Table 1.
List of representative networks with log-rank test p-values.
| Cluster # | # of unique genes | Representative network size | Log-rank test p-value |
Top enriched GO terms | Member genes of the representative network |
|---|---|---|---|---|---|
| 1 | 284 | 11 | 5.7 × 10-5 |
BP: extracellular matrix organization (8.22 × 10-7) BP (entire cluster): immune system process (1.01 × 10-46) MF: enzyme inhibitor activity (2.28 × 10-7) CC: proteinacious extracellular matrix (7.32 × 10-7) |
CLIC1, ILK, LGALS1, LGALS3, ANXA2, TIMP1, ANXA2P2, IQGAP1, EMP3, CAST, HEXB |
| 2 | 43 | 22 | 1.31 × 10-4 |
BP: chromatin organization (1.91 × 10-4) MF: deoxycytidyltransferase activity (2.28 × 10-7) CC: nucleoplasm (7.75 × 10-5) |
C10orf18, TAF5, SIRT1, FMR1, FBXO11, TCERG1, CXorf45, CASP8AP2, ARID4B, JMJD1C, TAF2, ELF2, CENPC1, ZNF131, NUP153, SUZ12, SR140, ATAD2B, HISPPD1, REV1, PMS1, ZCCHC11 |
| 3 | 34 | 16 | 2.21 × 10-4 |
BP: RNA processing (6.60 × 10-5) MF: poly(A)-specific ribonuclease activity (1.50 × 10-3) CC: nuclear speck (9.97 × 10-5) |
USP52, ZCCHC11, FNBP4, CROP, NKTR, SFRS18, RBM6, RBM5, CCNL2, C21orf66, DMTF1, WSB1, CDK5RAP3, ZNF692, LOC440350, LOC339047 |
| 4 | 27 | 25 | 4.52 × 10-4 |
BP: translation (2.06 × 10-5), ncRNA metabolic process (4.01 × 10-4) MF: structural constituent of ribosome (5.92 × 10-5) CC: ribonucleoprotein complex (2.03 × 10-7) |
RPP30, UCK2, BUB3, SMNDC1, SAR1A, MRPS16, GLRX3, TIMM23, UTP11L, HCCS, POLR3C, EIF2B3, MRPL9, SNRPD1, TFB2M, SUMO1, FASTKD3, HSPA14, DUSP11, ATPBD1C, MRPS15, MED28, GTF2B, MRPL22, POLE3 |
| 5 | 15 | 15 | 6.19 × 10-4 |
BP: RNA processing (2.18 × 10-10), RNA splicing (7.93 × 10-8) MF: RNA binding (2.00 × 10-12) CC: heterogeneous nuclear ribonucleoprotein complex (1.22 × 10-12) |
JARID1B, RBM12, ADNP, CPSF6, HNRPA3, ILF3, CTCF, HNRPD, HNRNPA0, SART3, HNRPDL, SFPQ, HNRNPR, TARDBP, TLK2 |
| 6 | 35 | 27 | 0.0016 |
BP: chromatin modification (1.64 × 10-9), histone acetylation (5.73 × 10-6) MF: transcription activator activity (1.18 × 10-5) CC: nucleolus (1.39 × 10-8) |
BAHCC1, CHD7, PHF2, TOP2B, TCF4, MYST3, SETD5, POGZ, BRD3, MED13, BPTF, GPATCH8, TARDBP, ILF3, HNRNPR, NASP, MDC1, ARID1A, TRIM33, CTCF, HNRPA3, RBM10, YLPM1, SMARCA4, SART3, SFRS8, EP400 |
| 7 | 12 | 12 | 0.002747 |
BP: pentose-phosphate shunt , oxidative branch (1.94 × 10-3) MF: 6-phosphoglucono-lactonase activity (1.29 × 10-3) CC: ribosome (7.42 × 10-3) |
PGLS, TMED1, CD320, MRPL4, RFXANK, TMEM161A, CLPP, STX10, TMEM147, EIF3G, C19orf56, UBA52 |
| 8 | 39 | 32 | 0.002782 |
BP: translation (8.30 × 10-7) MF: structural constituent of ribosome (8.92 × 10-9) CC: ribosome (1.59 × 10-9), mitochondrion (2.47 × 10-6) |
COMMD3, HSBP1, ZNF32, SUPT4H1, NFU1, LYRM4, RPS3A, RPS7, SNRPG, HAX1, MED28, UXT, MRPL22, FAM96B, UQCRQ, HBXIP, UBL5, MRPS15, NDUFA2, GTF2B, DUSP11, PSMA5, GTF2A2, PSMB4, ATP5F1, MRPL13, ATPBD1C, MRPL46, MRPL11, MRPS7, WDR61, BNIP1 |
| 9 | 25 | 25 | 0.003697 |
BP: RNA processing (1.06 × 10-3), mitotic cell cycle (1.66 × 10-3) MF: eukaryotic initiation factor 4G binding (1.29 × 10-3), RNA binding (4.08 × 10-3) CC: chromosomal part (2.64 × 10-3) |
DDX52, PRPSAP2, YWHAQ, ORC4L, MOBKL3, MYNN, CENPQ, C11orf73, MIS12, HMGN4, C14orf104, FASTKD3, SNRPD1, C4orf27, SFRS3, SUMO1, GIN1, FLJ13611, THAP1, ATPBD1C, DUSP11, EIF4E, PIGF, RY1, NIF3L1 |
| 10 | 14 | 14 | 0.004707 |
BP: nuclear-transcribed mRNA catabolic process (1.82 × 10-3) MF: RNA binding (3.02 × 10-3) CC: BRISC complex (2.94 × 10-3) |
DDX50, DIP2C, KIAA0157, KIAA1128, KIAA1279, LARP5, PAPD1, RAB11FIP2, SHOC2, TNKS2, UPF2, WAC, WDR37, ZMYND11 |
| 11 | 22 | 16 | 0.005489 |
BP: type I interferon-mediated signalling (4.49 × 10-14) pathway, immune system process (1.79 × 10-11) MF: MHC class I receptor activity (4.94 × 10-10) CC: MHC class I protein complex (1.80 × 10-9) |
CASP1, CASP4, PLSCR1, NMI, SP100, SP110, TRIM22, TRIM6-TRIM34, TRIM21, IFI35, PSMB9, PSMB8, HLA-F, HLA-B, HLA-C, HLA-E |
| 12 | 12 | 12 | 0.005663 |
BP: - MF: sequence-specific DNA binding transcription factor activity (2.43 × 10-2) CC: - |
ZNF134, ZNF180, ZNF211, ZNF222, ZNF223, ZNF228, ZNF230, ZNF304, ZNF419, ZNF45, ZNF606, ZNF8 |
| 13 | 21 | 21 | 0.006774 |
BP: mitotic cell cycle (6.43 × 10-5) MF: RNA trimethylguanosine synthase activity (1.13 × 10-3) CC: nucleoplasm (4.08 × 10-4) |
EED, POLD3, ELF2, CENPC1, HISPPD1, ZNF131, RBM12, CEP57, NOL11, COIL, NUP160, CEP76, ZNF140, ZNF143, TDG, TAF11, FASTKD3, TGS1, EXOSC9, YTHDF2, SAE2 |
| 14 | 18 | 18 | 0.006858 |
BP: arginine biosynthetic process via orthithine (9.69 × 10-4) MF: argininosuccinate lyase activity 9.67 × 10-4) CC: organelle envelope (4.11 × 10-3) |
ASL, ZMYM6, RAB32, CD58, MOBKL1B, TRAM1, CD164, RER1, CCDC109B, CLIC1, CASP4, SQRDL, SERPINB1, MR1, CASP1, CAPG, MGAT4A, ANXA4 |
| 15 | 22 | 22 | 0.007708 |
BP: multicellular organismal movement (4.97 × 10-4) MF: ATP-dependent helicase activity (2.22 × 10-4) CC: endopeptidase Clp complex (1.10 × 10-3) |
SEC24A, TMF1, KIAA0372, CLCC1, DHX29, SLC30A5, VPS54, CHD1, RPS6KB1, HISPPD1, ETAA1, CENPC1, CLPX, C1orf9, ZNF131, KLHL20, REV1, ZC3H7A, DDX46, NUP153, SMCHD1, PPWD1 |
| 16 | 15 | 15 | 0.008207 |
BP: ribulose-phosphate 3-epimerase activity (8.069 × 10-4) MF: mRNA 3'-end processing (1.429 × 10-3) CC: SPOTS complex (1.574 × 10-3) |
C15orf15, SELT, COMMD10, UBE2A, TMED2, CNOT8, NMD3, MRPL42, BZW1, NUDT21, SPTLC1, DCTN4, YIPF5, RPE, C20orf30 |
The p-values associated with the GO terms are based on Fisher's exact tests without Bonferroni correction (http://toppgene.cchmc.org).