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 TRAF3

Gene summary

Basic gene Info.	Gene symbol	TRAF3
	Gene name	TNF receptor-associated factor 3
	Synonyms	CAP-1\|CAP1\|CD40bp\|CRAF1\|IIAE5\|LAP1
	Cytomap	UCSC genome browser: 14q32.32
	Type of gene	protein-coding
	RefGenes	NM_001199427.1, NM_003300.3,NM_145725.2,NM_145726.2,
	Description	CD40 associated protein 1CD40 binding proteinCD40 receptor associated factor 1LMP1-associated protein 1
	Modification date	20141222
dbXrefs	MIM : 601896
	HGNC : HGNC
	Ensembl : ENSG00000131323
	HPRD : 03539
	Vega : OTTHUMG00000171902
Protein	UniProt: Q13114 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_TRAF3
	BioGPS: 7187
Pathway	NCI Pathway Interaction Database: TRAF3
	KEGG: TRAF3
	REACTOME: TRAF3
	Pathway Commons: TRAF3
Context	iHOP: TRAF3
	ligand binding site mutation search in PubMed: TRAF3
	UCL Cancer Institute: TRAF3
Assigned class in mutLBSgeneDB	C: This gene just belongs to mutLBSgenes.

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

GO ID

GO Term

PubMed ID

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Ligand binding site mutations for TRAF3

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

LBS	AAchange of nsSNV	Cancer type	# samples
C68	E67K	COAD	1
D463	D463N	UCEC	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 TRAF3

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
D463	D463N	-0.94406974
C68	E67K	-0.8309165

(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 TRAF3 from PDB

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Differential gene expression and gene-gene network for TRAF3

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 TRAF3 and the right PPI network was created from samples without mutations in the LBS of TRAF3. 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 TRAF3

Gene level disease information (DisGeNet)

Disease ID	Disease name	# PubMed	Association type
umls:C3553868	HERPES SIMPLEX ENCEPHALITIS, SUSCEPTIBILITY TO, 3	1	GeneticVariation

Mutation level pathogenic information (ClinVar annotation)

Allele ID

AA change

Clinical significance

Origin

Phenotype IDs

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Pharmacological information for TRAF3

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.