Table 1 Gene set enrichment analysis of the modules from dual evaluationa
From: Dense module searching for gene networks associated with multiple sclerosis
GO term | # contributing genes/ term sizeb | Contributing genesc | p-value | adj. p-valued |
|---|---|---|---|---|
Molecular Function | ||||
Phosphotyrosine residue binding | 3/18 | GRB2, MAPK1, MAPK3 | 1.916 × 10− 5 | 1.674 × 10− 3 |
Phosphatidylinositol-4,5-bisphosphate 3-kinase activity | 4/62 | CD80, CD86, GRB2, PIK3R2 | 3.318 × 10− 5 | 1.674 × 10− 3 |
Virus receptor activity | 4/71 | CD80, CD86, ITGB3, TNFRSF14 | 5.667 × 10−5 | 1.674 × 10−3 |
Phosphatidylinositol bisphosphate kinase activity | 4/72 | CD80, CD86, GRB2, PIK3R2 | 5.987 × 10−5 | 1.674 × 10−3 |
Protein phosphorylated amino acid binding | 3/28 | GRB2, MAPK1, MAPK2 | 7.533 × 10−5 | 1.674 × 10−3 |
Biological Process | ||||
T cell costimulation | 7/82 | CD80, CD86, CSK, CTLA4, GRB2, MAP3K14, TNFRSF14 | 3.704 × 10−9 | 2.113 × 10−6 |
Lymphocyte costimulation | 7/83 | CD80, CD86, CSK, CTLA4, GRB2, MAP3K14, TNFRSF14 | 4.037 × 10−9 | 2.113 × 10−6 |
JAK-STAT cascade involved in growth hormone signaling pathway | 4/15 | MAPK1, MAPK3, STAT3, STAT5A | 8.415 × 10−8 | 2.937 × 10−5 |
Growth hormone receptor signaling pathway | 4/24 | MAPK1, MAPK3, STAT3, STAT5A | 6.425 × 10−7 | 1.598 × 10− 4 |
Cellular response to growth hormone stimulus | 4/25 | MAPK1, MAPK3, STAT3, STAT5A | 7.633 × 10−7 | 1.598 × 10−4 |
Cellular Component | ||||
Nuclear pore | 5/84 | KPNB1, NUP153, RAN, SENP2, SNUPN | 4.311 × 10−6 | 3.794 × 10−4 |
Clathrin-coated pit | 4/69 | AMN, CLTC, EPN1, EPS15L1 | 4.666 × 10−5 | 2.053 × 10−3 |
Endoplasmic reticulum tubular network | 2/12 | KPNB1, RAB18 | 5.296 × 10−4 | 0.0136 |
Platelet alpha granule membrane | 2/13 | ITGB3, PECAM1 | 6.248 × 10−4 | 0.0136 |
Cytosolic large ribosomal subunit | 3/67 | RPL4, RPL5, RPL17 | 9.556 × 10−4 | 0.0136 |