Table 4

Top GO enrichment terms for expression modules
Module Size Rank p.Bonf Fraction Ontology Term name
1 1520 1 1.20E-14 0.65147 CC membrane-bounded organelle
1 1520 2 1.90E-14 0.65007 CC intracellular membrane-bounded organelle
2 703 1 1.30E-05 0.04885 CC ribosome
2 703 2 1.50E-05 0.07481 BP translation
3 658 1 0.00018 0.16382 CC extracellular region
4 647 1 0.011 0.63711 CC membrane-bounded organelle
6 442 1 7.60E-07 0.27229 BP response to stress
6 442 2 2.80E-06 0.34217 BP signal transduction
7 426 1 9.40E-07 0.18734 BP immune system process
8 407 1 0.0042 0.66755 CC intracellular membrane-bounded organelle
9 387 1 1.70E-05 0.82961 CC intracellular part
10 355 1 1.80E-05 0.07855 BP ncRNA metabolic process
10 355 2 3.60E-05 0.19335 CC mitochondrion
12 306 1 2.00E-16 0.1134 CC ribosome
12 306 2 4.00E-16 0.17182 CC ribonucleoprotein complex
12 306 3 1.20E-14 0.14777 BP translation
12 306 4 2.30E-14 0.09278 BP viral transcription
13 260 1 0.00041 0.025 CC hemoglobin complex
13 260 2 0.011 0.025 BP heme biosynthetic process
14 237 1 0.014 0.61086 MF protein binding
15 118 1 0.018 0.25688 BP intracellular signal transduction
15 118 2 0.032 0.12844 BP small GTPase mediated signal transduction
16 108 1 1.30E-05 0.18478 BP translation
16 108 2 0.00017 0.1087 BP ribosome biogenesis
17 99 1 2.30E-09 0.36957 CC mitochondrion
18 72 1 3.30E-06 0.1791 BP platelet activation
18 72 2 1.20E-05 0.22388 BP blood coagulation
19 60 1 1.40E-17 0.31034 MF structural constituent of ribosome
19 60 2 2.90E-17 0.32759 CC ribosome
20 52 1 7.10E-23 0.32653 BP type I interferon-mediated signaling pathway
20 52 2 7.10E-23 0.32653 BP cellular response to type I interferon
23 32 1 0.053 0.17241 CC external side of plasma membrane

For each module we list the top enriched GO terms. Columns list the module label, module size, rank of the enrichment p-value for that particular module, the Bonferroni-corrected enrichment p-value (the correction is performed with respect to the number of GO terms), fraction of the module genes also in the GO term, GO ontology, and GO term name. Multiple expression modules exhibit significant enrichment. Row shading separates modules for easier reading. The enrichment provides evidence that the modules are biologically meaningful.

van Eijk et al.

van Eijk et al. BMC Genomics 2012 13:636   doi:10.1186/1471-2164-13-636

Open Data