SZGR2

Summary ?

GeneID	3659
Symbol	IRF1
Synonyms	IRF-1\|MAR
Description	interferon regulatory factor 1
Reference	MIM:147575\|HGNC:HGNC:6116\|Ensembl:ENSG00000125347\|HPRD:00961\|Vega:OTTHUMG00000059497
Gene type	protein-coding
Map location	5q31.1
Pascal p-value	0.095
Sherlock p-value	0.963
Fetal beta	-0.854
DMG	1 (# studies)
eGene	Myers' cis & trans

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:PGCnp	Genome-wide Association Study	GWAS
DMG:Jaffe_2016	Genome-wide DNA methylation analysis	This dataset includes 2,104 probes/CpGs associated with SZ patients (n=108) compared to 136 controls at Bonferroni-adjusted P < 0.05.	1
GSMA_I	Genome scan meta-analysis	Psr: 0.0032

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg22594055	5	131832675	IRF1	2.02E-8	-0.009	6.99E-6	DMG:Jaffe_2016

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	qvalue	eQTL type
rs1342707	chr1	147264296	IRF1	3659	0	trans
rs10495652	chr2	17139288	IRF1	3659	0.03	trans
rs6531271	chr2	17139932	IRF1	3659	0.03	trans
rs12620194	chr2	17148003	IRF1	3659	0.03	trans
rs277655	chr3	100044586	IRF1	3659	0.17	trans
rs6551878	chr4	65690588	IRF1	3659	0.04	trans
rs10516136	chr5	176381368	IRF1	3659	0.1	trans
rs9397692	chr6	154487314	IRF1	3659	0.07	trans
rs9384190	chr6	154524473	IRF1	3659	0.14	trans
rs1111835	chr13	79482717	IRF1	3659	0.11	trans

Section II. Transcriptome annotation

General gene expression (GTEx)

Gene expression during devlopment (BrainCloud)

Footnote:
A total of 269 time points ploted, with n=38 fetal samples (x=1:38). Each triangle represents one time point.

Gene expression of temporal and spatial changes (BrainSpan)

Footnote:
SC: sub-cortical regions; SM: sensory-motor regions; FC: frontal cortex; and TP: temporal-parietal cortex
ST1: fetal (13 - 26 postconception weeks), ST2: early infancy to late childhood (4 months to 11 years), and ST3: adolescence to adulthood (13 - 23 years)
The bar shown representes the lower 25% and upper 25% of the expression distribution.

Top co-expressed genes in brain regions

Top 10 positively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
SELPLG	0.81	0.81
CSF1R	0.81	0.82
CYBB	0.79	0.75
P2RY13	0.79	0.70
APBB1IP	0.78	0.77
PTPRC	0.77	0.77
LAPTM5	0.77	0.77
CTSS	0.75	0.72
P2RY12	0.74	0.72
LPAR5	0.73	0.74

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
BCL7C	-0.34	-0.41
RP9P	-0.30	-0.41
SH2B2	-0.30	-0.30
AC132872.1	-0.29	-0.29
SNHG12	-0.28	-0.30
ST20	-0.28	-0.34
PPP1R14B	-0.28	-0.37
NUDT8	-0.28	-0.23
FAM167B	-0.28	-0.29
RPL23A	-0.28	-0.34

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0003700	transcription factor activity	IEA		-
GO:0043565	sequence-specific DNA binding	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0006350	transcription	IEA		-
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	IEA		-
GO:0045084	positive regulation of interleukin-12 biosynthetic process	IEA		-
GO:0045786	negative regulation of cell cycle	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005634	nucleus	IEA		-

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
CSNK2A1	CK2A1 \| CKII	casein kinase 2, alpha 1 polypeptide	An unspecified isoform of CK2-alpha interacts with IRF-1 promoter.	BIND	15893730
CSNK2B	CK2B \| CK2N \| CSK2B \| G5A \| MGC138222 \| MGC138224	casein kinase 2, beta polypeptide	CK2-beta interacts with IRF-1 promoter.	BIND	15893730
CTDP1	CCFDN \| FCP1	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) phosphatase, subunit 1	An unspecified isoform of CTD interacts with IRF-1 promoter.	BIND	15893730
DR1	NC2 \| NC2-BETA	down-regulator of transcription 1, TBP-binding (negative cofactor 2)	Dr1 interacts with IRF-1 promoter.	BIND	15893730
DRAP1	NC2-alpha	DR1-associated protein 1 (negative cofactor 2 alpha)	DRAP1 interacts with IRF-1 promoter.	BIND	15893730
ERCC3	BTF2 \| GTF2H \| RAD25 \| TFIIH \| XPB	excision repair cross-complementing rodent repair deficiency, complementation group 3 (xeroderma pigmentosum group B complementing)	TFIIH interacts with IRF-1 promoter.	BIND	15893730
GTF2F1	BTF4 \| RAP74 \| TF2F1 \| TFIIF	general transcription factor IIF, polypeptide 1, 74kDa	TFIIF interacts with IRF-1 promoter.	BIND	15893730
HMGA1	HMG-R \| HMGA1A \| HMGIY \| MGC12816 \| MGC4242 \| MGC4854	high mobility group AT-hook 1	-	HPRD,BioGRID	10357819
IRF8	H-ICSBP \| ICSBP \| ICSBP1 \| IRF-8	interferon regulatory factor 8	-	HPRD,BioGRID	7768900 \|9742224
KAT2A	GCN5 \| GCN5L2 \| MGC102791 \| PCAF-b \| hGCN5	K(lysine) acetyltransferase 2A	Reconstituted Complex	BioGRID	10022868
KAT2B	CAF \| P \| P/CAF \| PCAF	K(lysine) acetyltransferase 2B	-	HPRD,BioGRID	10022868 \|11304541
MED23	CRSP130 \| CRSP133 \| CRSP3 \| DKFZp434H0117 \| DRIP130 \| SUR2	mediator complex subunit 23	An unspecified isoform of MED23 interacts with IRF-1 promoter.	BIND	15893730
NFKB1	DKFZp686C01211 \| EBP-1 \| KBF1 \| MGC54151 \| NF-kappa-B \| NFKB-p105 \| NFKB-p50 \| p105	nuclear factor of kappa light polypeptide gene enhancer in B-cells 1	-	HPRD	8746784
POLR2D	HSRBP4 \| HSRPB4 \| RBP4	polymerase (RNA) II (DNA directed) polypeptide D	Rbp4 interacts with IRF-1 promoter.	BIND	15893730
POLR2D	HSRBP4 \| HSRPB4 \| RBP4	polymerase (RNA) II (DNA directed) polypeptide D	Rbp4 interacts with IRF-1.	BIND	15893730
STAT1	DKFZp686B04100 \| ISGF-3 \| STAT91	signal transducer and activator of transcription 1, 91kDa	-	HPRD,BioGRID	10764778
SUB1	MGC102747 \| P15 \| PC4 \| p14	SUB1 homolog (S. cerevisiae)	PC4 interacts with IRF-1 promoter.	BIND	15893730
TBP	GTF2D \| GTF2D1 \| MGC117320 \| MGC126054 \| MGC126055 \| SCA17 \| TFIID	TATA box binding protein	TBP interacts with IRF-1 promoter.	BIND	15893730

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
PID TELOMERASE PATHWAY	68	48	All SZGR 2.0 genes in this pathway
PID REG GR PATHWAY	82	60	All SZGR 2.0 genes in this pathway
PID IFNG PATHWAY	40	34	All SZGR 2.0 genes in this pathway
PID IL6 7 PATHWAY	47	40	All SZGR 2.0 genes in this pathway
PID IL12 STAT4 PATHWAY	33	29	All SZGR 2.0 genes in this pathway
REACTOME TRAF6 MEDIATED IRF7 ACTIVATION	30	26	All SZGR 2.0 genes in this pathway
REACTOME FACTORS INVOLVED IN MEGAKARYOCYTE DEVELOPMENT AND PLATELET PRODUCTION	132	101	All SZGR 2.0 genes in this pathway
REACTOME INTERFERON GAMMA SIGNALING	63	48	All SZGR 2.0 genes in this pathway
REACTOME INTERFERON ALPHA BETA SIGNALING	64	50	All SZGR 2.0 genes in this pathway
REACTOME INTERFERON SIGNALING	159	116	All SZGR 2.0 genes in this pathway
REACTOME RIG I MDA5 MEDIATED INDUCTION OF IFN ALPHA BETA PATHWAYS	73	57	All SZGR 2.0 genes in this pathway
REACTOME HEMOSTASIS	466	331	All SZGR 2.0 genes in this pathway
REACTOME INNATE IMMUNE SYSTEM	279	178	All SZGR 2.0 genes in this pathway
REACTOME IMMUNE SYSTEM	933	616	All SZGR 2.0 genes in this pathway
REACTOME CYTOKINE SIGNALING IN IMMUNE SYSTEM	270	204	All SZGR 2.0 genes in this pathway
BERTUCCI MEDULLARY VS DUCTAL BREAST CANCER UP	206	111	All SZGR 2.0 genes in this pathway
GARY CD5 TARGETS UP	473	314	All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA DN	77	52	All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY SERUM DEPRIVATION UP	552	347	All SZGR 2.0 genes in this pathway
GRAESSMANN RESPONSE TO MC AND SERUM DEPRIVATION UP	211	136	All SZGR 2.0 genes in this pathway
BARIS THYROID CANCER DN	59	45	All SZGR 2.0 genes in this pathway
PEREZ TP53 TARGETS	1174	695	All SZGR 2.0 genes in this pathway
DACOSTA UV RESPONSE VIA ERCC3 XPCS UP	28	16	All SZGR 2.0 genes in this pathway
RASHI RESPONSE TO IONIZING RADIATION 2	127	92	All SZGR 2.0 genes in this pathway
RASHI NFKB1 TARGETS	19	18	All SZGR 2.0 genes in this pathway
SCHLOSSER SERUM RESPONSE UP	134	93	All SZGR 2.0 genes in this pathway
BOWIE RESPONSE TO EXTRACELLULAR MATRIX	17	11	All SZGR 2.0 genes in this pathway
BOWIE RESPONSE TO TAMOXIFEN	18	10	All SZGR 2.0 genes in this pathway
DACOSTA UV RESPONSE VIA ERCC3 UP	309	199	All SZGR 2.0 genes in this pathway
YAN ESCAPE FROM ANOIKIS	24	19	All SZGR 2.0 genes in this pathway
SASAI RESISTANCE TO NEOPLASTIC TRANSFROMATION	50	31	All SZGR 2.0 genes in this pathway
NUYTTEN EZH2 TARGETS UP	1037	673	All SZGR 2.0 genes in this pathway
BUYTAERT PHOTODYNAMIC THERAPY STRESS UP	811	508	All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 48HR DN	428	306	All SZGR 2.0 genes in this pathway
BENPORATH ES CORE NINE CORRELATED	100	68	All SZGR 2.0 genes in this pathway
SHIN B CELL LYMPHOMA CLUSTER 1	13	11	All SZGR 2.0 genes in this pathway
ZHANG RESPONSE TO IKK INHIBITOR AND TNF UP	223	140	All SZGR 2.0 genes in this pathway
GRANDVAUX IFN RESPONSE NOT VIA IRF3	14	10	All SZGR 2.0 genes in this pathway
DER IFN ALPHA RESPONSE UP	74	48	All SZGR 2.0 genes in this pathway
RADAEVA RESPONSE TO IFNA1 UP	52	40	All SZGR 2.0 genes in this pathway
DER IFN BETA RESPONSE UP	102	67	All SZGR 2.0 genes in this pathway
BROCKE APOPTOSIS REVERSED BY IL6	144	98	All SZGR 2.0 genes in this pathway
DER IFN GAMMA RESPONSE UP	71	45	All SZGR 2.0 genes in this pathway
SANSOM APC TARGETS DN	366	238	All SZGR 2.0 genes in this pathway
ABBUD LIF SIGNALING 1 UP	46	29	All SZGR 2.0 genes in this pathway
ZHAN V2 LATE DIFFERENTIATION GENES	45	34	All SZGR 2.0 genes in this pathway
NATSUME RESPONSE TO INTERFERON BETA UP	71	49	All SZGR 2.0 genes in this pathway
JIANG VHL TARGETS	138	91	All SZGR 2.0 genes in this pathway
ZHU CMV ALL UP	120	89	All SZGR 2.0 genes in this pathway
GEISS RESPONSE TO DSRNA UP	38	29	All SZGR 2.0 genes in this pathway
HEDENFALK BREAST CANCER BRCA1 VS BRCA2	163	113	All SZGR 2.0 genes in this pathway
ZHU CMV 24 HR UP	93	65	All SZGR 2.0 genes in this pathway
BURTON ADIPOGENESIS 11	57	40	All SZGR 2.0 genes in this pathway
WALLACE PROSTATE CANCER RACE UP	299	167	All SZGR 2.0 genes in this pathway
ACEVEDO LIVER CANCER DN	540	340	All SZGR 2.0 genes in this pathway
MITSIADES RESPONSE TO APLIDIN UP	439	257	All SZGR 2.0 genes in this pathway
BOQUEST STEM CELL CULTURED VS FRESH UP	425	298	All SZGR 2.0 genes in this pathway
WEST ADRENOCORTICAL TUMOR DN	546	362	All SZGR 2.0 genes in this pathway
QI PLASMACYTOMA UP	259	185	All SZGR 2.0 genes in this pathway
ISHIKAWA STING SIGNALING	8	6	All SZGR 2.0 genes in this pathway
FERRARI RESPONSE TO FENRETINIDE UP	22	16	All SZGR 2.0 genes in this pathway
ICHIBA GRAFT VERSUS HOST DISEASE D7 UP	107	67	All SZGR 2.0 genes in this pathway
PARK TRETINOIN RESPONSE AND PML RARA FUSION	30	21	All SZGR 2.0 genes in this pathway
ZHANG INTERFERON RESPONSE	23	14	All SZGR 2.0 genes in this pathway
HINATA NFKB TARGETS KERATINOCYTE UP	91	63	All SZGR 2.0 genes in this pathway
HINATA NFKB TARGETS FIBROBLAST UP	84	60	All SZGR 2.0 genes in this pathway
LIU VAV3 PROSTATE CARCINOGENESIS UP	89	61	All SZGR 2.0 genes in this pathway
WORSCHECH TUMOR EVASION AND TOLEROGENICITY DN	14	11	All SZGR 2.0 genes in this pathway
HOSHIDA LIVER CANCER SUBCLASS S1	237	159	All SZGR 2.0 genes in this pathway
ZHAN MULTIPLE MYELOMA LB DN	44	23	All SZGR 2.0 genes in this pathway
TIAN TNF SIGNALING VIA NFKB	28	21	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 2HR UP	39	30	All SZGR 2.0 genes in this pathway
MARTENS BOUND BY PML RARA FUSION	456	287	All SZGR 2.0 genes in this pathway
MARTENS TRETINOIN RESPONSE UP	857	456	All SZGR 2.0 genes in this pathway
KIM GLIS2 TARGETS UP	84	61	All SZGR 2.0 genes in this pathway
FEVR CTNNB1 TARGETS UP	682	433	All SZGR 2.0 genes in this pathway
KRIEG KDM3A TARGETS NOT HYPOXIA	208	107	All SZGR 2.0 genes in this pathway
ALFANO MYC TARGETS	239	156	All SZGR 2.0 genes in this pathway
PHONG TNF TARGETS UP	63	43	All SZGR 2.0 genes in this pathway
PHONG TNF RESPONSE NOT VIA P38	337	236	All SZGR 2.0 genes in this pathway
GHANDHI DIRECT IRRADIATION DN	33	23	All SZGR 2.0 genes in this pathway
ZWANG CLASS 1 TRANSIENTLY INDUCED BY EGF	516	308	All SZGR 2.0 genes in this pathway
ZWANG EGF INTERVAL DN	214	124	All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA family	Target position			miRNA ID	miRNA seq
miRNA family	UTR start	UTR end	Match method	miRNA ID	miRNA seq
miR-124/506	680	686	m8	hsa-miR-506	UAAGGCACCCUUCUGAGUAGA
miR-124/506	680	686	m8	hsa-miR-124^brain	UAAGGCACGCGGUGAAUGCC
miR-130/301	410	417	1A,m8	hsa-miR-130a^brain	CAGUGCAAUGUUAAAAGGGCAU
				hsa-miR-301	CAGUGCAAUAGUAUUGUCAAAGC
				hsa-miR-130b^brain	CAGUGCAAUGAUGAAAGGGCAU
				hsa-miR-454-3p	UAGUGCAAUAUUGCUUAUAGGGUUU
miR-17-5p/20/93.mr/106/519.d	589	595	m8	hsa-miR-17-5p	CAAAGUGCUUACAGUGCAGGUAGU
				hsa-miR-20a^brain	UAAAGUGCUUAUAGUGCAGGUAG
				hsa-miR-106a	AAAAGUGCUUACAGUGCAGGUAGC
				hsa-miR-106b^SZ	UAAAGUGCUGACAGUGCAGAU
				hsa-miR-20b^SZ	CAAAGUGCUCAUAGUGCAGGUAG
				hsa-miR-519d	CAAAGUGCCUCCCUUUAGAGUGU
miR-23	487	494	1A,m8	hsa-miR-23a^brain	AUCACAUUGCCAGGGAUUUCC
miR-23	487	494	1A,m8	hsa-miR-23b^brain	AUCACAUUGCCAGGGAUUACC
miR-323	487	493	1A	hsa-miR-323^brain	GCACAUUACACGGUCGACCUCU
miR-383	618	625	1A,m8	hsa-miR-383^brain	AGAUCAGAAGGUGAUUGUGGCU

SZ: miRNAs which differentially expressed in brain cortex of schizophrenia patients comparing with control samples using microarray. Click here to see the list of SZ related miRNAs.
Brain: miRNAs which are expressed in brain based on miRNA microarray expression studies. Click here to see the list of brain related miRNAs.

Gene Page: IRF1