SZGR2

Summary ?

GeneID	4760
Symbol	NEUROD1
Synonyms	BETA2\|BHF-1\|MODY6\|NEUROD\|bHLHa3
Description	neuronal differentiation 1
Reference	MIM:601724\|HGNC:HGNC:7762\|Ensembl:ENSG00000162992\|HPRD:03428\|Vega:OTTHUMG00000132583
Gene type	protein-coding
Map location	2q32
Pascal p-value	0.323
Fetal beta	2.508
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.
Literature	High-throughput literature-search	Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenias	Click to show details
GO_Annotation	Mapping neuro-related keywords to Gene Ontology annotations	Hits with neuro-related keywords: 2
Network	Shortest path distance of core genes in the Human protein-protein interaction network	Contribution to shortest path in PPI network: 0.0024

Section I. Genetics and epigenetics annotation

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	qvalue	eQTL type
rs16829545	chr2	151977407	NEUROD1	4760	1.658E-14	trans
rs7584986	chr2	184111432	NEUROD1	4760	6.239E-6	trans
rs7609691	chr3	143427927	NEUROD1	4760	0.2	trans
rs2183142	chr4	159232695	NEUROD1	4760	0.01	trans
rs10491487	chr5	80323367	NEUROD1	4760	0.02	trans
rs6996695	chr8	77540580	NEUROD1	4760	0.06	trans
rs11139116	chr9	83896951	NEUROD1	4760	0	trans
rs12098525	chr10	87501764	NEUROD1	4760	0.12	trans
rs16955618	chr15	29937543	NEUROD1	4760	1.335E-12	trans
rs16945437	chr17	11797650	NEUROD1	4760	0.07	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
TRIP6	0.79	0.78
SYDE1	0.76	0.75
TRIP10	0.76	0.76
INPPL1	0.76	0.76
FKBP10	0.75	0.75
MOV10	0.75	0.77
LAMB2	0.74	0.76
CTDSP1	0.74	0.76
SIX5	0.73	0.75
TEAD3	0.72	0.71

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
RALYL	-0.55	-0.59
PPP3CB	-0.53	-0.56
HMGCLL1	-0.51	-0.57
PRKACB	-0.50	-0.55
FBXW7	-0.50	-0.54
RGS7	-0.50	-0.49
RAP1GDS1	-0.49	-0.53
C20orf7	-0.49	-0.58
ELOVL4	-0.49	-0.53
C1orf52	-0.49	-0.51

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0003700	transcription factor activity	IDA		10545951
GO:0003702	RNA polymerase II transcription factor activity	IDA		10545951
GO:0008134	transcription factor binding	IPI		10545951
GO:0016563	transcription activator activity	IEA		-
GO:0046982	protein heterodimerization activity	IPI		10545951
GO:0043565	sequence-specific DNA binding	IDA		10545951
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0022008	neurogenesis	TAS	neurogenesis (GO term level: 6)	8786144
GO:0030902	hindbrain development	IEA	Brain (GO term level: 8)	-
GO:0006355	regulation of transcription, DNA-dependent	IEA		-
GO:0007263	nitric oxide mediated signal transduction	IDA		17941991
GO:0009952	anterior/posterior pattern formation	IEA		-
GO:0009749	response to glucose stimulus	IMP		10545951
GO:0007275	multicellular organismal development	IEA		-
GO:0043066	negative regulation of apoptosis	ISS		9308961
GO:0031018	endocrine pancreas development	ISS		9308961
GO:0042593	glucose homeostasis	ISS		9308961
GO:0043010	camera-type eye development	IEA		-
GO:0045165	cell fate commitment	IEA		-
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	IEA		-
GO:0048562	embryonic organ morphogenesis	ISS		9308961
GO:0050796	regulation of insulin secretion	IC		10545951
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005634	nucleus	IEA		-
GO:0005737	cytoplasm	IEA		-

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
CALM1	CALML2 \| CAMI \| DD132 \| PHKD	calmodulin 1 (phosphorylase kinase, delta)	-	HPRD	10757985
CALM2	CAMII \| PHKD \| PHKD2	calmodulin 2 (phosphorylase kinase, delta)	-	HPRD	10757985
CALM3	PHKD \| PHKD3	calmodulin 3 (phosphorylase kinase, delta)	-	HPRD	10757985
CCND1	BCL1 \| D11S287E \| PRAD1 \| U21B31	cyclin D1	Affinity Capture-Western Phenotypic Suppression	BioGRID	11788592
EP300	KAT3B \| p300	E1A binding protein p300	-	HPRD,BioGRID	10545951
HAP1	HAP2 \| HIP5 \| HLP \| hHLP1	huntingtin-associated protein 1	-	HPRD,BioGRID	12881483
HTT	HD \| IT15	huntingtin	Affinity Capture-Western	BioGRID	12881483
MAFA	RIPE3b1 \| hMafA	v-maf musculoaponeurotic fibrosarcoma oncogene homolog A (avian)	-	HPRD,BioGRID	15665000
MAP3K10	MLK2 \| MST	mitogen-activated protein kinase kinase kinase 10	Affinity Capture-Western Biochemical Activity Two-hybrid	BioGRID	12881483
PDX1	GSF \| IDX-1 \| IPF1 \| IUF1 \| MODY4 \| PDX-1 \| STF-1	pancreatic and duodenal homeobox 1	-	HPRD,BioGRID	10636926
PITX1	BFT \| POTX \| PTX1	paired-like homeodomain 1	-	HPRD	9343431
RREB1	FINB \| HNT \| LZ321 \| RREB-1 \| Zep-1	ras responsive element binding protein 1	-	HPRD	12482979

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG MATURITY ONSET DIABETES OF THE YOUNG	25	19	All SZGR 2.0 genes in this pathway
REACTOME DEVELOPMENTAL BIOLOGY	396	292	All SZGR 2.0 genes in this pathway
REACTOME REGULATION OF BETA CELL DEVELOPMENT	30	23	All SZGR 2.0 genes in this pathway
REACTOME REGULATION OF GENE EXPRESSION IN BETA CELLS	20	15	All SZGR 2.0 genes in this pathway
WILCOX RESPONSE TO PROGESTERONE UP	152	90	All SZGR 2.0 genes in this pathway
SABATES COLORECTAL ADENOMA DN	291	176	All SZGR 2.0 genes in this pathway
GAUSSMANN MLL AF4 FUSION TARGETS C UP	170	114	All SZGR 2.0 genes in this pathway
RIZ ERYTHROID DIFFERENTIATION 6HR	40	23	All SZGR 2.0 genes in this pathway
HERNANDEZ ABERRANT MITOSIS BY DOCETACEL 4NM UP	23	15	All SZGR 2.0 genes in this pathway
MARTORIATI MDM4 TARGETS NEUROEPITHELIUM DN	164	111	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
BLALOCK ALZHEIMERS DISEASE DN	1237	837	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 14HR DN	298	200	All SZGR 2.0 genes in this pathway
ZHOU PANCREATIC ENDOCRINE PROGENITOR	14	11	All SZGR 2.0 genes in this pathway
ZHOU PANCREATIC BETA CELL	11	9	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
MIKKELSEN MCV6 HCP WITH H3K27ME3	435	318	All SZGR 2.0 genes in this pathway
SETLUR PROSTATE CANCER TMPRSS2 ERG FUSION DN	20	12	All SZGR 2.0 genes in this pathway
MIKKELSEN MEF HCP WITH H3K27ME3	590	403	All SZGR 2.0 genes in this pathway
CARD MIR302A TARGETS	77	62	All SZGR 2.0 genes in this pathway
VANDESLUIS COMMD1 TARGETS GROUP 4 DN	16	11	All SZGR 2.0 genes in this pathway
MADAN DPPA4 TARGETS	46	26	All SZGR 2.0 genes in this pathway
ROLEF GLIS3 TARGETS	37	29	All SZGR 2.0 genes in this pathway
RAO BOUND BY SALL4 ISOFORM B	517	302	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-101	1229	1236	1A,m8	hsa-miR-101	UACAGUACUGUGAUAACUGAAG
miR-103/107	90	96	1A	hsa-miR-103^brain	AGCAGCAUUGUACAGGGCUAUGA
miR-103/107	90	96	1A	hsa-miR-107^brain	AGCAGCAUUGUACAGGGCUAUCA
miR-124.1	613	619	m8	hsa-miR-124a	UUAAGGCACGCGGUGAAUGCCA
miR-124/506	613	619	1A	hsa-miR-506	UAAGGCACCCUUCUGAGUAGA
miR-124/506	613	619	1A	hsa-miR-124^brain	UAAGGCACGCGGUGAAUGCC
miR-128	36	42	m8	hsa-miR-128a	UCACAGUGAACCGGUCUCUUUU
miR-128	36	42	m8	hsa-miR-128b	UCACAGUGAACCGGUCUCUUUC
miR-130/301	898	904	m8	hsa-miR-130a^brain	CAGUGCAAUGUUAAAAGGGCAU
				hsa-miR-301	CAGUGCAAUAGUAUUGUCAAAGC
				hsa-miR-130b^brain	CAGUGCAAUGAUGAAAGGGCAU
				hsa-miR-454-3p	UAGUGCAAUAUUGCUUAUAGGGUUU
miR-137	318	325	1A,m8	hsa-miR-137	UAUUGCUUAAGAAUACGCGUAG
miR-138	394	400	1A	hsa-miR-138^brain	AGCUGGUGUUGUGAAUC
miR-138	394	400	1A	hsa-miR-138^brain	AGCUGGUGUUGUGAAUC
miR-144	1230	1236	1A	hsa-miR-144	UACAGUAUAGAUGAUGUACUAG
miR-145	1215	1221	1A	hsa-miR-145	GUCCAGUUUUCCCAGGAAUCCCUU
miR-153	334	341	1A,m8	hsa-miR-153	UUGCAUAGUCACAAAAGUGA
miR-17-5p/20/93.mr/106/519.d	701	707	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-18	183	189	1A	hsa-miR-18a	UAAGGUGCAUCUAGUGCAGAUA
miR-18	183	189	1A	hsa-miR-18b	UAAGGUGCAUCUAGUGCAGUUA
miR-19	897	903	m8	hsa-miR-19a	UGUGCAAAUCUAUGCAAAACUGA
				hsa-miR-19b	UGUGCAAAUCCAUGCAAAACUGA
				hsa-miR-19a	UGUGCAAAUCUAUGCAAAACUGA
				hsa-miR-19b	UGUGCAAAUCCAUGCAAAACUGA
				hsa-miR-19a	UGUGCAAAUCUAUGCAAAACUGA
				hsa-miR-19b	UGUGCAAAUCCAUGCAAAACUGA
miR-190	523	530	1A,m8	hsa-miR-190	UGAUAUGUUUGAUAUAUUAGGU
miR-217	1171	1177	m8	hsa-miR-217	UACUGCAUCAGGAACUGAUUGGAU
miR-24	1046	1052	m8	hsa-miR-24^SZ	UGGCUCAGUUCAGCAGGAACAG
miR-25/32/92/363/367	1298	1304	1A	hsa-miR-25^brain	CAUUGCACUUGUCUCGGUCUGA
				hsa-miR-32	UAUUGCACAUUACUAAGUUGC
				hsa-miR-92	UAUUGCACUUGUCCCGGCCUG
				hsa-miR-367	AAUUGCACUUUAGCAAUGGUGA
				hsa-miR-92b^SZ	UAUUGCACUCGUCCCGGCCUC
miR-299-5p	577	583	1A	hsa-miR-299-5p	UGGUUUACCGUCCCACAUACAU
miR-30-5p	59	66	1A,m8	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-328	358	364	1A	hsa-miR-328^brain	CUGGCCCUCUCUGCCCUUCCGU
miR-331	162	168	1A	hsa-miR-331^brain	GCCCCUGGGCCUAUCCUAGAA
miR-34b	145	151	m8	hsa-miR-34b	UAGGCAGUGUCAUUAGCUGAUUG
miR-363	99	105	1A	hsa-miR-363	AUUGCACGGUAUCCAUCUGUAA
miR-380-5p	391	397	1A	hsa-miR-380-5p	UGGUUGACCAUAGAACAUGCGC
miR-380-5p	391	397	1A	hsa-miR-563	AGGUUGACAUACGUUUCCC
miR-383	295	301	m8	hsa-miR-383^brain	AGAUCAGAAGGUGAUUGUGGCU
miR-448	335	341	1A	hsa-miR-448	UUGCAUAUGUAGGAUGUCCCAU
miR-494	967	973	m8	hsa-miR-494^brain	UGAAACAUACACGGGAAACCUCUU
miR-496	1163	1170	1A,m8	hsa-miR-496	AUUACAUGGCCAAUCUC
miR-496	1163	1170	1A,m8	hsa-miR-496	AUUACAUGGCCAAUCUC
miR-544	584	590	1A	hsa-miR-544	AUUCUGCAUUUUUAGCAAGU
miR-93.hd/291-3p/294/295/302/372/373/520	619	625	m8	hsa-miR-93^brain	AAAGUGCUGUUCGUGCAGGUAG
				hsa-miR-302a	UAAGUGCUUCCAUGUUUUGGUGA
				hsa-miR-302b	UAAGUGCUUCCAUGUUUUAGUAG
				hsa-miR-302c	UAAGUGCUUCCAUGUUUCAGUGG
				hsa-miR-302d	UAAGUGCUUCCAUGUUUGAGUGU
				hsa-miR-372	AAAGUGCUGCGACAUUUGAGCGU
				hsa-miR-373	GAAGUGCUUCGAUUUUGGGGUGU
				hsa-miR-520e	AAAGUGCUUCCUUUUUGAGGG
				hsa-miR-520a	AAAGUGCUUCCCUUUGGACUGU
				hsa-miR-520b	AAAGUGCUUCCUUUUAGAGGG
				hsa-miR-520c	AAAGUGCUUCCUUUUAGAGGGUU
				hsa-miR-520d	AAAGUGCUUCUCUUUGGUGGGUU

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: NEUROD1