mutLBSgeneDB

mutLBSgeneDB
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 symbol	TCF3
	Gene name	transcription factor 3
	Synonyms	E2A\|E47\|ITF1\|TCF-3\|VDIR\|bHLHb21
	Cytomap	UCSC genome browser: 19p13.3
	Type of gene	protein-coding
	RefGenes	NM_001136139.2, NM_003200.3,
	Description	VDR 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 date	20141207
dbXrefs	MIM : 147141
	HGNC : HGNC
	Ensembl : ENSG00000071564
	HPRD : 00918
	Vega : OTTHUMG00000180031
Protein	UniProt: P15923 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_TCF3
	BioGPS: 6929
Pathway	NCI Pathway Interaction Database: TCF3
	KEGG: TCF3
	REACTOME: TCF3
	Pathway Commons: TCF3
Context	iHOP: TCF3
	ligand binding site mutation search in PubMed: TCF3
	UCL Cancer Institute: TCF3
Assigned class in mutLBSgeneDB	B: This gene belongs to targetable_mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez

GO ID	GO Term	PubMed ID
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	14576336
GO:0002326	B cell lineage commitment	15030778
GO:0006351	transcription, DNA-templated	10775504
GO:0033152	immunoglobulin V(D)J recombination	16428437
GO:0045787	positive regulation of cell cycle	11509675
GO:0045893	positive regulation of transcription, DNA-templated	11509675
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	16043483
GO:0051091	positive regulation of sequence-specific DNA binding transcription factor activity	14752053
GO:2000045	regulation of G1/S transition of mitotic cell cycle	11509675

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Ligand binding site mutations for TCF3

Cancer type specific mutLBS sorted by frequency

LBS	AAchange of nsSNV	Cancer type	# samples
R561	R561W	BRCA	1
N555	R557W	COAD	1
R561	R563C	STAD	1

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 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.

LBS	AAchange of nsSNV	Relative stability change
R561	R563C	-1.0994248
R561	R561W	-0.99253994
N555	R557W	-0.77164232

(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

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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.

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Phenotype information for TCF3

Gene level disease information (DisGeNet)

Disease ID	Disease name	# PubMed	Association type
umls:C0023485	Precursor B-Cell Lymphoblastic Leukemia-Lymphoma	8	Biomarker, GeneticVariation
umls:C0006413	Burkitt Lymphoma	5	Biomarker

Mutation level pathogenic information (ClinVar annotation)

Allele ID

AA change

Clinical significance

Origin

Phenotype IDs

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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.