STANDARD_NAME	GSE18791_CTRL_VS_NEWCASTLE_VIRUS_DC_10H_UP
SYSTEMATIC_NAME	M4268
COLLECTION	C7:IMMUNESIGDB
MSIGDB_URL	https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/GSE18791_CTRL_VS_NEWCASTLE_VIRUS_DC_10H_UP
NAMESPACE	HUMAN_GENE_SYMBOL
DESCRIPTION_BRIEF	Genes up-regulated in comparison of control conventional dendritic cells (cDC) at 0 h versus cDCs infected with Newcastle disease virus (NDV) at 10 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_1543_200_UP
FILTERED_BY_SIMILARITY	
EXTERNAL_NAMES_FOR_SIMILAR_TERMS	
EXTERNAL_DETAILS_URL	
SOURCE_MEMBERS	ADORA2B,AKTIP,AP3M1,ARHGAP12,ARL3,ASB6,ASL,ASTE1,ATP2A3,ATPAF2,BAHD1,BLMH,BRIX1,C11orf82,C12orf29,C14orf167,C14orf169,C18orf55,C1orf131,C3orf75,C9orf80,CAMKK1,CARKD,CCDC12,CCDC76,CCDC99,CDC23,CDC40,CEP97,CERK,CLP1,CLPP,COPS6,COQ9,CSRP2BP,DAAM1,DCAF13,DCAF4,DDX28,DEM1,DIEXF,DIS3L,DNAAF2,DNAJC11,DNAJC28,DNAL1,DOK2,DSTYK,DUSP7,EDC3,ENDOG,EXOSC5,EXOSC7,FAM168B,FAM54A,FAM65A,FAM78A,FAM98A,FAM98B,FASTKD5,FBXO21,FBXO33,FKBP14,FLAD1,FLVCR2,FOS,FRAT2,FTSJ2,G2E3,GABPA,GATC,GBA2,GEMIN6,GMCL1,GPATCH1,GSPT2,GTF3C4,GTF3C5,GXYLT1,HENMT1,HRAS,HRH1,HS3ST1,HSD17B10,IFNGR1,IKBKAP,IMP4,IRF3,IRF5,KBTBD7,KLHDC5,LOC100507564,LOC152217,LOC729082,LRMP,LRR1,MAP7,MCEE,MED11,MED29,MED31,MKL1,MRPL12,MRPL4,MRPS11,MRPS2,MRPS33,MSH2,MTFMT,MTMR12,NAIF1,NAP1L5,NAPEPLD,NARFL,NAT9,NCRNA00292,NDUFA5,NFATC3,NFIA,NLRP2,NME6,NOL11,NUDT4,NUDT6,NUP37,OSGEPL1,PABPN1,PDE6D,PDIK1L,PEX1,PIK3R1,PIK3R4,PIP4K2B,PLEKHJ1,PLXNA1,PNP,PNPLA6,POLE3,POLR2D,POLR3B,POLR3H,POP1,POP5,PPP1R14B,PRADC1,PRMT7,PS1TP4,RANGRF,RG9MTD1,RNF166,RNF7,RPAP2,RPP40,RUNX1,SEC22C,SETD6,SGK1,SLC19A2,SLC2A9,SUV39H2,TARBP2,TATDN2,TEX264,THAP11,THNSL1,THYN1,TMTC4,TNFAIP8L2,TNRC18,TOMM40L,TP53RK,TRMT1,TSPYL5,TSSC1,TTC15,TTLL1,TUBB6,UBAC1,UMPS,UNG,URB2,USP38,USP46,UTP11L,VASH1,WDR53,WNT5B,YLPM1,ZCCHC17,ZCCHC24,ZNF180,ZNF227,ZNF30,ZNF319,ZNF35,ZNF559,ZNF641,ZNF642,ZNF789,ZNF813
GENE_SYMBOLS	ADORA2B,AKTIP,AP3M1,ARHGAP12,ARL3,ASB6,ASL,ASTE1,ATP2A3,ATPAF2,BAHD1,BLMH,BRIX1,DDIAS,RLIG1,DHRS4-AS1,RIOX1,TIMM21,FSAF1,ELP6,INIP,CAMKK1,NAXD,CCDC12,TRMT13,SPDL1,CDC23,CDC40,CEP97,CERK,CLP1,CLPP,COPS6,COQ9,KAT14,DAAM1,DCAF13,DCAF4,DDX28,EXO5,UTP25,DIS3L,DNAAF2,DNAJC11,DNAJC28,DNAL1,DOK2,DSTYK,DUSP7,EDC3,ENDOG,EXOSC5,EXOSC7,FAM168B,MTFR2,RIPOR1,FAM78A,FAM98A,FAM98B,FASTKD5,FBXO21,FBXO33,FKBP14,FLAD1,FLVCR2,FOS,FRAT2,MRM2,G2E3,GABPA,GATC,GBA2,GEMIN6,GMCL1,GPATCH1,GSPT2,GTF3C4,GTF3C5,GXYLT1,HENMT1,HRAS,HRH1,HS3ST1,HSD17B10,IFNGR1,ELP1,IMP4,IRF3,IRF5,KBTBD7,KLHL42,MAGOH-DT,NCBP2AS2,OIP5-AS1,IRAG2,LRR1,MAP7,MCEE,MED11,MED29,MED31,MRTFA,MRPL12,MRPL4,MRPS11,MRPS2,MRPS33,MSH2,MTFMT,MTMR12,NAIF1,NAP1L5,NAPEPLD,CIAO3,NAT9,FLVCR1-DT,NDUFA5,NFATC3,NFIA,NLRP2,NME6,NOL11,NUDT4,NUDT6,NUP37,OSGEPL1,PABPN1,PDE6D,PDIK1L,PEX1,PIK3R1,PIK3R4,PIP4K2B,PLEKHJ1,PLXNA1,PNP,PNPLA6,POLE3,POLR2D,POLR3B,POLR3H,POP1,POP5,PPP1R14B,PRADC1,PRMT7,,RANGRF,TRMT10C,RNF166,RNF7,RPAP2,RPP40,RUNX1,SEC22C,SETD6,SGK1,SLC19A2,SLC2A9,SUV39H2,TARBP2,TATDN2,TEX264,THAP11,THNSL1,THYN1,TMTC4,TNFAIP8L2,TNRC18,TOMM40L,TP53RK,TRMT1,TSPYL5,EIPR1,TRAPPC12,TTLL1,TUBB6,UBAC1,UMPS,UNG,URB2,USP38,USP46,UTP11,VASH1,WDR53,WNT5B,YLPM1,ZCCHC17,ZCCHC24,ZNF180,ZNF227,ZNF30,ZNF319,ZNF35,ZNF559,ZNF641,ZFP69,ZNF789,ZNF813
FOUNDER_NAMES