Gene Page:NEGR1

Summary?
GeneID 257194
Symbol NEGR1
Synonyms DMML2433|IGLON4|KILON|Ntra
Description neuronal growth regulator 1
Reference MIM:613173|HGNC:HGNC:17302|Ensembl:ENSG00000172260|HPRD:14820|
Gene type protein-coding
Map location 1p31.1
Pascal p-value 3.174E-4
Fetal beta -1.07
DMG 1 (# studies)
Support G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-CONSENSUS
G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-FULL
G2Cdb.human_BAYES-COLLINS-MOUSE-PSD-CONSENSUS
G2Cdb.human_clathrin
G2Cdb.human_Synaptosome
CompositeSet

Gene in Data Sources
Gene set name Method of gene set Description Info
CV:GWAScat Genome-wide Association Studies This data set includes 560 SNPs associated with schizophrenia. A total of 486 genes were mapped to these SNPs within 50kb.
CV:PGC128 Genome-wide Association Study A multi-stage schizophrenia GWAS of up to 36,989 cases and 113,075 controls. Reported by the Schizophrenia Working Group of PGC. 128 independent associations spanning 108 loci
CV:PGCnp Genome-wide Association Study GWAS
DMG:Nishioka_2013 Genome-wide DNA methylation analysis The authors investigated the methylation profiles of DNA in peripheral blood cells from 18 patients with first-episode schizophrenia (FESZ) and from 15 normal controls. 1
PMID:cooccur High-throughput literature-search Systematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
GSMA_IIA Genome scan meta-analysis (All samples) Psr: 0.02692
Literature High-throughput literature-search 与精神分裂症Co-occurance关键词:schizophrenia,schizophrenic,schizophrenias Click to show details

Section I. Genetics and epigenetics annotation

@CV:PGC128

SNP ID Chromosome Position Allele P Function Gene Up/Down Distance
rs12129573 chr1 73768366 AC 2.346E-10 intergenic NEGR1,LINC01360 dist=1020089;dist=3487

@Differentially methylated gene

Probe Chromosome Position Nearest gene P (dis) Beta (dis) FDR (dis) Study
cg04645342 1 72748124 NEGR1 -0.024 0.58 DMG:Nishioka_2013


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.

No co-expressed genes in brain regions


Section III. Gene Ontology annotation

Molecular function GO term Evidence Neuro keywords PubMed ID
GO:0005515 protein binding IEA -
Biological process GO term Evidence Neuro keywords PubMed ID
GO:0007155 cell adhesion IEA -
Cellular component GO term Evidence Neuro keywords PubMed ID
GO:0005886 plasma membrane IEA -
GO:0031225 anchored to membrane IEA -

Section V. Pathway annotation

Pathway name Pathway size # SZGR 2.0 genes in pathway Info
KEGG CELL ADHESION MOLECULES CAMS 134 93 All SZGR 2.0 genes in this pathway
HORIUCHI WTAP TARGETS DN 310 188 All SZGR 2.0 genes in this pathway
TAKEDA TARGETS OF NUP98 HOXA9 FUSION 3D UP 182 110 All SZGR 2.0 genes in this pathway
TAKEDA TARGETS OF NUP98 HOXA9 FUSION 8D UP 157 91 All SZGR 2.0 genes in this pathway
TAKEDA TARGETS OF NUP98 HOXA9 FUSION 10D UP 194 122 All SZGR 2.0 genes in this pathway
TAKEDA TARGETS OF NUP98 HOXA9 FUSION 16D UP 175 108 All SZGR 2.0 genes in this pathway
JAATINEN HEMATOPOIETIC STEM CELL UP 316 190 All SZGR 2.0 genes in this pathway
GAUSSMANN MLL AF4 FUSION TARGETS G UP 238 135 All SZGR 2.0 genes in this pathway
MANTOVANI VIRAL GPCR SIGNALING UP 86 54 All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 48HR DN 428 306 All SZGR 2.0 genes in this pathway
PASQUALUCCI LYMPHOMA BY GC STAGE UP 283 177 All SZGR 2.0 genes in this pathway
BENPORATH ES WITH H3K27ME3 1118 744 All SZGR 2.0 genes in this pathway
WANG SMARCE1 TARGETS UP 280 183 All SZGR 2.0 genes in this pathway
KONDO EZH2 TARGETS 245 148 All SZGR 2.0 genes in this pathway
CAMPS COLON CANCER COPY NUMBER DN 74 34 All SZGR 2.0 genes in this pathway
GOBERT OLIGODENDROCYTE DIFFERENTIATION DN 1080 713 All SZGR 2.0 genes in this pathway
WAKABAYASHI ADIPOGENESIS PPARG RXRA BOUND 36HR 152 88 All SZGR 2.0 genes in this pathway
WAKABAYASHI ADIPOGENESIS PPARG RXRA BOUND 8D 882 506 All SZGR 2.0 genes in this pathway
WANG MLL TARGETS 289 188 All SZGR 2.0 genes in this pathway
ZWANG TRANSIENTLY UP BY 2ND EGF PULSE ONLY 1725 838 All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA family Target position microrna的ID miRNA seq
UTR start UTR end Match method
miR-101 3666 3672 m8 hsa-miR-101 UACAGUACUGUGAUAACUGAAG
miR-122 2053 2060 1A,m8 hsa-miR-122a UGGAGUGUGACAAUGGUGUUUGU
miR-124.1 3562 3569 1A,m8 hsa-miR-124a UUAAGGCACGCGGUGAAUGCCA
miR-124/506 3562 3568 1A hsa-miR-506 UAAGGCACCCUUCUGAGUAGA
hsa-miR-124brain UAAGGCACGCGGUGAAUGCC
hsa-miR-506 UAAGGCACCCUUCUGAGUAGA
hsa-miR-124brain UAAGGCACGCGGUGAAUGCC
miR-135 1560 1566 m8 hsa-miR-135a UAUGGCUUUUUAUUCCUAUGUGA
hsa-miR-135b UAUGGCUUUUCAUUCCUAUGUG
mir - 145 3599 3605 1A hsa-miR-145 GUCCAGUUUUCCCAGGAAUCCCUU
miR-181 2524 2531 1A,m8 hsa-miR-181abrain AACAUUCAACGCUGUCGGUGAGU
hsa-miR-181bSZ AACAUUCAUUGCUGUCGGUGGG
hsa-miR-181cbrain AACAUUCAACCUGUCGGUGAGU
hsa-miR-181dbrain AACAUUCAUUGUUGUCGGUGGGUU
miR-186 365 372 1A,m8 hsa-miR-186 CAAAGAAUUCUCCUUUUGGGCUU
miR-200bc/429 3526 3532 m8 hsa-miR-200b UAAUACUGCCUGGUAAUGAUGAC
hsa-miR-200c UAAUACUGCCGGGUAAUGAUGG
hsa-miR-429 UAAUACUGUCUGGUAAAACCGU
hsa-miR-200b UAAUACUGCCUGGUAAUGAUGAC
hsa-miR-200c UAAUACUGCCGGGUAAUGAUGG
hsa-miR-429 UAAUACUGUCUGGUAAAACCGU
miR-203.1 2694 2700 1A hsa-miR-203 UGAAAUGUUUAGGACCACUAG
miR-25/32/92/363/367 377 383 1A hsa-miR-25brain CAUUGCACUUGUCUCGGUCUGA
hsa-miR-32 UAUUGCACAUUACUAAGUUGC
hsa-miR-92 UAUUGCACUUGUCCCGGCCUG
hsa-miR-367 AAUUGCACUUUAGCAAUGGUGA
hsa-miR-92bSZ UAUUGCACUCGUCCCGGCCUC
miR-29 2085 2092 1A,m8 hsa-miR-29aSZ UAGCACCAUCUGAAAUCGGUU
hsa-miR-29bSZ UAGCACCAUUUGAAAUCAGUGUU
hsa-miR-29cSZ UAGCACCAUUUGAAAUCGGU
miR-30-3p 3183 3190 1A,m8 hsa-miR-30a-3p CUUUCAGUCGGAUGUUUGCAGC
hsa-miR-30e-3p CUUUCAGUCGGAUGUUUACAGC
miR-30-5p 332 338 1A hsa-miR-30a-5p UGUAAACAUCCUCGACUGGAAG
hsa-miR-30cbrain UGUAAACAUCCUACACUCUCAGC
hsa-miR-30dSZ UGUAAACAUCCCCGACUGGAAG
hsa-miR-30bSZ UGUAAACAUCCUACACUCAGCU
hsa-miR-30e-5p UGUAAACAUCCUUGACUGGA
miR-320 2038 2045 1A,m8 hsa-miR-320 AAAAGCUGGGUUGAGAGGGCGAA
miR-324-3p 351 357 1A hsa-miR-324-3p CCACUGCCCCAGGUGCUGCUGG
miR-377 2520 2527 1A,m8 hsa-miR-377 AUCACACAAAGGCAACUUUUGU
miR-382 283 289 m8 hsa-miR-382brain GAAGUUGUUCGUGGUGGAUUCG
miR-493-5p 2612 2618 1A hsa-miR-493-5p UUGUACAUGGUAGGCUUUCAUU
miR-494 400 406 1A hsa-miR-494brain UGAAACAUACACGGGAAACCUCUU
miR-496 3652 3658 1A hsa-miR-496 AUUACAUGGCCAAUCUC