 | YES
43 | RPS5 | RPS5 | RPS5 | 5278 | 0.042 | 0.37 | YES
44 | RPL14 | RPL14 | RPL14 | 5284 | 0.042 | 0.38 | YES
45 | RPS9 | RPS9 | RPS9 | 5288 | 0.042 | 0.39 | YES
46 | RPLP1 | RPLP1 | RPLP1 | 5334 | 0.041 | 0.4 | YES
47 | RPS7 | RPS7 | RPS7 | 5348 | 0.041 | 0.41 | YES
48 | RPL10 | RPL10 | RPL10 | 5428 | 0.04 | 0.41 | YES
49 | RPL24 | RPL24 | RPL24 | 5429 | 0.04 | 0.42 | YES
50 | RPS13 | RPS13 | RPS13 | 5577 | 0.038 | 0.42 | YES
51 | RPS11 | RPS11 | RPS11 | 5664 | 0.037 | 0.43 | YES
52 | RPL11 | RPL11 | RPL11 | 5717 | 0.036 | 0.43 | YES
53 | RPS21 | RPS21 | RPS21 | 5720 | 0.036 | 0.44 | YES
54 | RPL30 | RPL30 | RPL30 | 5769 | 0.035 | 0.44 | YES
55 | RPS16 | RPS16 | RPS16 | 5783 | 0.035 | 0.45 | YES
56 | RPS27A | RPS27A | RPS27A | 5809 | 0.035 | 0.46 | YES
57 | RPL27A | RPL27A | RPL27A | 5854 | 0.034 | 0.46 | YES
58 | RPS3 | RPS3 | RPS3 | 5858 | 0.034 | 0.47 | YES
59 | RPS6 | RPS6 | RPS6 | 5872 | 0.034 | 0.48 | YES
60 | RPS19 | RPS19 | RPS19 | 5890 | 0.034 | 0.49 | YES
61 | RPL15 | RPL15 | RPL15 | 5903 | 0.034 | 0.49 | YES
62 | FAU | FAU | FAU | 5975 | 0.033 | 0.5 | YES
63 | RPLP0 | RPLP0 | RPLP0 | 5994 | 0.033 | 0.5 | YES
64 | RPS29 | RPS29 | RPS29 | 6231 | 0.03 | 0.5 | YES
65 | RPL3 | RPL3 | RPL3 | 6266 | 0.029 | 0.5 | YES
66 | RPL6 | RPL6 | RPL6 | 6307 | 0.028 | 0.51 | YES
67 | RPL8 | RPL8 | RPL8 | 6322 | 0.028 | 0.51 | YES
68 | RPL36AL | RPL36AL | RPL36AL | 6332 | 0.028 | 0.52 | YES
69 | RPS8 | RPS8 | RPS8 | 6342 | 0.028 | 0.52 | YES
70 | RPS12 | RPS12 | RPS12 | 6519 | 0.026 | 0.52 | YES
71 | RPL13A | RPL13A | RPL13A | 6646 | 0.024 | 0.52 | YES
72 | RSL24D1 | RSL24D1 | RSL24D1 | 6713 | 0.024 | 0.52 | YES
73 | UBA52 | UBA52 | UBA52 | 6773 | 0.023 | 0.52 | YES
74 | RPL5 | RPL5 | RPL5 | 6803 | 0.022 | 0.53 | YES
75 | RPS3A | RPS3A | RPS3A | 6807 | 0.022 | 0.53 | YES
76 | RPS27L | RPS27L | RPS27L | 6822 | 0.022 | 0.54 | YES
77 | RPL7A | RPL7A | RPL7A | 7555 | 0.013 | 0.5 | NO
78 | RPS25 | RPS25 | RPS25 | 7786 | 0.01 | 0.48 | NO
79 | RPL4 | RPL4 | RPL4 | 7983 | 0.0078 | 0.48 | NO
80 | RPL19 | RPL19 | RPL19 | 8017 | 0.0073 | 0.48 | NO
81 | RPL26L1 | RPL26L1 | RPL26L1 | 8488 | 0.0017 | 0.45 | NO
82 | MRPL13 | MRPL13 | MRPL13 | 9041 | -0.0048 | 0.42 | NO
83 | RPL7 | RPL7 | RPL7 | 9782 | -0.014 | 0.38 | NO
84 | RPS27 | RPS27 | RPS27 | 13088 | -0.088 | 0.2 | NO
85 | RPS4Y1 | RPS4Y1 | RPS4Y1 | 14512 | -0.16 | 0.16 | NO

Figure S53. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX.

Figure S54. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME FORMATION OF THE TERNARY COMPLEX AND SUBSEQUENTLY THE 43S COMPLEX, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

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

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

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | RPSAP9 | RPSAP9 | RPSAP9 | 981 | 0.21 | -0.024 | YES
2 | RPS26 | RPS26 | RPS26 | 1570 | 0.16 | -0.032 | YES
3 | RPL9 | RPL9 | RPL9 | 1646 | 0.15 | -0.012 | YES
4 | POLR2H | POLR2H | POLR2H | 1990 | 0.13 | -0.01 | YES
5 | POLR2I | POLR2I | POLR2I | 2124 | 0.13 | 0.0024 | YES
6 | RPL36A | RPL36A | RPL36A | 2319 | 0.12 | 0.01 | YES
7 | RPL21 | RPL21 | RPL21 | 2469 | 0.11 | 0.02 | YES
8 | CALR | CALR | CALR | 2851 | 0.096 | 0.013 | YES
9 | RPL37 | RPL37 | RPL37 | 2989 | 0.092 | 0.02 | YES
10 | RPL36 | RPL36 | RPL36 | 3302 | 0.083 | 0.015 | YES
11 | RPL12 | RPL12 | RPL12 | 3427 | 0.079 | 0.021 | YES
12 | RPS15 | RPS15 | RPS15 | 3447 | 0.079 | 0.032 | YES
13 | RPL35A | RPL35A | RPL35A | 3459 | 0.079 | 0.044 | YES
14 | RPL39 | RPL39 | RPL39 | 3594 | 0.075 | 0.049 | YES
15 | RPL31 | RPL31 | RPL31 | 3739 | 0.072 | 0.052 | YES
16 | POLR2F | POLR2F | POLR2F | 3781 | 0.071 | 0.061 | YES
17 | RPS17 | RPS17 | RPS17 | 3843 | 0.069 | 0.069 | YES
18 | RPL29 | RPL29 | RPL29 | 3854 | 0.069 | 0.079 | YES
19 | RPL10A | RPL10A | RPL10A | 3899 | 0.068 | 0.088 | YES
20 | RPL23 | RPL23 | RPL23 | 3936 | 0.067 | 0.096 | YES
21 | RPS28 | RPS28 | RPS28 | 4069 | 0.064 | 0.099 | YES
22 | RPL28 | RPL28 | RPL28 | 4148 | 0.063 | 0.1 | YES
23 | RPL26 | RPL26 | RPL26 | 4178 | 0.062 | 0.11 | YES
24 | RPL13 | RPL13 | RPL13 | 4188 | 0.062 | 0.12 | YES
25 | HSPA1B | HSPA1B | HSPA1B | 4224 | 0.061 | 0.13 | YES
26 | RPS4X | RPS4X | RPS4X | 4284 | 0.06 | 0.14 | YES
27 | RPL18 | RPL18 | RPL18 | 4314 | 0.059 | 0.14 | YES
28 | RPS10 | RPS10 | RPS10 | 4324 | 0.059 | 0.15 | YES
29 | RPL41 | RPL41 | RPL41 | 4385 | 0.058 | 0.16 | YES
30 | RPL17 | RPL17 | RPL17 | 4475 | 0.056 | 0.16 | YES
31 | RPS15A | RPS15A | RPS15A | 4511 | 0.055 | 0.17 | YES
32 | RPL34 | RPL34 | RPL34 | 4515 | 0.055 | 0.18 | YES
33 | RPL32 | RPL32 | RPL32 | 4525 | 0.055 | 0.19 | YES
34 | RPL38 | RPL38 | RPL38 | 4542 | 0.055 | 0.2 | YES
35 | RPL22 | RPL22 | RPL22 | 4610 | 0.053 | 0.2 | YES
36 | RPL37A | RPL37A | RPL37A | 4626 | 0.053 | 0.21 | YES
37 | GTF2F1 | GTF2F1 | GTF2F1 | 4704 | 0.052 | 0.21 | YES
38 | RPL18A | RPL18A | RPL18A | 4743 | 0.051 | 0.22 | YES
39 | RPS14 | RPS14 | RPS14 | 4763 | 0.051 | 0.22 | YES
40 | RPS24 | RPS24 | RPS24 | 4772 | 0.051 | 0.23 | YES
41 | RPS20 | RPS20 | RPS20 | 4802 | 0.05 | 0.24 | YES
42 | RPL35 | RPL35 | RPL35 | 4891 | 0.048 | 0.24 | YES
43 | RPL27 | RPL27 | RPL27 | 4987 | 0.047 | 0.24 | YES
44 | RPLP2 | RPLP2 | RPLP2 | 4996 | 0.047 | 0.25 | YES
45 | RPS2 | RPS2 | RPS2 | 5025 | 0.046 | 0.26 | YES
46 | RPSA | RPSA | RPSA | 5045 | 0.046 | 0.26 | YES
47 | RPS23 | RPS23 | RPS23 | 5068 | 0.045 | 0.27 | YES
48 | RPS18 | RPS18 | RPS18 | 5225 | 0.043 | 0.27 | YES
49 | RPL23A | RPL23A | RPL23A | 5256 | 0.043 | 0.27 | YES
50 | RPS5 | RPS5 | RPS5 | 5278 | 0.042 | 0.28 | YES
51 | RPL14 | RPL14 | RPL14 | 5284 | 0.042 | 0.28 | YES
52 | AAAS | AAAS | AAAS | 5285 | 0.042 | 0.29 | YES
53 | RPS9 | RPS9 | RPS9 | 5288 | 0.042 | 0.3 | YES
54 | POLR2L | POLR2L | POLR2L | 5300 | 0.042 | 0.3 | YES
55 | RPLP1 | RPLP1 | RPLP1 | 5334 | 0.041 | 0.31 | YES
56 | RPS7 | RPS7 | RPS7 | 5348 | 0.041 | 0.32 | YES
57 | RPL10 | RPL10 | RPL10 | 5428 | 0.04 | 0.32 | YES
58 | RPL24 | RPL24 | RPL24 | 5429 | 0.04 | 0.32 | YES
59 | RPS13 | RPS13 | RPS13 | 5577 | 0.038 | 0.32 | YES
60 | RPS11 | RPS11 | RPS11 | 5664 | 0.037 | 0.32 | YES
61 | RPL11 | RPL11 | RPL11 | 5717 | 0.036 | 0.32 | YES
62 | RPS21 | RPS21 | RPS21 | 5720 | 0.036 | 0.33 | YES
63 | RPL30 | RPL30 | RPL30 | 5769 | 0.035 | 0.33 | YES
64 | POLR2A | POLR2A | POLR2A | 5779 | 0.035 | 0.34 | YES
65 | POM121 | POM121 | POM121 | 5781 | 0.035 | 0.34 | YES
66 | RPS16 | RPS16 | RPS16 | 5783 | 0.035 | 0.35 | YES
67 | RPS27A | RPS27A | RPS27A | 5809 | 0.035 | 0.35 | YES
68 | RPL27A | RPL27A | RPL27A | 5854 | 0.034 | 0.36 | YES
69 | RPS3 | RPS3 | RPS3 | 5858 | 0.034 | 0.36 | YES
70 | RPS6 | RPS6 | RPS6 | 5872 | 0.034 | 0.37 | YES
71 | RPS19 | RPS19 | RPS19 | 5890 | 0.034 | 0.37 | YES
72 | RPL15 | RPL15 | RPL15 | 5903 | 0.034 | 0.38 | YES
73 | FAU | FAU | FAU | 5975 | 0.033 | 0.38 | YES
74 | RPLP0 | RPLP0 | RPLP0 | 5994 | 0.033 | 0.38 | YES
75 | RPS29 | RPS29 | RPS29 | 6231 | 0.03 | 0.37 | YES
76 | RPL3 | RPL3 | RPL3 | 6266 | 0.029 | 0.38 | YES
77 | RPL6 | RPL6 | RPL6 | 6307 | 0.028 | 0.38 | YES
78 | RPL8 | RPL8 | RPL8 | 6322 | 0.028 | 0.38 | YES
79 | RPS8 | RPS8 | RPS8 | 6342 | 0.028 | 0.38 | YES
80 | RPS12 | RPS12 | RPS12 | 6519 | 0.026 | 0.38 | YES
81 | RAN | RAN | RAN | 6539 | 0.026 | 0.38 | YES
82 | NUP188 | NUP188 | NUP188 | 6590 | 0.025 | 0.38 | YES
83 | RPL13A | RPL13A | RPL13A | 6646 | 0.024 | 0.38 | YES
84 | RAE1 | RAE1 | RAE1 | 6726 | 0.023 | 0.38 | YES
85 | POLR2D | POLR2D | POLR2D | 6756 | 0.023 | 0.38 | YES
86 | UBA52 | UBA52 | UBA52 | 6773 | 0.023 | 0.39 | YES
87 | SEH1L | SEH1L | SEH1L | 6777 | 0.023 | 0.39 | YES
88 | NUP214 | NUP214 | NUP214 | 6792 | 0.023 | 0.39 | YES
89 | POLR2J | POLR2J | POLR2J | 6798 | 0.022 | 0.4 | YES
90 | RPL5 | RPL5 | RPL5 | 6803 | 0.022 | 0.4 | YES
91 | RPS3A | RPS3A | RPS3A | 6807 | 0.022 | 0.4 | YES
92 | NUP85 | NUP85 | NUP85 | 7033 | 0.02 | 0.39 | NO
93 | HSP90AA1 | HSP90AA1 | HSP90AA1 | 7134 | 0.018 | 0.39 | NO
94 | RPL7A | RPL7A | RPL7A | 7555 | 0.013 | 0.37 | NO
95 | NUP107 | NUP107 | NUP107 | 7609 | 0.012 | 0.37 | NO
96 | POLR2C | POLR2C | POLR2C | 7765 | 0.01 | 0.36 | NO
97 | NUP54 | NUP54 | NUP54 | 7773 | 0.01 | 0.36 | NO
98 | RPS25 | RPS25 | RPS25 | 7786 | 0.01 | 0.36 | NO
99 | NUP153 | NUP153 | NUP153 | 7800 | 0.01 | 0.36 | NO
100 | POLR2G | POLR2G | POLR2G | 7844 | 0.0095 | 0.36 | NO
101 | XPO1 | XPO1 | XPO1 | 7854 | 0.0093 | 0.36 | NO
102 | NUP35 | NUP35 | NUP35 | 7961 | 0.008 | 0.36 | NO
103 | RPL4 | RPL4 | RPL4 | 7983 | 0.0078 | 0.36 | NO
104 | RPL19 | RPL19 | RPL19 | 8017 | 0.0073 | 0.36 | NO
105 | NUPL2 | NUPL2 | NUPL2 | 8384 | 0.003 | 0.34 | NO
106 | GRSF1 | GRSF1 | GRSF1 | 8480 | 0.0018 | 0.33 | NO
107 | RPL26L1 | RPL26L1 | RPL26L1 | 8488 | 0.0017 | 0.33 | NO
108 | IPO5 | IPO5 | IPO5 | 8737 | -0.0013 | 0.32 | NO
109 | NUP88 | NUP88 | NUP88 | 9031 | -0.0047 | 0.3 | NO
110 | POLR2E | POLR2E | POLR2E | 9135 | -0.0061 | 0.3 | NO
111 | NUP43 | NUP43 | NUP43 | 9251 | -0.0074 | 0.29 | NO
112 | NUP62 | NUP62 | NUP62 | 9261 | -0.0076 | 0.29 | NO
113 | CLTA | CLTA | CLTA | 9539 | -0.011 | 0.28 | NO
114 | KPNB1 | KPNB1 | KPNB1 | 9551 | -0.011 | 0.28 | NO
115 | CANX | CANX | CANX | 9634 | -0.012 | 0.28 | NO
116 | RPL7 | RPL7 | RPL7 | 9782 | -0.014 | 0.27 | NO
117 | GTF2F2 | GTF2F2 | GTF2F2 | 9819 | -0.015 | 0.27 | NO
118 | NUP93 | NUP93 | NUP93 | 9857 | -0.015 | 0.27 | NO
119 | NUP205 | NUP205 | NUP205 | 9905 | -0.016 | 0.27 | NO
120 | NUP133 | NUP133 | NUP133 | 10258 | -0.021 | 0.25 | NO
121 | POLR2B | POLR2B | POLR2B | 10287 | -0.021 | 0.25 | NO
122 | POLR2K | POLR2K | POLR2K | 10313 | -0.021 | 0.26 | NO
123 | NUP37 | NUP37 | NUP37 | 10623 | -0.026 | 0.24 | NO
124 | TPR | TPR | TPR | 10637 | -0.027 | 0.25 | NO
125 | DNAJC3 | DNAJC3 | DNAJC3 | 11174 | -0.035 | 0.22 | NO
126 | KPNA1 | KPNA1 | KPNA1 | 11259 | -0.037 | 0.22 | NO
127 | NUP210 | NUP210 | NUP210 | 11480 | -0.041 | 0.22 | NO
128 | RANBP2 | RANBP2 | RANBP2 | 11779 | -0.048 | 0.2 | NO
129 | NUP50 | NUP50 | NUP50 | 11823 | -0.048 | 0.21 | NO
130 | NUPL1 | NUPL1 | NUPL1 | 12304 | -0.061 | 0.19 | NO
131 | NUP155 | NUP155 | NUP155 | 12495 | -0.066 | 0.19 | NO
132 | CLTC | CLTC | CLTC | 12602 | -0.07 | 0.2 | NO
133 | RPS27 | RPS27 | RPS27 | 13088 | -0.088 | 0.18 | NO
134 | RPS4Y1 | RPS4Y1 | RPS4Y1 | 14512 | -0.16 | 0.13 | NO
135 | FAM153A | FAM153A | FAM153A | 15115 | -0.21 | 0.12 | NO

Figure S55. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE.

Figure S56. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME SRP DEPENDENT COTRANSLATIONAL PROTEIN TARGETING TO MEMBRANE, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

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

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

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | RPSAP9 | RPSAP9 | RPSAP9 | 981 | 0.21 | -0.022 | YES
2 | RPS26 | RPS26 | RPS26 | 1570 | 0.16 | -0.03 | YES
3 | RPL9 | RPL9 | RPL9 | 1646 | 0.15 | -0.0089 | YES
4 | RPL36A | RPL36A | RPL36A | 2319 | 0.12 | -0.028 | YES
5 | RPL21 | RPL21 | RPL21 | 2469 | 0.11 | -0.018 | YES
6 | RPL37 | RPL37 | RPL37 | 2989 | 0.092 | -0.033 | YES
7 | GSPT2 | GSPT2 | GSPT2 | 3108 | 0.088 | -0.025 | YES
8 | RPL36 | RPL36 | RPL36 | 3302 | 0.083 | -0.023 | YES
9 | RPL12 | RPL12 | RPL12 | 3427 | 0.079 | -0.016 | YES
10 | RPS15 | RPS15 | RPS15 | 3447 | 0.079 | -0.0044 | YES
11 | RPL35A | RPL35A | RPL35A | 3459 | 0.079 | 0.0082 | YES
12 | RPL39 | RPL39 | RPL39 | 3594 | 0.075 | 0.013 | YES
13 | RPL31 | RPL31 | RPL31 | 3739 | 0.072 | 0.017 | YES
14 | RPS17 | RPS17 | RPS17 | 3843 | 0.069 | 0.022 | YES
15 | RPL29 | RPL29 | RPL29 | 3854 | 0.069 | 0.033 | YES
16 | RPL10A | RPL10A | RPL10A | 3899 | 0.068 | 0.042 | YES
17 | RPL23 | RPL23 | RPL23 | 3936 | 0.067 | 0.051 | YES
18 | RPS28 | RPS28 | RPS28 | 4069 | 0.064 | 0.054 | YES
19 | SEC61A2 | SEC61A2 | SEC61A2 | 4075 | 0.064 | 0.065 | YES
20 | RPL28 | RPL28 | RPL28 | 4148 | 0.063 | 0.071 | YES
21 | RPL26 | RPL26 | RPL26 | 4178 | 0.062 | 0.08 | YES
22 | RPL13 | RPL13 | RPL13 | 4188 | 0.062 | 0.09 | YES
23 | EIF4EBP1 | EIF4EBP1 | EIF4EBP1 | 4232 | 0.061 | 0.097 | YES
24 | RPS4X | RPS4X | RPS4X | 4284 | 0.06 | 0.1 | YES
25 | RPL18 | RPL18 | RPL18 | 4314 | 0.059 | 0.11 | YES
26 | RPS10 | RPS10 | RPS10 | 4324 | 0.059 | 0.12 | YES
27 | RPL41 | RPL41 | RPL41 | 4385 | 0.058 | 0.13 | YES
28 | RPL17 | RPL17 | RPL17 | 4475 | 0.056 | 0.13 | YES
29 | SRPRB | SRPRB | SRPRB | 4478 | 0.056 | 0.14 | YES
30 | RPS15A | RPS15A | RPS15A | 4511 | 0.055 | 0.15 | YES
31 | RPL34 | RPL34 | RPL34 | 4515 | 0.055 | 0.16 | YES
32 | RPL32 | RPL32 | RPL32 | 4525 | 0.055 | 0.17 | YES
33 | RPL38 | RPL38 | RPL38 | 4542 | 0.055 | 0.18 | YES
34 | EEF1B2 | EEF1B2 | EEF1B2 | 4595 | 0.054 | 0.18 | YES
35 | RPL22 | RPL22 | RPL22 | 4610 | 0.053 | 0.19 | YES
36 | RPL37A | RPL37A | RPL37A | 4626 | 0.053 | 0.2 | YES
37 | EIF2B4 | EIF2B4 | EIF2B4 | 4668 | 0.052 | 0.2 | YES
38 | EIF4A2 | EIF4A2 | EIF4A2 | 4714 | 0.052 | 0.21 | YES
39 | RPL18A | RPL18A | RPL18A | 4743 | 0.051 | 0.22 | YES
40 | RPS14 | RPS14 | RPS14 | 4763 | 0.051 | 0.22 | YES
41 | RPS24 | RPS24 | RPS24 | 4772 | 0.051 | 0.23 | YES
42 | RPS20 | RPS20 | RPS20 | 4802 | 0.05 | 0.24 | YES
43 | RPL35 | RPL35 | RPL35 | 4891 | 0.048 | 0.24 | YES
44 | RPL27 | RPL27 | RPL27 | 4987 | 0.047 | 0.24 | YES
45 | RPLP2 | RPLP2 | RPLP2 | 4996 | 0.047 | 0.25 | YES
46 | RPS2 | RPS2 | RPS2 | 5025 | 0.046 | 0.26 | YES
47 | RPSA | RPSA | RPSA | 5045 | 0.046 | 0.26 | YES
48 | RPS23 | RPS23 | RPS23 | 5068 | 0.045 | 0.27 | YES
49 | RPS18 | RPS18 | RPS18 | 5225 | 0.043 | 0.27 | YES
50 | RPL23A | RPL23A | RPL23A | 5256 | 0.043 | 0.27 | YES
51 | RPS5 | RPS5 | RPS5 | 5278 | 0.042 | 0.28 | YES
52 | RPL14 | RPL14 | RPL14 | 5284 | 0.042 | 0.29 | YES
53 | RPS9 | RPS9 | RPS9 | 5288 | 0.042 | 0.29 | YES
54 | RPLP1 | RPLP1 | RPLP1 | 5334 | 0.041 | 0.3 | YES
55 | RPS7 | RPS7 | RPS7 | 5348 | 0.041 | 0.3 | YES
56 | RPL10 | RPL10 | RPL10 | 5428 | 0.04 | 0.31 | YES
57 | RPL24 | RPL24 | RPL24 | 5429 | 0.04 | 0.31 | YES
58 | RPS13 | RPS13 | RPS13 | 5577 | 0.038 | 0.31 | YES
59 | RPS11 | RPS11 | RPS11 | 5664 | 0.037 | 0.31 | YES
60 | RPL11 | RPL11 | RPL11 | 5717 | 0.036 | 0.32 | YES
61 | RPS21 | RPS21 | RPS21 | 5720 | 0.036 | 0.32 | YES
62 | RPL30 | RPL30 | RPL30 | 5769 | 0.035 | 0.32 | YES
63 | RPS16 | RPS16 | RPS16 | 5783 | 0.035 | 0.33 | YES
64 | RPS27A | RPS27A | RPS27A | 5809 | 0.035 | 0.33 | YES
65 | EIF5 | EIF5 | EIF5 | 5812 | 0.035 | 0.34 | YES
66 | RPL27A | RPL27A | RPL27A | 5854 | 0.034 | 0.34 | YES
67 | RPS3 | RPS3 | RPS3 | 5858 | 0.034 | 0.35 | YES
68 | RPS6 | RPS6 | RPS6 | 5872 | 0.034 | 0.35 | YES
69 | SEC61G | SEC61G | SEC61G | 5882 | 0.034 | 0.36 | YES
70 | EIF3B | EIF3B | EIF3B | 5887 | 0.034 | 0.36 | YES
71 | RPS19 | RPS19 | RPS19 | 5890 | 0.034 | 0.37 | YES
72 | RPL15 | RPL15 | RPL15 | 5903 | 0.034 | 0.38 | YES
73 | FAU | FAU | FAU | 5975 | 0.033 | 0.38 | YES
74 | RPLP0 | RPLP0 | RPLP0 | 5994 | 0.033 | 0.38 | YES
75 | RPS29 | RPS29 | RPS29 | 6231 | 0.03 | 0.37 | YES
76 | SSR4 | SSR4 | SSR4 | 6264 | 0.029 | 0.38 | YES
77 | RPL3 | RPL3 | RPL3 | 6266 | 0.029 | 0.38 | YES
78 | RPL6 | RPL6 | RPL6 | 6307 | 0.028 | 0.38 | YES
79 | RPL8 | RPL8 | RPL8 | 6322 | 0.028 | 0.39 | YES
80 | SEC61B | SEC61B | SEC61B | 6339 | 0.028 | 0.39 | YES
81 | RPS8 | RPS8 | RPS8 | 6342 | 0.028 | 0.39 | YES
82 | ETF1 | ETF1 | ETF1 | 6410 | 0.027 | 0.4 | YES
83 | SPCS1 | SPCS1 | SPCS1 | 6431 | 0.027 | 0.4 | YES
84 | RPS12 | RPS12 | RPS12 | 6519 | 0.026 | 0.4 | YES
85 | EIF2S3 | EIF2S3 | EIF2S3 | 6596 | 0.025 | 0.4 | YES
86 | RPL13A | RPL13A | RPL13A | 6646 | 0.024 | 0.4 | YES
87 | EIF4A1 | EIF4A1 | EIF4A1 | 6651 | 0.024 | 0.4 | YES
88 | UBA52 | UBA52 | UBA52 | 6773 | 0.023 | 0.4 | YES
89 | EEF2 | EEF2 | EEF2 | 6781 | 0.023 | 0.4 | YES
90 | RPL5 | RPL5 | RPL5 | 6803 | 0.022 | 0.4 | YES
91 | RPS3A | RPS3A | RPS3A | 6807 | 0.022 | 0.41 | YES
92 | EIF2B5 | EIF2B5 | EIF2B5 | 7000 | 0.02 | 0.4 | NO
93 | SSR2 | SSR2 | SSR2 | 7043 | 0.02 | 0.4 | NO
94 | EIF3E | EIF3E | EIF3E | 7047 | 0.02 | 0.4 | NO
95 | EIF3I | EIF3I | EIF3I | 7060 | 0.019 | 0.41 | NO
96 | EIF1AX | EIF1AX | EIF1AX | 7314 | 0.016 | 0.4 | NO
97 | EEF1D | EEF1D | EEF1D | 7412 | 0.014 | 0.39 | NO
98 | SRP14 | SRP14 | SRP14 | 7519 | 0.013 | 0.39 | NO
99 | RPL7A | RPL7A | RPL7A | 7555 | 0.013 | 0.39 | NO
100 | EIF3J | EIF3J | EIF3J | 7564 | 0.013 | 0.39 | NO
101 | EIF4E | EIF4E | EIF4E | 7590 | 0.012 | 0.39 | NO
102 | EIF3F | EIF3F | EIF3F | 7677 | 0.012 | 0.39 | NO
103 | EIF3H | EIF3H | EIF3H | 7733 | 0.011 | 0.39 | NO
104 | EIF3G | EIF3G | EIF3G | 7762 | 0.01 | 0.39 | NO
105 | RPS25 | RPS25 | RPS25 | 7786 | 0.01 | 0.39 | NO
106 | EEF1A1 | EEF1A1 | EEF1A1 | 7810 | 0.0099 | 0.39 | NO
107 | EEF1G | EEF1G | EEF1G | 7916 | 0.0086 | 0.38 | NO
108 | RPL4 | RPL4 | RPL4 | 7983 | 0.0078 | 0.38 | NO
109 | RPL19 | RPL19 | RPL19 | 8017 | 0.0073 | 0.38 | NO
110 | EIF4H | EIF4H | EIF4H | 8270 | 0.0044 | 0.36 | NO
111 | EIF2B2 | EIF2B2 | EIF2B2 | 8318 | 0.0038 | 0.36 | NO
112 | SEC11C | SEC11C | SEC11C | 8373 | 0.0032 | 0.36 | NO
113 | RPL26L1 | RPL26L1 | RPL26L1 | 8488 | 0.0017 | 0.35 | NO
114 | RPN2 | RPN2 | RPN2 | 8505 | 0.0015 | 0.35 | NO
115 | EIF3C | EIF3C | EIF3C | 8519 | 0.0014 | 0.35 | NO
116 | SEC61A1 | SEC61A1 | SEC61A1 | 8673 | -0.00061 | 0.34 | NO
117 | EIF2B3 | EIF2B3 | EIF2B3 | 8726 | -0.0012 | 0.34 | NO
118 | DDOST | DDOST | DDOST | 8762 | -0.0016 | 0.34 | NO
119 | EIF3A | EIF3A | EIF3A | 8812 | -0.0022 | 0.34 | NO
120 | EIF3K | EIF3K | EIF3K | 8873 | -0.0029 | 0.33 | NO
121 | SRP19 | SRP19 | SRP19 | 8951 | -0.0037 | 0.33 | NO
122 | EIF2B1 | EIF2B1 | EIF2B1 | 9012 | -0.0044 | 0.33 | NO
123 | EIF5B | EIF5B | EIF5B | 9099 | -0.0056 | 0.32 | NO
124 | SRP72 | SRP72 | SRP72 | 9228 | -0.0072 | 0.32 | NO
125 | EIF4B | EIF4B | EIF4B | 9319 | -0.0082 | 0.31 | NO
126 | TRAM1 | TRAM1 | TRAM1 | 9397 | -0.0092 | 0.31 | NO
127 | SRP68 | SRP68 | SRP68 | 9450 | -0.01 | 0.31 | NO
128 | PABPC1 | PABPC1 | PABPC1 | 9502 | -0.011 | 0.31 | NO
129 | SRP9 | SRP9 | SRP9 | 9640 | -0.012 | 0.3 | NO
130 | EIF4G1 | EIF4G1 | EIF4G1 | 9722 | -0.014 | 0.3 | NO
131 | EIF3D | EIF3D | EIF3D | 9728 | -0.014 | 0.3 | NO
132 | RPL7 | RPL7 | RPL7 | 9782 | -0.014 | 0.3 | NO
133 | RPN1 | RPN1 | RPN1 | 9967 | -0.017 | 0.29 | NO
134 | SRPR | SRPR | SRPR | 9999 | -0.017 | 0.29 | NO
135 | EIF2S2 | EIF2S2 | EIF2S2 | 10207 | -0.02 | 0.28 | NO
136 | SSR3 | SSR3 | SSR3 | 10486 | -0.024 | 0.27 | NO
137 | SPCS3 | SPCS3 | SPCS3 | 10664 | -0.027 | 0.27 | NO
138 | LOC653566 | LOC653566 | LOC653566 | 10887 | -0.03 | 0.26 | NO
139 | SPCS2 | SPCS2 | SPCS2 | 10943 | -0.031 | 0.26 | NO
140 | SEC11A | SEC11A | SEC11A | 11625 | -0.044 | 0.23 | NO
141 | SRP54 | SRP54 | SRP54 | 11644 | -0.045 | 0.24 | NO
142 | EIF2S1 | EIF2S1 | EIF2S1 | 11703 | -0.046 | 0.24 | NO
143 | SSR1 | SSR1 | SSR1 | 11875 | -0.049 | 0.24 | NO
144 | RPS27 | RPS27 | RPS27 | 13088 | -0.088 | 0.18 | NO
145 | RPS4Y1 | RPS4Y1 | RPS4Y1 | 14512 | -0.16 | 0.12 | NO
146 | FAM153A | FAM153A | FAM153A | 15115 | -0.21 | 0.12 | NO

Figure S57. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S.

Figure S58. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME ACTIVATION OF THE MRNA UPON BINDING OF THE CAP BINDING COMPLEX AND EIFS AND SUBSEQUENT BINDING TO 43S, this volcano plot shows how much they are up/down-regulated and significant. The significance was calculated by empirical bayesian fit

genes ES table in pathway: REACTOME PEPTIDE CHAIN ELONGATION

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

Rank | GENE | SYMBOL | DESC | LIST.LOC | S2N | RES | CORE_ENRICHMENT
--- | --- | --- | --- | --- | --- | --- | ---
1 | RPSAP9 | RPSAP9 | RPSAP9 | 981 | 0.21 | -0.015 | YES
2 | RPS26 | RPS26 | RPS26 | 1570 | 0.16 | -0.017 | YES
3 | RPL9 | RPL9 | RPL9 | 1646 | 0.15 | 0.0092 | YES
4 | RPL36A | RPL36A | RPL36A | 2319 | 0.12 | -0.006 | YES
5 | RPL21 | RPL21 | RPL21 | 2469 | 0.11 | 0.0078 | YES
6 | RPL37 | RPL37 | RPL37 | 2989 | 0.092 | -0.0038 | YES
7 | RPL36 | RPL36 | RPL36 | 3302 | 0.083 | -0.0052 | YES
8 | RPL12 | RPL12 | RPL12 | 3427 | 0.079 | 0.0036 | YES
9 | RPS15 | RPS15 | RPS15 | 3447 | 0.079 | 0.018 | YES
10 | RPL35A | RPL35A | RPL35A | 3459 | 0.079 | 0.034 | YES
11 | RPL39 | RPL39 | RPL39 | 3594 | 0.075 | 0.041 | YES
12 | RPL31 | RPL31 | RPL31 | 3739 | 0.072 | 0.047 | YES
13 | RPS17 | RPS17 | RPS17 | 3843 | 0.069 | 0.055 | YES
14 | RPL29 | RPL29 | RPL29 | 3854 | 0.069 | 0.069 | YES
15 | RPL10A | RPL10A | RPL10A | 3899 | 0.068 | 0.08 | YES
16 | RPL23 | RPL23 | RPL23 | 3936 | 0.067 | 0.091 | YES
17 | RPS28 | RPS28 | RPS28 | 4069 | 0.064 | 0.096 | YES
18 | RPL28 | RPL28 | RPL28 | 4148 | 0.063 | 0.1 | YES
19 | RPL26 | RPL26 | RPL26 | 4178 | 0.062 | 0.12 | YES
20 | RPL13 | RPL13 | RPL13 | 4188 | 0.062 | 0.13 | YES
21 | RPS4X | RPS4X | RPS4X | 4284 | 0.06 | 0.13 | YES
22 | RPL18 | RPL18 | RPL18 | 4314 | 0.059 | 0.14 | YES
23 | RPS10 | RPS10 | RPS10 | 4324 | 0.059 | 0.16 | YES
24 | RPL41 | RPL41 | RPL41 | 4385 | 0.058 | 0.16 | YES
25 | RPL17 | RPL17 | RPL17 | 4475 | 0.056 | 0.17 | YES
26 | RPS15A | RPS15A | RPS15A | 4511 | 0.055 | 0.18 | YES
27 | RPL34 | RPL34 | RPL34 | 4515 | 0.055 | 0.19 | YES
28 | RPL32 | RPL32 | RPL32 | 4525 | 0.055 | 0.2 | YES
29 | RPL38 | RPL38 | RPL38 | 4542 | 0.055 | 0.21 | YES
30 | RPL22 | RPL22 | RPL22 | 4610 | 0.053 | 0.22 | YES
31 | RPL37A | RPL37A | RPL37A | 4626 | 0.053 | 0.23 | YES
32 | EIF4A2 | EIF4A2 | EIF4A2 | 4714 | 0.052 | 0.23 | YES
33 | RPL18A | RPL18A | RPL18A | 4743 | 0.051 | 0.24 | YES
34 | RPS14 | RPS14 | RPS14 | 4763 | 0.051 | 0.25 | YES
35 | RPS24 | RPS24 | RPS24 | 4772 | 0.051 | 0.26 | YES
36 | RPS20 | RPS20 | RPS20 | 4802 | 0.05 | 0.27 | YES
37 | RPL35 | RPL35 | RPL35 | 4891 | 0.048 | 0.27 | YES
38 | RPL27 | RPL27 | RPL27 | 4987 | 0.047 | 0.28 | YES
39 | RPLP2 | RPLP2 | RPLP2 | 4996 | 0.047 | 0.29 | YES
40 | RPS2 | RPS2 | RPS2 | 5025 | 0.046 | 0.3 | YES
41 | RPSA | RPSA | RPSA | 5045 | 0.046 | 0.3 | YES
42 | RPS23 | RPS23 | RPS23 | 5068 | 0.045 | 0.31 | YES
43 | RPS18 | RPS18 | RPS18 | 5225 | 0.043 | 0.31 | YES
44 | RPL23A | RPL23A | RPL23A | 5256 | 0.043 | 0.32 | YES
45 | RPS5 | RPS5 | RPS5 | 5278 | 0.042 | 0.32 | YES
46 | RPL14 | RPL14 | RPL14 | 5284 | 0.042 | 0.33 | YES
47 | RPS9 | RPS9 | RPS9 | 5288 | 0.042 | 0.34 | YES
48 | RPLP1 | RPLP1 | RPLP1 | 5334 | 0.041 | 0.35 | YES
49 | RPS7 | RPS7 | RPS7 | 5348 | 0.041 | 0.36 | YES
50 | RPL10 | RPL10 | RPL10 | 5428 | 0.04 | 0.36 | YES
51 | RPL24 | RPL24 | RPL24 | 5429 | 0.04 | 0.37 | YES
52 | RPS13 | RPS13 | RPS13 | 5577 | 0.038 | 0.36 | YES
53 | RPS11 | RPS11 | RPS11 | 5664 | 0.037 | 0.37 | YES
54 | RPL11 | RPL11 | RPL11 | 5717 | 0.036 | 0.37 | YES
55 | RPS21 | RPS21 | RPS21 | 5720 | 0.036 | 0.38 | YES
56 | RPL30 | RPL30 | RPL30 | 5769 | 0.035 | 0.38 | YES
57 | RPS16 | RPS16 | RPS16 | 5783 | 0.035 | 0.39 | YES
58 | RPS27A | RPS27A | RPS27A | 5809 | 0.035 | 0.4 | YES
59 | RPL27A | RPL27A | RPL27A | 5854 | 0.034 | 0.4 | YES
60 | RPS3 | RPS3 | RPS3 | 5858 | 0.034 | 0.41 | YES
61 | RPS6 | RPS6 | RPS6 | 5872 | 0.034 | 0.41 | YES
62 | EIF3B | EIF3B | EIF3B | 5887 | 0.034 | 0.42 | YES
63 | RPS19 | RPS19 | RPS19 | 5890 | 0.034 | 0.43 | YES
64 | RPL15 | RPL15 | RPL15 | 5903 | 0.034 | 0.43 | YES
65 | FAU | FAU | FAU | 5975 | 0.033 | 0.43 | YES
66 | RPLP0 | RPLP0 | RPLP0 | 5994 | 0.033 | 0.44 | YES
67 | RPS29 | RPS29 | RPS29 | 6231 | 0.03 | 0.43 | YES
68 | RPL3 | RPL3 | RPL3 | 6266 | 0.029 | 0.44 | YES
69 | RPL6 | RPL6 | RPL6 | 6307 | 0.028 | 0.44 | YES
70 | RPL8 | RPL8 | RPL8 | 6322 | 0.028 | 0.44 | YES
71 | RPS8 | RPS8 | RPS8 | 6342 | 0.028 | 0.45 | YES
72 | RPS12 | RPS12 | RPS12 | 6519 | 0.026 | 0.44 | YES
73 | EIF2S3 | EIF2S3 | EIF2S3 | 6596 | 0.025 | 0.44 | YES
74 | RPL13A | RPL13A | RPL13A | 6646 | 0.024 | 0.45 | YES
75 | EIF4A1 | EIF4A1 | EIF4A1 | 6651 | 0.024 | 0.45 | YES
76 | UBA52 | UBA52 | UBA52 | 6773 | 0.023 | 0.45 | YES
77 | RPL5 | RPL5 | RPL5 | 6803 | 0.022 | 0.45 | YES
78 | RPS3A | RPS3A | RPS3A | 6807 | 0.022 | 0.46 | YES
79 | EIF3E | EIF3E | EIF3E | 7047 | 0.02 | 0.45 | NO
80 | EIF3I | EIF3I | EIF3I | 7060 | 0.019 | 0.45 | NO
81 | EIF1AX | EIF1AX | EIF1AX | 7314 | 0.016 | 0.44 | NO
82 | RPL7A | RPL7A | RPL7A | 7555 | 0.013 | 0.43 | NO
83 | EIF3J | EIF3J | EIF3J | 7564 | 0.013 | 0.43 | NO
84 | EIF4E | EIF4E | EIF4E | 7590 | 0.012 | 0.43 | NO
85 | EIF3F | EIF3F | EIF3F | 7677 | 0.012 | 0.43 | NO
86 | EIF3H | EIF3H | EIF3H | 7733 | 0.011 | 0.43 | NO
87 | EIF3G | EIF3G | EIF3G | 7762 | 0.01 | 0.43 | NO
88 | RPS25 | RPS25 | RPS25 | 7786 | 0.01 | 0.43 | NO
89 | RPL4 | RPL4 | RPL4 | 7983 | 0.0078 | 0.42 | NO
90 | RPL19 | RPL19 | RPL19 | 8017 | 0.0073 | 0.42 | NO
91 | EIF4H | EIF4H | EIF4H | 8270 | 0.0044 | 0.4 | NO
92 | RPL26L1 | RPL26L1 | RPL26L1 | 8488 | 0.0017 | 0.39 | NO
93 | EIF3C | EIF3C | EIF3C | 8519 | 0.0014 | 0.39 | NO
94 | EIF3A | EIF3A | EIF3A | 8812 | -0.0022 | 0.37 | NO
95 | EIF3K | EIF3K | EIF3K | 8873 | -0.0029 | 0.37 | NO
96 | EIF4B | EIF4B | EIF4B | 9319 | -0.0082 | 0.34 | NO
97 | PABPC1 | PABPC1 | PABPC1 | 9502 | -0.011 | 0.34 | NO
98 | EIF4G1 | EIF4G1 | EIF4G1 | 9722 | -0.014 | 0.33 | NO
99 | EIF3D | EIF3D | EIF3D | 9728 | -0.014 | 0.33 | NO
100 | RPL7 | RPL7 | RPL7 | 9782 | -0.014 | 0.33 | NO
101 | EIF2S2 | EIF2S2 | EIF2S2 | 10207 | -0.02 | 0.31 | NO
102 | EIF2S1 | EIF2S1 | EIF2S1 | 11703 | -0.046 | 0.23 | NO
103 | RPS27 | RPS27 | RPS27 | 13088 | -0.088 | 0.17 | NO
104 | RPS4Y1 | RPS4Y1 | RPS4Y1 | 14512 | -0.16 | 0.12 | NO
105 | FAM153A | FAM153A | FAM153A | 15115 | -0.21 | 0.12 | NO

Figure S59. Get High-res Image This plot shows mRNAseq_cNMF expression data heatmap (on the left) a RunningEnrichmentScore(RES) plot (on the top right) and a Signal2Noise(S2N) plot (on the bottom right) of genes in the pathway: REACTOME PEPTIDE CHAIN ELONGATION.

Figure S60. Get High-res Image For the top 5 core enriched genes in the pathway: REACTOME PEPTIDE CHAIN ELONGATION, 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

- up-regulated, please check the list of up-regulated genes

- down-regulated, please check the list of down-regulated genes

Expression level

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

- highly expressed genes, please check the list of high (top 30%) expressed genes

- low expressed genes, please check the list of low (bottom 30%) expressed genes

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

- significantly differently expressed genes by eBayes lm fit, please check the list of significant genes

Methods & Data
Input

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

- Expression data file = LAML-TB.uncv2.mRNAseq_RSEM_normalized_log2.txt

- Phenotype data file = LAML-TB.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.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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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