mutLBSgeneDB

mutLBSgeneDB
mutated Ligand Binding Site gene DataBase

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

Gene Summary

Ligand Binding Site Mutation Information

Protein Structure Related Information

Gene Expression and Gene-Gene Network

Phenotype Information

Pharmacological Information

Conservation Information for LBS

Gene summary for EPCAM
Gene summary
Basic gene Info.Gene symbolEPCAM
Gene nameepithelial cell adhesion molecule
SynonymsDIAR5|EGP-2|EGP314|EGP40|ESA|HNPCC8|KS1/4|KSA|M4S1|MIC18|MK-1|TACSTD1|TROP1
CytomapUCSC genome browser: 2p21
Type of geneprotein-coding
RefGenesNM_002354.2,
Descriptionadenocarcinoma-associated antigencell surface glycoprotein Trop-1epithelial glycoprotein 314human epithelial glycoprotein-2major gastrointestinal tumor-associated protein GA733-2membrane component, chromosome 4, surface marker (35kD glycoprotein)tum
Modification date20141222
dbXrefs MIM : 185535
HGNC : HGNC
Ensembl : ENSG00000119888
HPRD : 01709
Vega : OTTHUMG00000128853
ProteinUniProt: P16422
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_EPCAM
BioGPS: 4072
PathwayNCI Pathway Interaction Database: EPCAM
KEGG: EPCAM
REACTOME: EPCAM
Pathway Commons: EPCAM
ContextiHOP: EPCAM
ligand binding site mutation search in PubMed: EPCAM
UCL Cancer Institute: EPCAM
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO TermPubMed ID
GO:0008284positive regulation of cell proliferation15195135
GO:0045944positive regulation of transcription from RNA polymerase II promoter15195135
GO:2000048negative regulation of cell-cell adhesion mediated by cadherin9382878


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Ligand binding site mutations for EPCAM
Lollipop-style diagram of mutations at LBS in amino-acid sequence.
We represented ligand binding site mutations only. (You can see big image via clicking.)
 
: non-synonymous mutation on LBS, Circle size denotes number of samples.

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
V212A210TLUAD1
D232D232NSKCM1
Y174Y174CUCEC1
cf) Cancer type abbreviation. BLCA: Bladder urothelial carcinoma, BRCA: Breast invasive carcinoma, CESC: Cervical squamous cell carcinoma and endocervical adenocarcinoma, COAD: Colon adenocarcinoma, GBM: Glioblastoma multiforme, LGG: Brain lower grade glioma, HNSC: Head and neck squamous cell carcinoma, KICH: Kidney chromophobe, KIRC: Kidney renal clear cell carcinoma, KIRP: Kidney renal papillary cell carcinoma, LAML: Acute myeloid leukemia, LUAD: Lung adenocarcinoma, LUSC: Lung squamous cell carcinoma, OV: Ovarian serous cystadenocarcinoma, PAAD: Pancreatic adenocarcinoma, PRAD: Prostate adenocarcinoma, SKCM: Skin cutaneous melanoma, STAD: Stomach adenocarcinoma, THCA: Thyroid carcinoma, UCEC: Uterine corpus endometrial carcinoma.


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Protein structure related information for EPCAM
Relative protein structure stability change (ΔΔE) using Mupro 1.1
Mupro score denotes assessment of the effect of mutations on thermodynamic stability.
  (ΔΔE<0: mutation decreases stability, ΔΔE>0: mutation increases stability)
: nsSNV at non-LBS: nsSNV at LBS

nsSNVs sorted by the relative stability change of protein structure by each mutation
Blue: mutations of positive stability change. and red : the most recurrent mutation for this gene.
LBSAAchange of nsSNVRelative stability change
V212A210T-1.4429606
D232D232N-1.1902465
Y174Y174C-0.52426291
(MuPro1.1: Jianlin Cheng et al., Prediction of Protein Stability Changes for Single-Site Mutations Using Support Vector Machines, PROTEINS: Structure, Function, and Bioinformatics. 2006, 62:1125-1132)

Structure image for EPCAM from PDB

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Differential gene expression and gene-gene network for EPCAM
Differential gene expression between mutated and non-mutated LBS samples in all 16 major cancer types

Differential co-expressed gene network based on protein-protein interaction data (CePIN)
* Left PPI network was created from samples with mutations in the LBS of EPCAM and the right PPI network was created from samples without mutations in the LBS of EPCAM. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


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Phenotype information for EPCAM
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0007097Carcinoma44Biomarker, GeneticVariation
umls:C2750737Diarrhea 5, With Tufting Enteropathy, Congenital6Biomarker, GeneticVariation
umls:C0919267Ovarian Neoplasms2AlteredExpression, Biomarker
umls:C0030297Pancreatic Neoplasms2Biomarker
umls:C2931459Lynch syndrome I (site-specific colonic cancer)1Biomarker
umls:C0024667Mammary Neoplasms, Animal1Biomarker
umls:C0024668Mammary Neoplasms, Experimental1Biomarker
umls:C0033578Prostatic Neoplasms1Biomarker

Mutation level pathogenic information (ClinVar annotation)
Allele IDAA changeClinical significanceOriginPhenotype IDs

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Pharmacological information for EPCAM
Gene expression profile of anticancer drug treated cell-lines (CCLE)
Heatmap showing the correlation between gene expression and drug response across all the cell-lines. We chose the top 20 among 138 drugs.We used Pearson's correlation coefficient.

Gene-centered drug-gene interaction network
Drug information targeting mutLBSgene (Approved drugs only)
Drug statusDrugBank IDNameTypeDrug structure
InvestigationalDB05319oportuzumab monatoxBiotech
InvestigationalDB05831ING-1Small molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of EPCAM go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
DMUDECYL-BETA-D-MALTOPYRANOSIDE4mzvAY174 V212 D232


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Conservation information for LBS of EPCAM
Multiple alignments for P16422 in multiple species
LBSAA sequence# speciesSpecies
D219YYFEKDVKGES4Homo sapiens, Mus musculus, Rattus norvegicus, Macaca mulatta
D219YYFEKDVKDDS1Gallus gallus
D219YYFEKDVKDES1Bos taurus
D232SSKSMDLRVNG2Mus musculus, Rattus norvegicus
D232SKK-MDLTVNG1Homo sapiens
D232NNK-LNMNIDN1Gallus gallus
D232SKR-MDLRVNG1Bos taurus
D232SKK-MDLRVNG1Macaca mulatta
F216DVAYYFEKDVK6Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus, Bos taurus, Macaca mulatta
I146TYWIIIELKHK5Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus, Macaca mulatta
I146TTWIIIEMRHA1Gallus gallus
I170ALQKEITTRYQ1Homo sapiens
I170YLKDTITSRYM1Gallus gallus
I170ALQEAFTSRYK1Mus musculus
I170ALQDTFASRYM1Rattus norvegicus
I170ALKDVITNRYQ1Bos taurus
I170ALEEAIKTRYQ1Macaca mulatta
I193NNVITIDLMQN2Mus musculus, Rattus norvegicus
I193NNVITIDLVQN1Homo sapiens
I193NPTITIDLKQN1Gallus gallus
I193NDVITIDLVQN1Bos taurus
I193DNVITIDLVQN1Macaca mulatta
K221FEKDVKGESLF4Homo sapiens, Mus musculus, Rattus norvegicus, Macaca mulatta
K221FEKDVKDDSIF1Gallus gallus
K221FEKDVKDESLF1Bos taurus
K229SLFHSKK-MDL2Homo sapiens, Macaca mulatta
K229SLFHSSKSMDL2Mus musculus, Rattus norvegicus
K229SIFLNNK-LNM1Gallus gallus
K229SLFHSKR-MDL1Bos taurus
L166SLRTALQKEIT1Homo sapiens
L166SLTRYLKDTIT1Gallus gallus
L166SLQTALQEAFT1Mus musculus
L166SLHTALQDTFA1Rattus norvegicus
L166SLQSALKDVIT1Bos taurus
L166SLRTALEEAIK1Macaca mulatta
P244QLDLDPGQTLI2Homo sapiens, Macaca mulatta
P244ELKFD--NMMV1Gallus gallus
P244PLDLDPGQTLI1Mus musculus
P244LLDLDPGQTLI1Rattus norvegicus
P244LLDLDPGRTSI1Bos taurus
R173KEITTRYQLDP1Homo sapiens
R173DTITSRYMLDG1Gallus gallus
R173EAFTSRYKLNQ1Mus musculus
R173DTFASRYMLNP1Rattus norvegicus
R173DVITNRYQLDP1Bos taurus
R173EAIKTRYQLDP1Macaca mulatta
V212VDIADVAYYFE5Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus, Macaca mulatta
V212VDITDVAYYFE1Gallus gallus
V220YFEKDVKGESL4Homo sapiens, Mus musculus, Rattus norvegicus, Macaca mulatta
V220YFEKDVKDDSI1Gallus gallus
V220YFEKDVKDESL1Bos taurus
Y174EITTRYQLDPK1Homo sapiens
Y174TITSRYMLDGR1Gallus gallus
Y174AFTSRYKLNQK1Mus musculus
Y174TFASRYMLNPK1Rattus norvegicus
Y174VITNRYQLDPK1Bos taurus
Y174AIKTRYQLDPK1Macaca mulatta


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