Gene Page:NEUROD1

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 系统ematic 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 pvalue qvalue TSS distance 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)

Not available

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

前10名中的基因
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 去的术语 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 新闻学会 10545951
GO:0016563 transcription activator activity IEA -
GO:0046982 protein heterodimerization activity 新闻学会 10545951
GO:0043565 sequence-specific DNA binding IDA 10545951
Biological process 去的术语 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 去的术语 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 高清| 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
UTR start UTR end Match method
miR-101 1229 1236 1A,m8 hsa-miR-101 UACAGUACUGUGAUAACUGAAG
miR-103/107 90 96 1A hsa-miR-103brain AGCAGCAUUGUACAGGGCUAUGA
hsa-miR-107brain AGCAGCAUUGUACAGGGCUAUCA
miR-124.1 613 619 m8 hsa-miR-124a UUAAGGCACGCGGUGAAUGCCA
miR-124/506 613 619 1A hsa-miR-506 UAAGGCACCCUUCUGAGUAGA
hsa-miR-124brain UAAGGCACGCGGUGAAUGCC
miR-128 36 42 m8 hsa-miR-128a UCACAGUGAACCGGUCUCUUUU
hsa-miR-128b UCACAGUGAACCGGUCUCUUUC
miR-130/301 898 904 m8 hsa-miR-130abrain CAGUGCAAUGUUAAAAGGGCAU
hsa-miR-301 CAGUGCAAUAGUAUUGUCAAAGC
hsa-miR-130bbrain CAGUGCAAUGAUGAAAGGGCAU
hsa-miR-454-3p UAGUGCAAUAUUGCUUAUAGGGUUU
miR-137 318 325 1A,m8 hsa-miR-137 UAUUGCUUAAGAAUACGCGUAG
miR-138 394 400 1A hsa-miR-138brain AGCUGGUGUUGUGAAUC
hsa-miR-138brain 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-20abrain UAAAGUGCUUAUAGUGCAGGUAG
hsa-miR-106a AAAAGUGCUUACAGUGCAGGUAGC
hsa-miR-106bSZ UAAAGUGCUGACAGUGCAGAU
hsa-miR-20bSZ CAAAGUGCUCAUAGUGCAGGUAG
hsa-miR-519d CAAAGUGCCUCCCUUUAGAGUGU
miR-18 183 189 1A hsa-miR-18a UAAGGUGCAUCUAGUGCAGAUA
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-24SZ UGGCUCAGUUCAGCAGGAACAG
miR-25/32/92/363/367 1298 1304 1A hsa-miR-25brain CAUUGCACUUGUCUCGGUCUGA
hsa-miR-32 UAUUGCACAUUACUAAGUUGC
hsa-miR-92 UAUUGCACUUGUCCCGGCCUG
hsa-miR-367 AAUUGCACUUUAGCAAUGGUGA
hsa-miR-92bSZ 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-30cbrain UGUAAACAUCCUACACUCUCAGC
hsa-miR-30dSZ UGUAAACAUCCCCGACUGGAAG
hsa-miR-30bSZ UGUAAACAUCCUACACUCAGCU
hsa-miR-30e-5p UGUAAACAUCCUUGACUGGA
miR-328 358 364 1A hsa-miR-328brain CUGGCCCUCUCUGCCCUUCCGU
miR-331 162 168 1A hsa-miR-331brain 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
hsa-miR-563 AGGUUGACAUACGUUUCCC
miR-383 295 301 m8 hsa-miR-383brain AGAUCAGAAGGUGAUUGUGGCU
miR-448 335 341 1A hsa-miR-448 UUGCAUAUGUAGGAUGUCCCAU
miR-494 967 973 m8 hsa-miR-494brain UGAAACAUACACGGGAAACCUCUU
miR-496 1163 1170 1A,m8 hsa-miR-496 AUUACAUGGCCAAUCUC
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-93brain 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