Skip to main content

Table 2 GO ontology enrichment analysis for ten macro bipartite networks

From: Mining the tissue-tissue gene co-expression network for tumor microenvironment study and biomarker prediction

  BiNets density Tumor Genes Top Enriched GO Terms (p-value) Stroma Genes Top Enrich GO Terms (p-value)
1 25 0.365644 118 BP: cardiovascular system development (2.309E-14); CC: extracellular matrix (1.098E-20) 154 BP: muscle organ development (5.371E-9); CC: extracellular matrix (8.853E-19)
2 3 0.534566 73 BP: adenylate cyclase-activating G-protein coupled receptor signaling pathway (1.547E-6) 4 BP: protein-chromophore linkage (2.271E-3)
3 58 0.332754 278 BP: response to iron ion (1.948E-5), epithelial cell development (4.760E-5), response to estrogen stimulus (2.065E-4) 224 BP: gland development (8.306E-6), development of primary male sexual characteristics (1.596E-5), male sex differentiation (2.602E-5); MF: enzyme binding (1.636E-4); CC cell projection (6.956E-8)
4 13 0.326076 113 BP: cell-cell signaling (1.934E-8); MF: receptor binding (8.154E-6) 89 BP: cell-cell signaling (2.233E-9); MF: receptor binding (5.040E-7)
5 103 0.320424 521 BP: mitotic cell cycle (3.640E-32), cell cycle phase (3.333E-30), cell cycle process (5.346E-27), cell cycle (4.043E-25); MF: RNA binding (3.610E-9) 629 BP: mitotic cell cycle (7.256E-41), cell cycle phase (9.357E-39), cell cycle process (1.771E-32), cell cycle (1.319E-28); MF: RNA binding (2.821E-11)
6 16 0.3014 117 BP: defense response to virus (2.621E-32), response to virus (2.914E-32); MF: double-stranded RNA binding (5.875E-12) 99 BP: defense response to virus (1.307E-34), response to virus (2.873E-33), innate immune response (2.983E-32); MF: double-stranded RNA binding (1.255E-12)
7 99 0.329521 525 BP: mitotic cell cycle (5.339E-29), cell cycle phase (3.764E-27), cell cycle process (1.512E-23); CC: mitochondrial part (9.680E-23) 489 BP: cell cycle phase (7.556E-34), mitotic cell cycle (4.042E-32), cell cycle process (1.732E-28); MF: RNA binding (1.179E-14); CC: mitochondrial part (5.769E-24)
8 2 0.464059 26 BP: response to progesterone stimulus (4.135E-4) 30 BP: immune response (1.287E-7)
9 41 0.348161 278 BP: respiratory electron transport chain (1.096E-28), electron transport chain (1.967E-24), cellular respiration (1.066E-23); CC: mitochondrial part (7.866E-24) 219 BP: respiratory electron transport chain (2.241E-27), cellular respiration (1.460E-25), electron transport chain (1.381E-23); MF: RNA binding (7.907E-16); CC: mitochondrial membrane part (1.505E-23), mitochondrial part (6.889E-23), mitochondrial inner membrane (2.245E-21), organelle inner membrane (2.951E-21)
10 12 0.417881 80 BP: immune response (7.503E-25) 110 BP: defense response (3.448E-22), immune response (4.224E-21)
  1. For each macro bipartite network, we list the numbers of genes in the tumor side and the stroma side separately as well as significant GO terms with the p-values obtained from ToppGenes. P-values were before Bonferroni corrections. BP, MF, and CC stand for Biological Process, Molecular Function and Cellular Component, respectively.