STANDARD_NAME GSE18791_UNSTIM_VS_NEWCATSLE_VIRUS_DC_1H_DN SYSTEMATIC_NAME M4286 COLLECTION C7:IMMUNESIGDB MSIGDB_URL https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/GSE18791_UNSTIM_VS_NEWCATSLE_VIRUS_DC_1H_DN NAMESPACE HUMAN_GENE_SYMBOL DESCRIPTION_BRIEF Genes down-regulated in comparison of control conventional dendritic cells (cDC) at 1 h versus cDCs infected with Newcastle disease virus (NDV) at 1 h. DESCRIPTION_FULL The dendritic cell (DC) is a master regulator of immune responses. Pathogenic viruses subvert normal immune function in DCs through the expression of immune antagonists. Understanding how these antagonists interact with the host immune system requires knowledge of the underlying genetic regulatory network that operates during an uninhibited antiviral response. In order to isolate and identify this network, we studied DCs infected with Newcastle Disease Virus (NDV), which is able to stimulate innate immunity and DC maturation through activation of RIG-I signaling, but lacks the ability to evade the human interferon response. To analyze this experimental model, we developed a new approach integrating genome-wide expression kinetics and time-dependent promoter analysis. We found that the genetic program underlying the antiviral cell state transition during the first 18-hours post-infection could be explained by a single regulatory network. Gene expression changes were driven by a step-wise multi-factor cascading control mechanism, where the specific transcription factors controlling expression changed over time. Within this network, most individual genes are regulated by multiple factors, indicating robustness against virus-encoded immune evasion genes. In addition to effectively recapitulating current biological knowledge, we predicted, and validated experimentally, antiviral roles for several novel transcription factors. More generally, our results show how a genetic program can be temporally controlled through a single regulatory network to achieve the large-scale genetic reprogramming characteristic of cell state transitions. PMID 20164420 GEOID GSE18791 AUTHORS Zaslavsky E,Hershberg U,Seto J,Pham AM,Marquez S,Duke JL,Wetmur JG,Tenoever BR,Sealfon SC,Kleinstein SH CONTRIBUTOR Jernej Godec CONTRIBUTOR_ORG Dana-Farber Cancer Institute EXACT_SOURCE GSE18791_1548_200_DN FILTERED_BY_SIMILARITY EXTERNAL_NAMES_FOR_SIMILAR_TERMS EXTERNAL_DETAILS_URL SOURCE_MEMBERS ACADL,ACO2,AGK,AK5,AKNAD1,ALAD,ALKBH1,ANKRD30B,ARHGAP27,ARID3A,ASNSD1,ATP6AP2,BACH1,BAP1,BEST4,BNIP1,BRWD3,C14orf118,C14orf56,C16orf62,C16orf80,C1orf110,C2orf63,C5orf48,C6orf141,C6orf162,C7orf31,C7orf44,C8orf31,CA10,CABP2,CADPS,CAPN7,CCDC122,CCDC160,CCDC34,CCDC76,CCDC77,CCT7,CDC42EP3,CDH18,CDK7,CEACAM7,CENPQ,CHRDL1,CHTOP,CLMP,COG3,COG7,CREB3,CRYBB2P1,CSGALNACT1,CTAGE9,CTXN3,CYLC2,DCAF13,DGKG,DHFRL1,DHRS7B,DHX57,DMRTC2,DNAJC27,DPF3,DTX3L,EFTUD2,EIF5A2,ELMOD3,ENPP3,ETAA1,FAM126B,FAM168B,FGF13,FKTN,FLJ35424,FLJ39534,FLJ40434,FNBP4,FUBP3,GFM1,GIP,GRAMD1C,GSTM5,GTF3C3,HMGB3,HNRNPM,HSPA12A,HTN1,IRAK1BP1,IRF2BPL,IRS4,KAT5,KIAA0100,KIAA0232,LCOR,LHX2,LOC100128640,LOC100131067,LOC100131763,LOC100505893,LOC220980,LOC283357,LOC284950,LOC441025,LOC652993,LOC728288,LRFN5,LRIF1,LRRC19,LRRCC1,MAP4K4,MBIP,MDGA2,MECOM,MED7,MEGF9,METTL3,METTL4,MGC45800,MIA3,MTX3,MVP,MYH13,MYO1A,MYO5C,NAA35,NAP1L5,NCRNA00029,NCRNA00255,NDUFA5,NIP7,OPA1,OR3A2,PAFAH1B2,PCDH11X,PCDH8,PCDHGB6,PGLYRP4,PI4K2B,PKN3,PLAC8L1,POC5,POLI,PPP2CB,PPPDE2,PRPF3,PTGFR,RAB2B,RBM45,RIPK3,RIPK4,RNASEL,RNF166,SCN11A,SENP2,SEPSECS,SERPINB4,SIGLEC6,SLC19A2,SLC20A2,SLC25A27,SLC30A7,SLC35F1,SMPD3,SNRPA1,SNX1,SPRYD4,SPTLC2,SQRDL,SRR,STYX,SVOP,TAS2R14,TBX5,TFAP2C,TGIF1,TIGD6,TMEM213,TOR1AIP1,TRIM23,TSIX,TTC35,TTC8,UCK2,UGGT2,VPS35,WDR63,WDR67,ZDHHC13,ZFYVE26,ZNF157,ZNF207,ZNF271,ZNF616,ZNF620,ZNF680,ZNF696,ZNF805,ZSCAN23,ZUFSP,ZW10 GENE_SYMBOLS ACADL,ACO2,AGK,AK5,AKNAD1,ALAD,ALKBH1,ANKRD30B,ARHGAP27,ARID3A,ASNSD1,ATP6AP2,BACH1,BAP1,BEST4,BNIP1,BRWD3,GPATCH2L,,VPS35L,CFAP20,CCDC190,CLHC1,TEX43,C6orf141,SMIM8,C7orf31,COA1,LINC02904,CA10,CABP2,CADPS,CAPN7,CCDC122,CCDC160,CCDC34,TRMT13,CCDC77,CCT7,CDC42EP3,CDH18,CDK7,CEACAM7,CENPQ,CHRDL1,CHTOP,CLMP,COG3,COG7,CREB3,CRYBB2P1,CSGALNACT1,CTAGE9,CTXN3,CYLC2,DCAF13,DGKG,DHFR2,DHRS7B,DHX57,DMRTC2,DNAJC27,DPF3,DTX3L,EFTUD2,EIF5A2,ELMOD3,ENPP3,ETAA1,HYCC2,FAM168B,FGF13,FKTN,LINC00955,KIF9-AS1,SLC25A3P1,FNBP4,FUBP3,GFM1,GIP,GRAMD1C,GSTM5,GTF3C3,HMGB3,HNRNPM,HSPA12A,HTN1,IRAK1BP1,IRF2BPL,IRS4,KAT5,BLTP2,KIAA0232,LCOR,LHX2,ACVR2B-AS1,CKMT2-AS1,,SLIT2-IT1,TMEM72-AS1,,,LINC02483,,,LRFN5,LRIF1,LRRC19,LRRCC1,MAP4K4,MBIP,MDGA2,MECOM,MED7,MEGF9,METTL3,METTL4,,MIA3,MTX3,MVP,MYH13,MYO1A,MYO5C,NAA35,NAP1L5,LINC00029,RAD21-AS1,NDUFA5,NIP7,OPA1,OR3A2,PAFAH1B2,PCDH11X,PCDH8,PCDHGB6,PGLYRP4,PI4K2B,PKN3,PLAC8L1,POC5,POLI,PPP2CB,DESI1,PRPF3,PTGFR,RAB2B,RBM45,RIPK3,RIPK4,RNASEL,RNF166,SCN11A,SENP2,SEPSECS,SERPINB4,SIGLEC6,SLC19A2,SLC20A2,SLC25A27,SLC30A7,SLC35F1,SMPD3,SNRPA1,SNX1,SPRYD4,SPTLC2,SQOR,SRR,STYX,SVOP,TAS2R14,TBX5,TFAP2C,TGIF1,TIGD6,TMEM213,TOR1AIP1,TRIM23,TSIX,EMC2,TTC8,UCK2,UGGT2,VPS35,DNAI3,TBC1D31,ZDHHC13,ZFYVE26,ZNF157,ZNF207,ZNF271P,ZNF616,ZNF620,ZNF680,ZNF696,ZNF805,ZSCAN23,ZUP1,ZW10 FOUNDER_NAMES