Gene Page: SEMA3B

Summary ?
GeneID7869
SymbolSEMA3B
SynonymsLUCA-1|SEMA5|SEMAA|SemA|semaV
Descriptionsemaphorin 3B
ReferenceMIM:601281|HGNC:HGNC:10724|Ensembl:ENSG00000012171|HPRD:03179|Vega:OTTHUMG00000156970
Gene typeprotein-coding
Map location3p21.3
Pascal p-value0.066
Sherlock p-value0.438
Fetal beta-1.584
DMG1 (# studies)
eGeneMyers' cis & trans

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
DMG:Wockner_2014Genome-wide DNA methylation analysisThis dataset includes 4641 differentially methylated probes corresponding to 2929 unique genes between schizophrenia patients (n=24) and controls (n=24). 3
GO_AnnotationMapping neuro-related keywords to Gene Ontology annotationsHits with neuro-related keywords: 1 

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg18165186350314180SEMA3B6.19E-50.2550.023DMG:Wockner_2014
cg24784036350306878SEMA3B2.163E-4-0.4240.036DMG:Wockner_2014
cg09811393350313213SEMA3B2.515E-40.270.037DMG:Wockner_2014

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs1956962chr1437030834SEMA3B78690.09trans
rs418682chr1437038359SEMA3B78690.15trans

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
ABAT0.840.86
SLC30A10.830.81
FAM120A0.820.83
SPRED10.820.81
ACADSB0.810.80
PTPN110.800.76
PURA0.800.79
PTPRE0.790.78
APLP20.790.80
ADAM90.790.79
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
RP9P-0.45-0.49
SNHG12-0.44-0.51
AL022328.1-0.44-0.41
ACSM3-0.44-0.42
FAM159B-0.43-0.54
AC120053.1-0.43-0.45
AC135724.1-0.41-0.38
RPS21-0.40-0.48
IL32-0.40-0.32
RPL31-0.39-0.47

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0004872receptor activityIEA-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0007411axon guidanceTASaxon (GO term level: 13)8633026 
GO:0007267cell-cell signalingTAS8633026 
GO:0007275multicellular organismal developmentIEA-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005576extracellular regionIEA-
GO:0005783endoplasmic reticulumTAS8633026 
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
DAVICIONI MOLECULAR ARMS VS ERMS DN 182111All SZGR 2.0 genes in this pathway
DOANE BREAST CANCER ESR1 UP 11272All SZGR 2.0 genes in this pathway
BORCZUK MALIGNANT MESOTHELIOMA DN 10459All SZGR 2.0 genes in this pathway
SENESE HDAC1 AND HDAC2 TARGETS DN 232139All SZGR 2.0 genes in this pathway
SENESE HDAC2 TARGETS DN 13377All SZGR 2.0 genes in this pathway
SENESE HDAC3 TARGETS DN 536332All SZGR 2.0 genes in this pathway
NAGASHIMA NRG1 SIGNALING UP 176123All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY SERUM DEPRIVATION UP 552347All SZGR 2.0 genes in this pathway
GAUSSMANN MLL AF4 FUSION TARGETS E UP 9760All SZGR 2.0 genes in this pathway
BEGUM TARGETS OF PAX3 FOXO1 FUSION DN 4534All SZGR 2.0 genes in this pathway
SHI SPARC TARGETS DN 138All SZGR 2.0 genes in this pathway
MOHANKUMAR TLX1 TARGETS UP 414287All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 48HR UP 487286All SZGR 2.0 genes in this pathway
KOYAMA SEMA3B TARGETS UP 292168All SZGR 2.0 genes in this pathway
BENPORATH ES WITH H3K27ME3 1118744All SZGR 2.0 genes in this pathway
ONDER CDH1 TARGETS 2 DN 464276All SZGR 2.0 genes in this pathway
LE EGR2 TARGETS DN 10884All SZGR 2.0 genes in this pathway
ZUCCHI METASTASIS DN 4429All SZGR 2.0 genes in this pathway
STOSSI RESPONSE TO ESTRADIOL 5035All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE INCIPIENT UP 390242All SZGR 2.0 genes in this pathway
CUI TCF21 TARGETS 2 DN 830547All SZGR 2.0 genes in this pathway
MACLACHLAN BRCA1 TARGETS DN 1612All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE UP 16911088All SZGR 2.0 genes in this pathway
LU AGING BRAIN UP 262186All SZGR 2.0 genes in this pathway
NIELSEN SCHWANNOMA UP 1816All SZGR 2.0 genes in this pathway
BAELDE DIABETIC NEPHROPATHY DN 434302All SZGR 2.0 genes in this pathway
WANG CISPLATIN RESPONSE AND XPC UP 202115All SZGR 2.0 genes in this pathway
DURCHDEWALD SKIN CARCINOGENESIS UP 8847All SZGR 2.0 genes in this pathway
CREIGHTON ENDOCRINE THERAPY RESISTANCE 1 528324All SZGR 2.0 genes in this pathway
SANSOM APC MYC TARGETS 217138All SZGR 2.0 genes in this pathway
SANSOM APC TARGETS REQUIRE MYC 210123All SZGR 2.0 genes in this pathway
KYNG DNA DAMAGE BY GAMMA RADIATION 8159All SZGR 2.0 genes in this pathway
KYNG DNA DAMAGE DN 195135All SZGR 2.0 genes in this pathway
LEE METASTASIS AND ALTERNATIVE SPLICING DN 4531All SZGR 2.0 genes in this pathway
SARRIO EPITHELIAL MESENCHYMAL TRANSITION DN 154101All SZGR 2.0 genes in this pathway
AMBROSINI FLAVOPIRIDOL TREATMENT TP53 10963All SZGR 2.0 genes in this pathway
ACEVEDO LIVER CANCER UP 973570All SZGR 2.0 genes in this pathway
SMID BREAST CANCER RELAPSE IN BONE UP 9761All SZGR 2.0 genes in this pathway
SMID BREAST CANCER LUMINAL B UP 172109All SZGR 2.0 genes in this pathway
SMID BREAST CANCER BASAL DN 701446All SZGR 2.0 genes in this pathway
LABBE WNT3A TARGETS DN 9753All SZGR 2.0 genes in this pathway
WEST ADRENOCORTICAL TUMOR DN 546362All SZGR 2.0 genes in this pathway
HUPER BREAST BASAL VS LUMINAL DN 5944All SZGR 2.0 genes in this pathway
YAUCH HEDGEHOG SIGNALING PARACRINE DN 264159All SZGR 2.0 genes in this pathway
CHEN METABOLIC SYNDROM NETWORK 1210725All SZGR 2.0 genes in this pathway
MILI PSEUDOPODIA CHEMOTAXIS DN 457302All SZGR 2.0 genes in this pathway
YAO TEMPORAL RESPONSE TO PROGESTERONE CLUSTER 15 3523All SZGR 2.0 genes in this pathway
BAE BRCA1 TARGETS DN 3227All SZGR 2.0 genes in this pathway
DUTERTRE ESTRADIOL RESPONSE 6HR UP 229149All SZGR 2.0 genes in this pathway
DUTERTRE ESTRADIOL RESPONSE 24HR UP 324193All SZGR 2.0 genes in this pathway
BHAT ESR1 TARGETS NOT VIA AKT1 UP 211131All SZGR 2.0 genes in this pathway
BHAT ESR1 TARGETS VIA AKT1 UP 281183All SZGR 2.0 genes in this pathway
ISSAEVA MLL2 TARGETS 6235All SZGR 2.0 genes in this pathway
PLASARI TGFB1 SIGNALING VIA NFIC 1HR DN 10677All SZGR 2.0 genes in this pathway
FORTSCHEGGER PHF8 TARGETS DN 784464All SZGR 2.0 genes in this pathway
ZHOU CELL CYCLE GENES IN IR RESPONSE 2HR 85All SZGR 2.0 genes in this pathway
ZHOU CELL CYCLE GENES IN IR RESPONSE 6HR 8549All SZGR 2.0 genes in this pathway
ZHOU CELL CYCLE GENES IN IR RESPONSE 24HR 12873All 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-273543601Ahsa-miR-27abrainUUCACAGUGGCUAAGUUCCGC
hsa-miR-27bbrainUUCACAGUGGCUAAGUUCUGC