Table 2.

Top 10 networks generated from IPA for polysome-bound RNAs affected by radiation

Network IDGenes in networkScoreNo. focus genesTop categories
1ALAS2, BATF, BGLAP, CASR, CCL2, CXCR4, DKK1, FOSL1, FY, HMGCS2, JUN, MAP2K4, MAP3K8, MMP9, NPTX2, NR1H2, NR1H4, NR2F1, NR2F2, PIAS2, PIN1, RARB, RCN2, RQCD1, RXRA, SOCS3, STAT1, STAT4, TAF1B, TFPI, THBS1, TIEG, TOP2A, TOP2B, VDR3735Gene expression, cellular growth and proliferation, skeletal and muscular system development and function
2AR, BIRC5, CAMK1, CAMK2B, CASP7, CASP8, CASP8AP2, CAST (CALPASTATIN), CCNA2, CDC2, CDC34, CDKN1B, EEF2, GADD45A, GADD45G, HMGA2, JAG1, KLF4, M6PRBP1, MARCKS, MDM2, MSH2, NUP50, PCNA, PLEC1, PRKR, RAD9A, RFC3, SYN1, TAX1BP1, TNFRSF6, TNFSF13, TP73L, UBE2A, ZNF1483735Cell cycle, cancer, cell death
3CBL, CCNT1, CCNT2, CCRK, CD2AP, CDK9, EFEMP1, EGF, ERBB2, ERBB3, GRN, IL11RA, IL6ST, IRF7, KLF2, LAMR1, LAT, LIF, MYBL2, PMAIP1, POLR2C, POLR2H, PRDX2, PSG2, PTPRC, RNGTT, SMAD4, SMAD5, SPRY2, SPTBN1, SUPT5H, SYK, TCF7L2, TEGT, VAV13735Cellular development, gene expression, viral function
4ACTL6B, ACTR2, ACTR3, ALDOA, ARID4A, ARPC4, CBFA2T1, CDH11, CPA3, CSNK1G2, DAG1, FABP5, FIBP, FMR1, GNAI2, HMGB2, IGFBP6, MAPK6, NFYB, OGDH, PIK3CB, PIK3R3, PSMC3, PSMC6, PSMD2, PSMD10, PSMD13, RFX5, SAP30, SGCD, SGCG, SMARCA2, SNCA, STAU, TH3735Cardiovascular disease, organismal injury and abnormalities, small molecule biochemistry
5ASK, CDC7, CDC10, CEP2, CLK2, CPNE3, CR1, DCAMKL1, G3BP, HNRPA2B1, IL2RB, ITSN2, JAK3, LCK, LSM8, MBP, MCM2, MCM3, MCM4, MCM5, MCM6, MCM7, MMP9, NEDD5, NFKBIA, NRBP, NRG1, PGD, PNUTL1, POU3F1, PTPRC, SEPT6, STX4A, VCP, VRK11321Cell cycle, DNA replication, recombination, and repair, cell death
6ACTB, ATP5I, CCT3, CCT4, CETN3, CLK1, COX17, COX5B, DCTN1, DCTN2, DNCH1, DNCI1, DST, H3F3A, JRK, KIF11, MAGOH, MAPRE1, MAPRE3, NUDC, NXF1, PAFAH1B1, PPIH, PRPF3, PRPF4, PRPF18, PRPF4B, RPL36A, RSN, SFRS1, SFRS6, SFRS12, SRPK1, SRPK2, U2AF11018RNA post-transcriptional modification, protein folding, protein synthesis
7ACVR2, ACVR1B, ALDOC, BLOC1S1, BLOC1S2, BLOC1S3, BTEB1, CPSF1, DEK, ELF1, HAT1, HMGA1, INHA, INHBA, MYCN, MYST3, MYST4, NME1, PAH, PCAF, PLDN, RNF6, RPL29, RPS15, RPS23, SRRM1, STAF42, STAF65 (gamma), SUPT3H, TADA3L, TAF5, TAF12, TAF5L, TAF6L, TCF11018Post-translational modification, protein synthesis, DNA replication, recombination, and repair
8AKAP8, ANAPC1, ANAPC4, ANAPC10, APOBEC1, AQP2, AQP3, ARVCF, BAG4, C3orf15, CDC27, CDH1, CFTR, DNAJA1, DNAJB11, EGFR, EIF2S2, EIF5A, FKBP4, GPR37, HSPA8, HSPA1B, MYCBP, MYO7A, PDZK1, PRKACA, PRKACB, PRKACG, PRKAG1, PRKAR1A, PRKAR2B, PRKDC, SDCBP, STUB1, XRCC41018Protein folding, protein synthesis, cancer
9ACTN1, ANXA2, BRD2, CASP3, CDKN1A, DDX21, E2F2, E2F4, ENO1, FOS, GBP2, GEM, HIF1A, LAMP2, MYC, MYCN, PEG3, PGK1, PLS3, PRDX3, ROCK1, ROCK2, RPL23, RPS13, SUCLA2, TMSB4X, TP53915Cell cycle, cellular development, cellular growth and proliferation
10ANGPT1, ASE-1, BMX, CHUK, ELF2, GRB14, HSPA1L, HSPCB, IKBKB, IKBKE, IKBKG, IL1R1, IRAK1, MAP3K14, NFKBIB, STIP1, TANK, TBK1, TEBP, TEK, TERF1, TINF2, TLR2, TLR4, TLR5, TNFAIP3, TNFRSF8, TNFRSF1B, TNKS2, TOLLIP, TRAF3, TRAF5, TRAF6, TTRAP, ZA20D2917Endocrine system development and function, organismal survival, cell death
  • NOTE: The polysome-bound mRNAs whose levels were modified by radiation by ≥2-fold were subjected to IPA; the top 10 networks and their top 3 network function categories are shown. The score is the negative log of P and indicates the likelihood of the focus genes in a network being found together due to chance. No. focus genes refers to the genes affected by radiation within an IPA defined network; the maximum number of genes allowed by the IPA in a network is 35. Bold: genes increased by radiation; italicized bold: genes decreased by radiation; standard text: genes in network not affected by radiation.