Gene Page: CDH13

Summary ?
GeneID1012
SymbolCDH13
SynonymsCDHH|P105
Descriptioncadherin 13
ReferenceMIM:601364|HGNC:HGNC:1753|Ensembl:ENSG00000140945|HPRD:03219|Vega:OTTHUMG00000176635
Gene typeprotein-coding
Map location16q23.3
Fetal beta-1.819
DMG1 (# studies)
eGeneMyers' cis & trans
Meta
SupportCELL ADHESION AND TRANSSYNAPTIC SIGNALING
G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-CONSENSUS
G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-FULL
G2Cdb.human_BAYES-COLLINS-MOUSE-PSD-CONSENSUS
CompositeSet

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
DMG:Jaffe_2016Genome-wide DNA methylation analysisThis dataset includes 2,104 probes/CpGs associated with SZ patients (n=108) compared to 136 controls at Bonferroni-adjusted P < 0.05. 1
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,schizophreniasClick to show details
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
cg059491711682660596CDH134.32E-10-0.0367.89E-7DMG:Jaffe_2016

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs12201810chr651409683CDH1310120.14trans

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
NCAPH0.980.66
DTL0.970.69
GTSE10.970.70
NUSAP10.970.71
TIMELESS0.970.63
KIF2C0.970.70
CDC45L0.970.68
ORC1L0.970.63
MCM100.970.71
TACC30.970.66
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
FBXO2-0.40-0.55
C5orf53-0.40-0.57
ASPHD1-0.39-0.54
HLA-F-0.38-0.50
SLC9A3R2-0.38-0.39
CCNI2-0.38-0.59
ADAP1-0.38-0.43
LHPP-0.37-0.48
PTH1R-0.37-0.45
CA4-0.37-0.57

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0005509calcium ion bindingIEA-
GO:0042803protein homodimerization activityIEA-
GO:0030169low-density lipoprotein bindingIDA16013438 
GO:0045296cadherin bindingIDA10601632 
GO:0055100adiponectin bindingIEA-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0002040sprouting angiogenesisIDA16873731 
GO:0001938positive regulation of endothelial cell proliferationIMP15364621 
GO:0001954positive regulation of cell-matrix adhesionIMP17573778 
GO:0030100regulation of endocytosisIMP17573778 
GO:0007162negative regulation of cell adhesionIDA14729458 
GO:0007156homophilic cell adhesionIEA-
GO:0007266Rho protein signal transductionIMP15703273 
GO:0008285negative regulation of cell proliferationIDA10737605 
GO:0016601Rac protein signal transductionIMP15703273 
GO:0016339calcium-dependent cell-cell adhesionIDA10601632 
GO:0050927positive regulation of positive chemotaxisIDA16013438 
GO:0042058regulation of epidermal growth factor receptor signaling pathwayIMP17573778 
GO:0030335positive regulation of cell migrationIDA14729458 
GO:0030032lamellipodium biogenesisIDA15703273 
GO:0045885positive regulation of survival gene product expressionIMP16099944 
GO:0050850positive regulation of calcium-mediated signalingIDA16013438 
GO:0043542endothelial cell migrationIDA14729458 
GO:0043616keratinocyte proliferationIDA15816843 
GO:0048661positive regulation of smooth muscle cell proliferationIMP15364621 
GO:0055096low density lipoprotein mediated signalingIDA16013438 
GO:0051668localization within membraneIMP17573778 
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0043005neuron projectionIDAneuron, axon, neurite, dendrite (GO term level: 5)10737605 
GO:0005615extracellular spaceIDA16873731 
GO:0005737cytoplasmIDA10737605 
GO:0009897external side of plasma membraneIEA-
GO:0005901caveolaIDA9650591 
GO:0005886plasma membraneIEA-
GO:0031225anchored to membraneIEA-

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
REACTOME CELL CELL COMMUNICATION 12077All SZGR 2.0 genes in this pathway
REACTOME ADHERENS JUNCTIONS INTERACTIONS 2720All SZGR 2.0 genes in this pathway
REACTOME CELL CELL JUNCTION ORGANIZATION 5631All SZGR 2.0 genes in this pathway
REACTOME CELL JUNCTION ORGANIZATION 7843All SZGR 2.0 genes in this pathway
DAVICIONI MOLECULAR ARMS VS ERMS UP 332228All SZGR 2.0 genes in this pathway
CHARAFE BREAST CANCER LUMINAL VS BASAL DN 455304All SZGR 2.0 genes in this pathway
HORIUCHI WTAP TARGETS UP 306188All SZGR 2.0 genes in this pathway
SENESE HDAC1 TARGETS DN 260143All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA ANAPLASTIC UP 722443All SZGR 2.0 genes in this pathway
ENK UV RESPONSE KERATINOCYTE DN 485334All SZGR 2.0 genes in this pathway
CHIN BREAST CANCER COPY NUMBER DN 1610All SZGR 2.0 genes in this pathway
MAHADEVAN GIST MORPHOLOGICAL SWITCH 1511All SZGR 2.0 genes in this pathway
SILIGAN BOUND BY EWS FLT1 FUSION 4734All SZGR 2.0 genes in this pathway
DAIRKEE TERT TARGETS UP 380213All SZGR 2.0 genes in this pathway
HATADA METHYLATED IN LUNG CANCER UP 390236All SZGR 2.0 genes in this pathway
SCHLESINGER METHYLATED DE NOVO IN CANCER 8864All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 48HR UP 487286All SZGR 2.0 genes in this pathway
BENPORATH SUZ12 TARGETS 1038678All SZGR 2.0 genes in this pathway
CHEN NEUROBLASTOMA COPY NUMBER GAINS 5035All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE DN 1237837All SZGR 2.0 genes in this pathway
TRAYNOR RETT SYNDROM DN 1914All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 24HR DN 148102All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 14HR DN 298200All SZGR 2.0 genes in this pathway
KAYO AGING MUSCLE DN 12376All SZGR 2.0 genes in this pathway
KAAB HEART ATRIUM VS VENTRICLE DN 261183All SZGR 2.0 genes in this pathway
MCCLUNG CREB1 TARGETS UP 10072All SZGR 2.0 genes in this pathway
MCDOWELL ACUTE LUNG INJURY DN 4833All SZGR 2.0 genes in this pathway
MARCHINI TRABECTEDIN RESISTANCE DN 4934All SZGR 2.0 genes in this pathway
ACEVEDO METHYLATED IN LIVER CANCER DN 940425All SZGR 2.0 genes in this pathway
HOQUE METHYLATED IN CANCER 5645All SZGR 2.0 genes in this pathway
BONOME OVARIAN CANCER SURVIVAL SUBOPTIMAL DEBULKING 510309All SZGR 2.0 genes in this pathway
ZHANG TLX TARGETS 36HR UP 221150All SZGR 2.0 genes in this pathway
ZHANG TLX TARGETS 60HR UP 293203All SZGR 2.0 genes in this pathway
ZHANG TLX TARGETS UP 10878All SZGR 2.0 genes in this pathway
MIKKELSEN PARTIALLY REPROGRAMMED TO PLURIPOTENCY 106All SZGR 2.0 genes in this pathway
MEISSNER BRAIN HCP WITH H3K4ME3 AND H3K27ME3 1069729All SZGR 2.0 genes in this pathway
HOSHIDA LIVER CANCER LATE RECURRENCE UP 6242All SZGR 2.0 genes in this pathway
LI PROSTATE CANCER EPIGENETIC 3022All SZGR 2.0 genes in this pathway
NAKAMURA ADIPOGENESIS LATE UP 10467All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 30MIN DN 15099All SZGR 2.0 genes in this pathway
AZARE NEOPLASTIC TRANSFORMATION BY STAT3 UP 12170All SZGR 2.0 genes in this pathway
LEE BMP2 TARGETS UP 745475All SZGR 2.0 genes in this pathway
KOINUMA TARGETS OF SMAD2 OR SMAD3 824528All SZGR 2.0 genes in this pathway
IKEDA MIR30 TARGETS DN 2724All SZGR 2.0 genes in this pathway
WAKABAYASHI ADIPOGENESIS PPARG BOUND 8D 658397All SZGR 2.0 genes in this pathway
PEDRIOLI MIR31 TARGETS DN 418245All SZGR 2.0 genes in this pathway
ROESSLER LIVER CANCER METASTASIS UP 10772All SZGR 2.0 genes in this pathway
LIM MAMMARY STEM CELL UP 489314All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA familyTarget positionmiRNA IDmiRNA seq
UTR startUTR endMatch method
miR-181224230m8hsa-miR-181abrainAACAUUCAACGCUGUCGGUGAGU
hsa-miR-181bSZAACAUUCAUUGCUGUCGGUGGG
hsa-miR-181cbrainAACAUUCAACCUGUCGGUGAGU
hsa-miR-181dbrainAACAUUCAUUGUUGUCGGUGGGUU
miR-30-5p83891Ahsa-miR-30a-5pUGUAAACAUCCUCGACUGGAAG
hsa-miR-30cbrainUGUAAACAUCCUACACUCUCAGC
hsa-miR-30dSZUGUAAACAUCCCCGACUGGAAG
hsa-miR-30bSZUGUAAACAUCCUACACUCAGCU
hsa-miR-30e-5pUGUAAACAUCCUUGACUGGA
miR-3702652711Ahsa-miR-370brainGCCUGCUGGGGUGGAACCUGG
miR-493-5p8738801A,m8hsa-miR-493-5pUUGUACAUGGUAGGCUUUCAUU
miR-495993999m8hsa-miR-495brainAAACAAACAUGGUGCACUUCUUU
miR-543225231m8hsa-miR-543AAACAUUCGCGGUGCACUUCU