SZGR2

Summary ?

GeneID	1960
Symbol	EGR3
Synonyms	EGR-3\|PILOT
Description	early growth response 3
Reference	MIM:602419\|HGNC:HGNC:3240\|Ensembl:ENSG00000179388\|HPRD:03881\|Vega:OTTHUMG00000097825
Gene type	protein-coding
Map location	8p23-p21
Pascal p-value	0.773
Fetal beta	-4.408
eGene	Myers' cis & trans

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:PGCnp	Genome-wide Association Study	GWAS
PMID:cooccur	High-throughput literature-search	Systematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
Association	A combined odds ratio method (Sun et al. 2008), association studies	2	Link to SZGene
GSMA_I	Genome scan meta-analysis	Psr: 0.031
GSMA_IIA	Genome scan meta-analysis (All samples)	Psr: 0.03086
GSMA_IIE	Genome scan meta-analysis (European-ancestry samples)	Psr: 0.00057
Literature	High-throughput literature-search	Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenic,schizophrenias	Click to show details
GO_Annotation	Mapping neuro-related keywords to Gene Ontology annotations	Hits with neuro-related keywords: 1

Section I. Genetics and epigenetics annotation

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	qvalue	eQTL type
rs5944689	chrX	24860329	EGR3	1960	0.14	trans
rs5973369	chrX	35392270	EGR3	1960	0.17	trans
rs5973375	chrX	35489060	EGR3	1960	0.2	trans
rs2171999	chrX	35498985	EGR3	1960	0.19	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
NONO	0.96	0.93
INTS7	0.96	0.95
XRN2	0.96	0.93
EIF2S3	0.96	0.95
RBMX	0.96	0.93
CSGALNACT2	0.95	0.94
USP3	0.95	0.82
MCPH1	0.95	0.94
ANP32A	0.95	0.93
CAPRIN1	0.95	0.94

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
AIFM3	-0.69	-0.83
HLA-F	-0.69	-0.79
C5orf53	-0.68	-0.76
PTH1R	-0.67	-0.78
FXYD1	-0.67	-0.91
AF347015.31	-0.67	-0.87
IFI27	-0.67	-0.90
TSC22D4	-0.67	-0.82
MT-CO2	-0.66	-0.88
HEPN1	-0.66	-0.77

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0003700	transcription factor activity	TAS		1906159 \|9731539
GO:0008270	zinc ion binding	IEA		-
GO:0046872	metal ion binding	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0007274	neuromuscular synaptic transmission	IEA	neuron, Synap (GO term level: 7)	-
GO:0006355	regulation of transcription, DNA-dependent	IEA		-
GO:0006350	transcription	IEA		-
GO:0007517	muscle development	TAS		9731539
GO:0007623	circadian rhythm	TAS		9488654
GO:0007422	peripheral nervous system development	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005622	intracellular	IEA		-
GO:0005634	nucleus	IEA		-

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
BIOCARTA VIP PATHWAY	29	26	All SZGR 2.0 genes in this pathway
ST DIFFERENTIATION PATHWAY IN PC12 CELLS	45	35	All SZGR 2.0 genes in this pathway
PID NFAT TFPATHWAY	47	39	All SZGR 2.0 genes in this pathway
ONKEN UVEAL MELANOMA UP	783	507	All SZGR 2.0 genes in this pathway
HUTTMANN B CLL POOR SURVIVAL DN	60	39	All SZGR 2.0 genes in this pathway
OSWALD HEMATOPOIETIC STEM CELL IN COLLAGEN GEL UP	233	161	All SZGR 2.0 genes in this pathway
RHEIN ALL GLUCOCORTICOID THERAPY DN	362	238	All SZGR 2.0 genes in this pathway
MULLIGHAN MLL SIGNATURE 1 DN	242	165	All SZGR 2.0 genes in this pathway
MULLIGHAN MLL SIGNATURE 2 DN	281	186	All SZGR 2.0 genes in this pathway
TONKS TARGETS OF RUNX1 RUNX1T1 FUSION HSC DN	187	115	All SZGR 2.0 genes in this pathway
NAGASHIMA NRG1 SIGNALING UP	176	123	All SZGR 2.0 genes in this pathway
NAGASHIMA EGF SIGNALING UP	58	40	All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA ANAPLASTIC DN	537	339	All SZGR 2.0 genes in this pathway
GOZGIT ESR1 TARGETS DN	781	465	All SZGR 2.0 genes in this pathway
PACHER TARGETS OF IGF1 AND IGF2 UP	35	27	All SZGR 2.0 genes in this pathway
KOKKINAKIS METHIONINE DEPRIVATION 48HR UP	128	95	All SZGR 2.0 genes in this pathway
KOKKINAKIS METHIONINE DEPRIVATION 96HR UP	117	84	All SZGR 2.0 genes in this pathway
ENK UV RESPONSE EPIDERMIS DN	508	354	All SZGR 2.0 genes in this pathway
GAUSSMANN MLL AF4 FUSION TARGETS E UP	97	60	All SZGR 2.0 genes in this pathway
CHASSOT SKIN WOUND	10	9	All SZGR 2.0 genes in this pathway
FARMER BREAST CANCER APOCRINE VS LUMINAL	326	213	All SZGR 2.0 genes in this pathway
DIRMEIER LMP1 RESPONSE EARLY	66	48	All SZGR 2.0 genes in this pathway
THEODOROU MAMMARY TUMORIGENESIS	31	24	All SZGR 2.0 genes in this pathway
SCHLESINGER METHYLATED DE NOVO IN CANCER	88	64	All SZGR 2.0 genes in this pathway
BENPORATH SOX2 TARGETS	734	436	All SZGR 2.0 genes in this pathway
BENPORATH SUZ12 TARGETS	1038	678	All SZGR 2.0 genes in this pathway
BENPORATH EED TARGETS	1062	725	All SZGR 2.0 genes in this pathway
BENPORATH ES WITH H3K27ME3	1118	744	All SZGR 2.0 genes in this pathway
BENPORATH PRC2 TARGETS	652	441	All SZGR 2.0 genes in this pathway
BENPORATH MYC TARGETS WITH EBOX	230	156	All SZGR 2.0 genes in this pathway
AMIT EGF RESPONSE 40 HELA	42	29	All SZGR 2.0 genes in this pathway
AMIT EGF RESPONSE 40 MCF10A	19	11	All SZGR 2.0 genes in this pathway
AMIT SERUM RESPONSE 60 MCF10A	57	42	All SZGR 2.0 genes in this pathway
LIN SILENCED BY TUMOR MICROENVIRONMENT	108	73	All SZGR 2.0 genes in this pathway
FRASOR RESPONSE TO ESTRADIOL UP	37	28	All SZGR 2.0 genes in this pathway
BECKER TAMOXIFEN RESISTANCE UP	50	36	All SZGR 2.0 genes in this pathway
KUROKAWA LIVER CANCER CHEMOTHERAPY DN	41	28	All SZGR 2.0 genes in this pathway
FAELT B CLL WITH VH REARRANGEMENTS UP	48	34	All SZGR 2.0 genes in this pathway
THEILGAARD NEUTROPHIL AT SKIN WOUND UP	77	52	All SZGR 2.0 genes in this pathway
KANG IMMORTALIZED BY TERT DN	102	67	All SZGR 2.0 genes in this pathway
DEBIASI APOPTOSIS BY REOVIRUS INFECTION UP	314	201	All SZGR 2.0 genes in this pathway
IVANOVA HEMATOPOIESIS STEM CELL LONG TERM	302	191	All SZGR 2.0 genes in this pathway
WANG CISPLATIN RESPONSE AND XPC DN	228	146	All SZGR 2.0 genes in this pathway
ABE VEGFA TARGETS	20	15	All SZGR 2.0 genes in this pathway
ABE VEGFA TARGETS 30MIN	29	21	All SZGR 2.0 genes in this pathway
CREIGHTON ENDOCRINE THERAPY RESISTANCE 1	528	324	All SZGR 2.0 genes in this pathway
CREIGHTON ENDOCRINE THERAPY RESISTANCE 4	307	185	All SZGR 2.0 genes in this pathway
MASSARWEH TAMOXIFEN RESISTANCE DN	258	160	All SZGR 2.0 genes in this pathway
MASSARWEH RESPONSE TO ESTRADIOL	61	47	All SZGR 2.0 genes in this pathway
SMID BREAST CANCER BASAL DN	701	446	All SZGR 2.0 genes in this pathway
WEST ADRENOCORTICAL TUMOR DN	546	362	All SZGR 2.0 genes in this pathway
LIN NPAS4 TARGETS DN	68	48	All SZGR 2.0 genes in this pathway
SEKI INFLAMMATORY RESPONSE LPS UP	77	56	All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS UP	1305	895	All SZGR 2.0 genes in this pathway
LEE SP4 THYMOCYTE	14	11	All SZGR 2.0 genes in this pathway
MEISSNER BRAIN HCP WITH H3K4ME3 AND H3K27ME3	1069	729	All SZGR 2.0 genes in this pathway
ZHAN EARLY DIFFERENTIATION GENES DN	42	29	All SZGR 2.0 genes in this pathway
YAGI AML WITH INV 16 TRANSLOCATION	422	277	All SZGR 2.0 genes in this pathway
UZONYI RESPONSE TO LEUKOTRIENE AND THROMBIN	37	26	All SZGR 2.0 genes in this pathway
DANG BOUND BY MYC	1103	714	All SZGR 2.0 genes in this pathway
DORN ADENOVIRUS INFECTION 12HR UP	29	18	All SZGR 2.0 genes in this pathway
DORN ADENOVIRUS INFECTION 24HR DN	43	32	All SZGR 2.0 genes in this pathway
DORN ADENOVIRUS INFECTION 32HR DN	39	28	All SZGR 2.0 genes in this pathway
DORN ADENOVIRUS INFECTION 48HR DN	40	29	All SZGR 2.0 genes in this pathway
CHANDRAN METASTASIS DN	306	191	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 30MIN UP	56	38	All SZGR 2.0 genes in this pathway
LI INDUCED T TO NATURAL KILLER UP	307	182	All SZGR 2.0 genes in this pathway
MARTENS TRETINOIN RESPONSE UP	857	456	All SZGR 2.0 genes in this pathway
STAMBOLSKY TARGETS OF MUTATED TP53 UP	49	35	All SZGR 2.0 genes in this pathway
KIM ALL DISORDERS OLIGODENDROCYTE NUMBER CORR UP	756	494	All SZGR 2.0 genes in this pathway
KIM ALL DISORDERS CALB1 CORR UP	548	370	All SZGR 2.0 genes in this pathway
CHICAS RB1 TARGETS SENESCENT	572	352	All SZGR 2.0 genes in this pathway
GREGORY SYNTHETIC LETHAL WITH IMATINIB	145	83	All SZGR 2.0 genes in this pathway
DUTERTRE ESTRADIOL RESPONSE 6HR UP	229	149	All SZGR 2.0 genes in this pathway
SERVITJA ISLET HNF1A TARGETS UP	163	111	All SZGR 2.0 genes in this pathway
PEDERSEN METASTASIS BY ERBB2 ISOFORM 1	46	33	All SZGR 2.0 genes in this pathway
PLASARI TGFB1 TARGETS 1HR UP	34	26	All SZGR 2.0 genes in this pathway
WANG MLL TARGETS	289	188	All SZGR 2.0 genes in this pathway
LIM MAMMARY STEM CELL UP	489	314	All SZGR 2.0 genes in this pathway
SMIRNOV RESPONSE TO IR 6HR DN	114	69	All SZGR 2.0 genes in this pathway
ZWANG CLASS 2 TRANSIENTLY INDUCED BY EGF	51	29	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
let-7/98	1594	1601	1A,m8	hsa-let-7a^brain	UGAGGUAGUAGGUUGUAUAGUU
				hsa-let-7b^brain	UGAGGUAGUAGGUUGUGUGGUU
				hsa-let-7c^brain	UGAGGUAGUAGGUUGUAUGGUU
				hsa-let-7d^brain	AGAGGUAGUAGGUUGCAUAGU
				hsa-let-7e^brain	UGAGGUAGGAGGUUGUAUAGU
				hsa-let-7f^brain	UGAGGUAGUAGAUUGUAUAGUU
				hsa-miR-98^brain	UGAGGUAGUAAGUUGUAUUGUU
				hsa-let-7g^SZ	UGAGGUAGUAGUUUGUACAGU
				hsa-let-7i^brain	UGAGGUAGUAGUUUGUGCUGU
miR-142-5p	1827	1833	m8	hsa-miR-142-5p	CAUAAAGUAGAAAGCACUAC
miR-146	2250	2256	1A	hsa-miR-146a	UGAGAACUGAAUUCCAUGGGUU
miR-146	2250	2256	1A	hsa-miR-146b^brain	UGAGAACUGAAUUCCAUAGGCU
miR-17-5p/20/93.mr/106/519.d	1826	1832	1A	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-181	1724	1731	1A,m8	hsa-miR-181a^brain	AACAUUCAACGCUGUCGGUGAGU
				hsa-miR-181b^SZ	AACAUUCAUUGCUGUCGGUGGG
				hsa-miR-181c^brain	AACAUUCAACCUGUCGGUGAGU
				hsa-miR-181d^brain	AACAUUCAUUGUUGUCGGUGGGUU
miR-182	2291	2298	1A,m8	hsa-miR-182	UUUGGCAAUGGUAGAACUCACA
miR-200bc/429	2077	2083	m8	hsa-miR-200b	UAAUACUGCCUGGUAAUGAUGAC
				hsa-miR-200c	UAAUACUGCCGGGUAAUGAUGG
				hsa-miR-429	UAAUACUGUCUGGUAAAACCGU
miR-203.1	2590	2597	1A,m8	hsa-miR-203	UGAAAUGUUUAGGACCACUAG
miR-216	1359	1366	1A,m8	hsa-miR-216	UAAUCUCAGCUGGCAACUGUG
miR-219	2741	2748	1A,m8	hsa-miR-219^brain	UGAUUGUCCAAACGCAAUUCU
miR-23	2376	2382	1A	hsa-miR-23a^brain	AUCACAUUGCCAGGGAUUUCC
				hsa-miR-23b^brain	AUCACAUUGCCAGGGAUUACC
				hsa-miR-23a^brain	AUCACAUUGCCAGGGAUUUCC
				hsa-miR-23b^brain	AUCACAUUGCCAGGGAUUACC
miR-30-5p	1800	1806	1A	hsa-miR-30a-5p	UGUAAACAUCCUCGACUGGAAG
				hsa-miR-30c^brain	UGUAAACAUCCUACACUCUCAGC
				hsa-miR-30d^SZ	UGUAAACAUCCCCGACUGGAAG
				hsa-miR-30b^SZ	UGUAAACAUCCUACACUCAGCU
				hsa-miR-30e-5p	UGUAAACAUCCUUGACUGGA
miR-323	2101	2108	1A,m8	hsa-miR-323^brain	GCACAUUACACGGUCGACCUCU
miR-331	289	295	m8	hsa-miR-331^brain	GCCCCUGGGCCUAUCCUAGAA
miR-335	581	587	1A	hsa-miR-335^brain	UCAAGAGCAAUAACGAAAAAUGU
miR-380-5p	1014	1020	1A	hsa-miR-380-5p	UGGUUGACCAUAGAACAUGCGC
miR-380-5p	1014	1020	1A	hsa-miR-563	AGGUUGACAUACGUUUCCC
miR-381	2448	2454	1A	hsa-miR-381	UAUACAAGGGCAAGCUCUCUGU
miR-494	712	718	m8	hsa-miR-494^brain	UGAAACAUACACGGGAAACCUCUU
miR-7	690	697	1A,m8	hsa-miR-7^SZ	UGGAAGACUAGUGAUUUUGUUG
miR-9	438	444	m8	hsa-miR-9^SZ	UCUUUGGUUAUCUAGCUGUAUGA
miR-96	2292	2298	1A	hsa-miR-96^brain	UUUGGCACUAGCACAUUUUUGC

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: EGR3