Summary ?
GeneID10371
SymbolSEMA3A
SynonymsCOLL1|HH16|Hsema-I|Hsema-III|SEMA1|SEMAD|SEMAIII|SEMAL|SemD|coll-1
Descriptionsemaphorin 3A
ReferenceMIM:603961|HGNC:HGNC:10723|Ensembl:ENSG00000075213|HPRD:04908|Vega:OTTHUMG00000023443
Gene typeprotein-coding
Map location7p12.1
Pascal p-value0.002
Fetal beta2.459
eGeneMyers' cis & trans

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:GWAScatGenome-wide Association StudiesThis data set includes 560 SNPs associated with schizophrenia. A total of 486 genes were mapped to these SNPs within 50kb.
CV:GWASdbGenome-wide Association StudiesGWASdb records for schizophrenia
CV:PGCnpGenome-wide Association StudyGWAS
PMID:cooccurHigh-throughput literature-searchSystematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
LiteratureHigh-throughput literature-searchCo-occurance with Schizophrenia keywords: schizophrenia,schizophrenic,schizophreniasClick to show details
GO_AnnotationMapping neuro-related keywords to Gene Ontology annotationsHits with neuro-related keywords: 1 

Section I. Genetics and epigenetics annotation

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs4887786chr1674857551SEMA3A103710.12trans

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

Top 10 positively co-expressed genes
GenePearson's Correlation Spearman's Correlation
RAC30.920.90
NT5DC20.910.88
TUBB30.880.86
TUBA1A0.880.87
VPS37D0.880.87
FKBP1B0.880.86
FBL0.870.84
VAT10.870.81
DTD10.870.84
HN10.870.87
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
HLA-F-0.66-0.73
AF347015.27-0.64-0.79
TINAGL1-0.62-0.73
AF347015.33-0.62-0.77
MT-CO2-0.61-0.76
C5orf53-0.61-0.62
AF347015.31-0.61-0.75
CA4-0.61-0.68
AIFM3-0.61-0.65
ALDOC-0.60-0.60

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0004872receptor activityIEA-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0007399nervous system developmentIEAneurite (GO term level: 5)-
GO:0007275multicellular organismal developmentIEA-
GO:0030154cell differentiationIEA-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005576extracellular regionTAS8269517 
GO:0016020membraneIEA-

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
KEGG AXON GUIDANCE 129103All SZGR 2.0 genes in this pathway
REACTOME DEVELOPMENTAL BIOLOGY 396292All SZGR 2.0 genes in this pathway
REACTOME AXON GUIDANCE 251188All SZGR 2.0 genes in this pathway
REACTOME CRMPS IN SEMA3A SIGNALING 1414All SZGR 2.0 genes in this pathway
REACTOME SEMA3A PAK DEPENDENT AXON REPULSION 1514All SZGR 2.0 genes in this pathway
REACTOME SEMAPHORIN INTERACTIONS 6853All SZGR 2.0 genes in this pathway
REACTOME SEMA3A PLEXIN REPULSION SIGNALING BY INHIBITING INTEGRIN ADHESION 139All SZGR 2.0 genes in this pathway
PARENT MTOR SIGNALING UP 567375All SZGR 2.0 genes in this pathway
CHARAFE BREAST CANCER LUMINAL VS MESENCHYMAL DN 460312All SZGR 2.0 genes in this pathway
CHARAFE BREAST CANCER BASAL VS MESENCHYMAL DN 5036All SZGR 2.0 genes in this pathway
DITTMER PTHLH TARGETS DN 7351All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA ANAPLASTIC UP 722443All SZGR 2.0 genes in this pathway
MISSIAGLIA REGULATED BY METHYLATION DN 12267All SZGR 2.0 genes in this pathway
SEITZ NEOPLASTIC TRANSFORMATION BY 8P DELETION UP 7347All SZGR 2.0 genes in this pathway
NUYTTEN EZH2 TARGETS UP 1037673All SZGR 2.0 genes in this pathway
STARK PREFRONTAL CORTEX 22Q11 DELETION DN 517309All SZGR 2.0 genes in this pathway
ONDER CDH1 TARGETS 2 DN 464276All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 16HR DN 8662All SZGR 2.0 genes in this pathway
BACOLOD RESISTANCE TO ALKYLATING AGENTS UP 2617All SZGR 2.0 genes in this pathway
DOUGLAS BMI1 TARGETS DN 314188All SZGR 2.0 genes in this pathway
ZHANG GATA6 TARGETS DN 6446All SZGR 2.0 genes in this pathway
ZHENG GLIOBLASTOMA PLASTICITY UP 250168All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS UP 1305895All SZGR 2.0 genes in this pathway
SHEDDEN LUNG CANCER POOR SURVIVAL A6 456285All SZGR 2.0 genes in this pathway
CAIRO LIVER DEVELOPMENT UP 166105All SZGR 2.0 genes in this pathway
MIKKELSEN ES ICP WITH H3K4ME3 718401All SZGR 2.0 genes in this pathway
MIKKELSEN NPC ICP WITH H3K4ME3 445257All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE VIA TP53 GROUP D 280158All SZGR 2.0 genes in this pathway
IKEDA MIR30 TARGETS UP 11687All SZGR 2.0 genes in this pathway
PLASARI TGFB1 TARGETS 10HR DN 244157All SZGR 2.0 genes in this pathway
ZWANG CLASS 3 TRANSIENTLY INDUCED BY EGF 222159All SZGR 2.0 genes in this pathway
NABA ECM AFFILIATED 17189All SZGR 2.0 genes in this pathway
NABA MATRISOME ASSOCIATED 753411All SZGR 2.0 genes in this pathway
NABA MATRISOME 1028559All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA familyTarget positionmiRNA IDmiRNA seq
UTR startUTR endMatch method
miR-14529402946m8hsa-miR-145GUCCAGUUUUCCCAGGAAUCCCUU
hsa-miR-145GUCCAGUUUUCCCAGGAAUCCCUU
miR-15/16/195/424/49729662972m8hsa-miR-15abrainUAGCAGCACAUAAUGGUUUGUG
hsa-miR-16brainUAGCAGCACGUAAAUAUUGGCG
hsa-miR-15bbrainUAGCAGCACAUCAUGGUUUACA
hsa-miR-195SZUAGCAGCACAGAAAUAUUGGC
hsa-miR-424CAGCAGCAAUUCAUGUUUUGAA
hsa-miR-497CAGCAGCACACUGUGGUUUGU
hsa-miR-15abrainUAGCAGCACAUAAUGGUUUGUG
hsa-miR-16brainUAGCAGCACGUAAAUAUUGGCG
hsa-miR-15bbrainUAGCAGCACAUCAUGGUUUACA
hsa-miR-195SZUAGCAGCACAGAAAUAUUGGC
hsa-miR-424CAGCAGCAAUUCAUGUUUUGAA
hsa-miR-497CAGCAGCACACUGUGGUUUGU
miR-196267226781Ahsa-miR-196aUAGGUAGUUUCAUGUUGUUGG
hsa-miR-196bUAGGUAGUUUCCUGUUGUUGG
miR-203.130133019m8hsa-miR-203UGAAAUGUUUAGGACCACUAG
hsa-miR-203UGAAAUGUUUAGGACCACUAG
miR-216936991Ahsa-miR-21brainUAGCUUAUCAGACUGAUGUUGA
hsa-miR-590GAGCUUAUUCAUAAAAGUGCAG
miR-2176696761A,m8hsa-miR-217UACUGCAUCAGGAACUGAUUGGAU
miR-25/32/92/363/36766721Ahsa-miR-25brainCAUUGCACUUGUCUCGGUCUGA
hsa-miR-32UAUUGCACAUUACUAAGUUGC
hsa-miR-92UAUUGCACUUGUCCCGGCCUG
hsa-miR-367AAUUGCACUUUAGCAAUGGUGA
hsa-miR-92bSZUAUUGCACUCGUCCCGGCCUC
miR-30-5p1041111A,m8hsa-miR-30a-5pUGUAAACAUCCUCGACUGGAAG
hsa-miR-30cbrainUGUAAACAUCCUACACUCUCAGC
hsa-miR-30dSZUGUAAACAUCCCCGACUGGAAG
hsa-miR-30bSZUGUAAACAUCCUACACUCAGCU
hsa-miR-30e-5pUGUAAACAUCCUUGACUGGA
miR-320610616m8hsa-miR-320AAAAGCUGGGUUGAGAGGGCGAA
miR-3364701Ahsa-miR-33GUGCAUUGUAGUUGCAUUG
hsa-miR-33bGUGCAUUGCUGUUGCAUUGCA
miR-3306126181Ahsa-miR-330brainGCAAAGCACACGGCCUGCAGAGA
miR-3624364431A,m8hsa-miR-362AAUCCUUGGAACCUAGGUGUGAGU
miR-36591971Ahsa-miR-365UAAUGCCCCUAAAAAUCCUUAU
miR-379450456m8hsa-miR-379brainUGGUAGACUAUGGAACGUA