SZGR2

Summary ?

GeneID	3400
Symbol	ID4
Synonyms	IDB4\|bHLHb27
Description	inhibitor of DNA binding 4, HLH protein
Reference	MIM:600581\|HGNC:HGNC:5363\|HPRD:08995\|
Gene type	protein-coding
Map location	6p22.3
Pascal p-value	0.069
Sherlock p-value	0.145
Fetal beta	1.754
DMG	1 (# studies)
eGene	Myers' cis & trans

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:GWASdb	Genome-wide Association Studies	GWASdb records for schizophrenia
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: 0.033
GO_Annotation	Mapping neuro-related keywords to Gene Ontology annotations	Hits with neuro-related keywords: 5

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg02401132	6	19805404	ID4	1.26E-8	-0.014	5.09E-6	DMG:Jaffe_2016

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	pvalue	qvalue	TSS distance	eQTL type
rs409642	chr20	54250273	ID4	3400		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
ARFIP2	0.89	0.81
PSMC4	0.88	0.83
SARS	0.87	0.81
NSFL1C	0.87	0.82
PMPCA	0.87	0.81
TCF25	0.87	0.78
LCMT1	0.87	0.82
PSMD4	0.87	0.83
NDUFS2	0.87	0.79
AHSA1	0.87	0.82

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
AF347015.8	-0.75	-0.61
AF347015.2	-0.74	-0.61
AF347015.21	-0.74	-0.59
MT-CO2	-0.73	-0.58
AF347015.31	-0.73	-0.61
AF347015.33	-0.73	-0.62
MT-CYB	-0.72	-0.60
AF347015.26	-0.72	-0.63
AF347015.15	-0.72	-0.62
AF347015.27	-0.71	-0.63

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0003714	transcription corepressor activity	TAS		7665172
GO:0005515	protein binding	IEA		-
GO:0030528	transcription regulator activity	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0007420	brain development	IEA	Brain (GO term level: 7)	-
GO:0007405	neuroblast proliferation	IEA	neuron (GO term level: 8)	-
GO:0048712	negative regulation of astrocyte differentiation	IEA	astrocyte, Glial (GO term level: 12)	-
GO:0021895	cerebral cortex neuron differentiation	IEA	neuron, Brain (GO term level: 9)	-
GO:0045665	negative regulation of neuron differentiation	IEA	neuron (GO term level: 10)	-
GO:0000082	G1/S transition of mitotic cell cycle	IEA		-
GO:0006357	regulation of transcription from RNA polymerase II promoter	TAS		7665172
GO:0008284	positive regulation of cell proliferation	IEA		-
GO:0021766	hippocampus development	IEA		-
GO:0045449	regulation of transcription	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005634	nucleus	IEA		-

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG TGF BETA SIGNALING PATHWAY	86	64	All SZGR 2.0 genes in this pathway
LIU PROSTATE CANCER DN	481	290	All SZGR 2.0 genes in this pathway
ONKEN UVEAL MELANOMA DN	526	357	All SZGR 2.0 genes in this pathway
CHEMNITZ RESPONSE TO PROSTAGLANDIN E2 DN	391	222	All SZGR 2.0 genes in this pathway
TURASHVILI BREAST DUCTAL CARCINOMA VS DUCTAL NORMAL DN	198	110	All SZGR 2.0 genes in this pathway
TURASHVILI BREAST DUCTAL CARCINOMA VS LOBULAR NORMAL DN	69	43	All SZGR 2.0 genes in this pathway
TURASHVILI BREAST LOBULAR CARCINOMA VS DUCTAL NORMAL DN	91	53	All SZGR 2.0 genes in this pathway
TURASHVILI BREAST LOBULAR CARCINOMA VS LOBULAR NORMAL UP	94	59	All SZGR 2.0 genes in this pathway
ZHOU INFLAMMATORY RESPONSE LIVE UP	485	293	All SZGR 2.0 genes in this pathway
THUM SYSTOLIC HEART FAILURE UP	423	283	All SZGR 2.0 genes in this pathway
VECCHI GASTRIC CANCER EARLY DN	367	220	All SZGR 2.0 genes in this pathway
PAPASPYRIDONOS UNSTABLE ATEROSCLEROTIC PLAQUE DN	43	29	All SZGR 2.0 genes in this pathway
SENESE HDAC1 TARGETS DN	260	143	All SZGR 2.0 genes in this pathway
SENESE HDAC2 TARGETS DN	133	77	All SZGR 2.0 genes in this pathway
KIM WT1 TARGETS 8HR UP	164	122	All SZGR 2.0 genes in this pathway
KIM WT1 TARGETS 12HR UP	162	116	All SZGR 2.0 genes in this pathway
WAMUNYOKOLI OVARIAN CANCER GRADES 1 2 DN	67	43	All SZGR 2.0 genes in this pathway
ENK UV RESPONSE EPIDERMIS DN	508	354	All SZGR 2.0 genes in this pathway
DELYS THYROID CANCER DN	232	154	All SZGR 2.0 genes in this pathway
MARKEY RB1 ACUTE LOF DN	228	137	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
BERENJENO TRANSFORMED BY RHOA DN	394	258	All SZGR 2.0 genes in this pathway
MCBRYAN PUBERTAL BREAST 3 4WK UP	214	144	All SZGR 2.0 genes in this pathway
MCBRYAN PUBERTAL BREAST 4 5WK UP	271	175	All SZGR 2.0 genes in this pathway
MCBRYAN PUBERTAL TGFB1 TARGETS DN	62	44	All SZGR 2.0 genes in this pathway
BEGUM TARGETS OF PAX3 FOXO1 FUSION UP	60	45	All SZGR 2.0 genes in this pathway
PEREZ TP53 TARGETS	1174	695	All SZGR 2.0 genes in this pathway
PEREZ TP63 TARGETS	355	243	All SZGR 2.0 genes in this pathway
PEREZ TP53 AND TP63 TARGETS	205	145	All SZGR 2.0 genes in this pathway
BEGUM TARGETS OF PAX3 FOXO1 FUSION AND PAX3	7	5	All SZGR 2.0 genes in this pathway
MARTORIATI MDM4 TARGETS NEUROEPITHELIUM DN	164	111	All SZGR 2.0 genes in this pathway
DAWSON METHYLATED IN LYMPHOMA TCL1	59	45	All SZGR 2.0 genes in this pathway
SASAI RESISTANCE TO NEOPLASTIC TRANSFROMATION	50	31	All SZGR 2.0 genes in this pathway
HATADA METHYLATED IN LUNG CANCER UP	390	236	All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 48HR DN	428	306	All SZGR 2.0 genes in this pathway
KOYAMA SEMA3B TARGETS DN	411	249	All SZGR 2.0 genes in this pathway
BENPORATH ES CORE NINE CORRELATED	100	68	All SZGR 2.0 genes in this pathway
NIKOLSKY BREAST CANCER 6P24 P22 AMPLICON	21	17	All SZGR 2.0 genes in this pathway
JI METASTASIS REPRESSED BY STK11	27	17	All SZGR 2.0 genes in this pathway
JECHLINGER EPITHELIAL TO MESENCHYMAL TRANSITION DN	66	47	All SZGR 2.0 genes in this pathway
MATSUDA NATURAL KILLER DIFFERENTIATION	475	313	All SZGR 2.0 genes in this pathway
HASLINGER B CLL WITH 13Q14 DELETION	24	18	All SZGR 2.0 genes in this pathway
AFFAR YY1 TARGETS UP	214	133	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE INCIPIENT UP	390	242	All SZGR 2.0 genes in this pathway
DEBIASI APOPTOSIS BY REOVIRUS INFECTION UP	314	201	All SZGR 2.0 genes in this pathway
KAAB HEART ATRIUM VS VENTRICLE UP	249	170	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE UP	1691	1088	All SZGR 2.0 genes in this pathway
LU AGING BRAIN UP	262	186	All SZGR 2.0 genes in this pathway
WELCSH BRCA1 TARGETS UP	198	132	All SZGR 2.0 genes in this pathway
YEGNASUBRAMANIAN PROSTATE CANCER	128	60	All SZGR 2.0 genes in this pathway
RIGGI EWING SARCOMA PROGENITOR UP	430	288	All SZGR 2.0 genes in this pathway
GAUTSCHI SRC SIGNALING	8	6	All SZGR 2.0 genes in this pathway
SMID BREAST CANCER RELAPSE IN BONE DN	315	197	All SZGR 2.0 genes in this pathway
SMID BREAST CANCER LUMINAL B DN	564	326	All SZGR 2.0 genes in this pathway
SMID BREAST CANCER NORMAL LIKE UP	476	285	All SZGR 2.0 genes in this pathway
SMID BREAST CANCER BASAL UP	648	398	All SZGR 2.0 genes in this pathway
LE SKI TARGETS DN	8	6	All SZGR 2.0 genes in this pathway
WEST ADRENOCORTICAL TUMOR DN	546	362	All SZGR 2.0 genes in this pathway
HAN SATB1 TARGETS UP	395	249	All SZGR 2.0 genes in this pathway
COLINA TARGETS OF 4EBP1 AND 4EBP2	356	214	All SZGR 2.0 genes in this pathway
MCMURRAY TP53 HRAS COOPERATION RESPONSE DN	67	46	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
LOPEZ EPITHELIOID MESOTHELIOMA	17	11	All SZGR 2.0 genes in this pathway
WONG ADULT TISSUE STEM MODULE	721	492	All SZGR 2.0 genes in this pathway
GOBERT OLIGODENDROCYTE DIFFERENTIATION DN	1080	713	All SZGR 2.0 genes in this pathway
SERVITJA ISLET HNF1A TARGETS UP	163	111	All SZGR 2.0 genes in this pathway
PLASARI TGFB1 TARGETS 1HR UP	34	26	All SZGR 2.0 genes in this pathway
LIM MAMMARY STEM CELL UP	489	314	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-1/206	140	146	1A	hsa-miR-1	UGGAAUGUAAAGAAGUAUGUA
				hsa-miR-206^SZ	UGGAAUGUAAGGAAGUGUGUGG
				hsa-miR-613	AGGAAUGUUCCUUCUUUGCC
miR-10	939	945	m8	hsa-miR-10a	UACCCUGUAGAUCCGAAUUUGUG
miR-10	939	945	m8	hsa-miR-10b	UACCCUGUAGAACCGAAUUUGU
miR-101	586	592	1A	hsa-miR-101	UACAGUACUGUGAUAACUGAAG
miR-144	585	592	1A,m8	hsa-miR-144	UACAGUAUAGAUGAUGUACUAG
miR-149	35	41	m8	hsa-miR-149^brain	UCUGGCUCCGUGUCUUCACUCC
miR-188	1308	1314	1A	hsa-miR-188	CAUCCCUUGCAUGGUGGAGGGU
miR-19	187	193	m8	hsa-miR-19a	UGUGCAAAUCUAUGCAAAACUGA
miR-19	187	193	m8	hsa-miR-19b	UGUGCAAAUCCAUGCAAAACUGA
miR-192/215	996	1002	1A	hsa-miR-192	CUGACCUAUGAAUUGACAGCC
miR-192/215	996	1002	1A	hsa-miR-215	AUGACCUAUGAAUUGACAGAC
miR-194	494	500	1A	hsa-miR-194	UGUAACAGCAACUCCAUGUGGA
miR-203.1	522	529	1A,m8	hsa-miR-203	UGAAAUGUUUAGGACCACUAG
miR-27	246	252	1A	hsa-miR-27a^brain	UUCACAGUGGCUAAGUUCCGC
miR-27	246	252	1A	hsa-miR-27b^brain	UUCACAGUGGCUAAGUUCUGC
miR-320	390	396	1A	hsa-miR-320	AAAAGCUGGGUUGAGAGGGCGAA
miR-342	559	566	1A,m8	hsa-miR-342^brain	UCUCACACAGAAAUCGCACCCGUC
miR-374	593	599	1A	hsa-miR-374	UUAUAAUACAACCUGAUAAGUG
miR-374	593	599	1A	hsa-miR-374	UUAUAAUACAACCUGAUAAGUG
miR-486	937	943	m8	hsa-miR-486	UCCUGUACUGAGCUGCCCCGAG
miR-543	491	498	1A,m8	hsa-miR-543	AAACAUUCGCGGUGCACUUCU
miR-9	1201	1207	m8	hsa-miR-9^SZ	UCUUUGGUUAUCUAGCUGUAUGA
miR-9	1201	1207	m8	hsa-miR-9^SZ	UCUUUGGUUAUCUAGCUGUAUGA

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: ID4