mutated Ligand Binding Site gene DataBase





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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 TCF3
Gene summary
Basic gene Info.Gene symbolTCF3
Gene nametranscription factor 3
CytomapUCSC genome browser: 19p13.3
Type of geneprotein-coding
DescriptionVDR interacting repressorclass B basic helix-loop-helix protein 21helix-loop-helix protein HE47immunoglobulin transcription factor 1kappa-E2-binding factornegative vitamin D response element-binding proteintranscription factor 3 (E2A immunoglobulin
Modification date20141207
dbXrefs MIM : 147141
Ensembl : ENSG00000071564
HPRD : 00918
Vega : OTTHUMG00000180031
ProteinUniProt: P15923
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_TCF3
BioGPS: 6929
PathwayNCI Pathway Interaction Database: TCF3
Pathway Commons: TCF3
ContextiHOP: TCF3
ligand binding site mutation search in PubMed: TCF3
UCL Cancer Institute: TCF3
Assigned class in mutLBSgeneDBB: This gene belongs to targetable_mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO:0000122negative regulation of transcription from RNA polymerase II promoter14576336
GO:0002326B cell lineage commitment15030778
GO:0006351transcription, DNA-templated10775504
GO:0033152immunoglobulin V(D)J recombination16428437
GO:0045787positive regulation of cell cycle11509675
GO:0045893positive regulation of transcription, DNA-templated11509675
GO:0045944positive regulation of transcription from RNA polymerase II promoter16043483
GO:0051091positive regulation of sequence-specific DNA binding transcription factor activity14752053
GO:2000045regulation of G1/S transition of mitotic cell cycle11509675

Ligand binding site mutations for TCF3

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
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.

Protein structure related information for TCF3
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
(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 TCF3 from PDB

Differential gene expression and gene-gene network for TCF3
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 TCF3 and the right PPI network was created from samples without mutations in the LBS of TCF3. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for TCF3
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0023485Precursor B-Cell Lymphoblastic Leukemia-Lymphoma8Biomarker, GeneticVariation
umls:C0006413Burkitt Lymphoma5Biomarker

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

Pharmacological information for TCF3
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.
Drug information targeting mutLBSgene (Approved drugs only)
Drug statusDrugBank IDNameTypeDrug structure

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of TCF3 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS

Conservation information for LBS of TCF3
Multiple alignments for P15923 in multiple species
LBSAA sequence# speciesSpecies

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