Table I.
Functional annotation of CRC modules.
| Modulea | Annotationb | KEGG pathwaysb | Hub genes |
|---|---|---|---|
| Midnight blue (56) | Mitochondrial part (4.9E-3) 7 (3.2E-71) | C7ORF30, EIF3B, MRPS24 | |
| Tan (74) | CD55, DUSP4, LOC100507649 | ||
| Black (110) | Generation of precursor metabolites and energy (2.5E-3) | HSPA4L, LOC100507455, C1QBP | |
| Mitochondrion (7.7E-10)18 (2.0E-23) | |||
| Green (125) | X (6.2E-175)Xq28 (3.8E-17) | UBE2A, PHF16, NKRF | |
| Pink (99) | O-Glycan biosynthesis (2.7E-2) | ST6GALNAC1, SPINK4, REG4 | |
| Brown (370) | 20 (9.8E-57)20q13.13 (8.3E-5) | STAU1, DYNLRB1, DDX27 | |
| Light green (42) | 15 (5.0E-61)15q14 (2.0E-5) | COPS2, RSL24D1, MFAP1 | |
| Cyan (65) | 14 (7.7E-97)14q11.2 (5.6E-6) | C14ORF166, TMX1, TMED10 | |
| Turquoise (723) | Cell motion (4.0E-9) | Focal adhesion (1.8E-11) | SPARC, COL5A2, TIMP2 |
| Extracellular matrix (5.0E-23) | ECM-receptor interaction (2.8E-9) | ||
| Yellow (208) | Immune response (6.3E-32) | Antigen processing and presentation (3.4E-7) | CD53, LAPTM5, FCER1G |
| MHC class II protein complex (7.7E-9) | Intestinal immune network for IgA production (1.1E-6) | ||
| Grey (42) | RNA splicing (1.4E-7) | Spliceosome (4.0E-3) | NCRNA00201, NKTR, PNISR |
| Nuclear speck (4.8E-6) | |||
| Salmon (73) | Carbonate dehydratase (6.5E-3) | ZG16, CA1, CA4 | |
| Green yellow (77) | Regulation of protein localization (4.6E-2) | Pathways in cancer (2.5E-3) | DDX3X, PTPN11, G3BP2 |
| Membrane fraction (2.9E-2) | |||
| Light cyan (49) | 20 (4.5E-73)20q13 (8.9E-21) | PSMF1, MKKS, SNRPB | |
| Magenta (97) | Nucleoplasm (3.8E-3) 13 (1.8E-153)13q34 (5.8E-17) | CUL4A, IPO5, UCHL3 | |
| Red (120) | 8 (7.8E-165)8q24.3 (4.1E-18) | DCAF13, SLC25A32, ARMC1 | |
| Blue (455) | Mitotic cell cycle (5.5E-34) | Proteasome (7.8E-10) | BUB1B, OIP5, PRC1 |
| Nuclear lumen (1.9E-23) | Spliceosome (1.4E-8) | ||
| DNA replication (6.5E-8) | |||
| Purple (78) | Immune response (1.2E-17) | Antigen processing and presentation (3.9E-4) | IFIT3, CMPK2, IFIT1 |
| MHC class I protein complex (9.5E-5) |
a
Number of genes in the given module (the no. of genes is presented in the parentheses).
b
Annotation includes GO biological process, cellular component, molecular function, and chromosome. Representative functional terms overrepresented in the given module (Fisher's exact test P-values are presented in parentheses).