Table 3.
Gene set enrichment analysis:
| A. BioCarta pathways showing gene enrichment. | ||||
|---|---|---|---|---|
| BioCarta pathway name | Size (genes) | Enrichment Score | p-val | Change direction |
| VEGFPATHWAY | 25 | 0.657942 | 0.008163 | Decreased |
| CDMACPATHWAY | 15 | 0.699933 | 0.02268 | Decreased |
| INTEGRINPATHWAY | 33 | 0.549887 | 0.03527 | Decreased |
| ECMPATHWAY | 20 | 0.629207 | 0.038855 | Decreased |
| PROTEASOMEPATHWAY | 16 | 0.760643 | 0.041929 | Decreased |
| ATMPATHWAY | 18 | 0.529419 | 0.04918 | Decreased |
| MCALPAINPATHWAY | 22 | 0.62423 | 0.049587 | Decreased |
| CYTOKINEPATHWAY | 18 | −0.79414 | 0.006211 | Increased |
| B. GSEA cytokine pathway constituents (listed by Running ES rank). | ||||
|---|---|---|---|---|
| Gene Symbol | Gene Name | Rank Metric Scorea | Running ESb | Core Enrichment |
| IL18 | Interleukin 18 (interferon-gamma-inducing factor) | −0.031 | −0.7628 | Yes |
| IL5 | Interleukin 5 (colony-stimulating factor, eosinophil) | −0.061 | −0.7613 | Yes |
| LTA | Lymphotoxin alpha (TNF superfamily, member 1; TNFβ) | −0.075 | −0.7345 | Yes |
| IFNG | Interferon, gamma | −0.098 | −0.7007 | Yes |
| IL15 | Interleukin 15 | −0.106 | −0.6492 | Yes |
| IL12A | Interleukin 12a (natural killer cell stimulatory factor 1, cytotoxic lymphocyte maturation factor 1, p35) | −0.113 | −0.5942 | Yes |
| IL1A | Interleukin 1, alpha | −0.114 | −0.5334 | Yes |
| IL10 | Interleukin 10 | −0.131 | −0.4741 | Yes |
| IL8 | Interleukin 8 | −0.137 | −0.4033 | Yes |
| IL13 | Interleukin 13 | −0.167 | −0.3277 | Yes |
| IL2 | Interleukin 2 | −0.208 | −0.2289 | Yes |
| IL9 | Interleukin 9 | −0.228 | −0.1106 | Yes |
| IL3 | Interleukin 3 (colony-stimulating factor, multiple) | −0.245 | 0.0182 | Yes |
| IL6 | Interleukin 6 | 0.074 | −0.6347 | No |
| IL4 | Interleukin 4 | 0.036 | −0.6943 | No |
| IL12B | Interleukin 12b (natural killer cell stimulatory | 0.016 | −0.7183 | No |
| factor 2, cytotoxic lymphocyte maturation factor 2, p40) | ||||
| IL16 | Interleukin 16 (lymphocyte chemoattractant factor) | 0.007 | −0.7297 | No |
| TNF | Tumor necrosis factor (TNF super family, member 2 [TNFα]) | −0.011 | −0.7515 | No |
a
Rank metric: GSEA uses the signal-to-noise metric to rank the genes (for details, see “Metrics for Ranking Genes” at http://www.broadinstitute.org/gsea/doc/GSEAUserGuideFrame.html?Run_GSEA_Page). The larger the signal-to-noise ratio, the larger the differences of the means (relative to the standard deviations). A high signal-to-noise metric indicates greater separation between phenotypes.
b
Running ES: Running enrichment score, which reflects the degree to which a gene set is overrepresented at the top or bottom of a ranked list of genes (for details, see “GSEA Statistics” at http://www.broadinstitute.org/gsea/doc/GSEAUserGuideFrame.html?Run_GSEA_Page).