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 TRAF4

Gene summary

Basic gene Info.	Gene symbol	TRAF4
	Gene name	TNF receptor-associated factor 4
	Synonyms	CART1\|MLN62\|RNF83
	Cytomap	UCSC genome browser: 17q11-q12
	Type of gene	protein-coding
	RefGenes	NM_004295.3, NM_145751.1,
	Description	MLN 62RING finger protein 83cysteine-rich domain associated with RING and Traf domains protein 1cysteine-rich domain associated with ring and TRAF domainmalignant 62metastatic lymph node gene 62 proteintumor necrosis receptor-associated factor 4A
	Modification date	20141207
dbXrefs	MIM : 602464
	HGNC : HGNC
	Ensembl : ENSG00000076604
	HPRD : 03915
	Vega : OTTHUMG00000132677
Protein	UniProt: Q9BUZ4 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_TRAF4
	BioGPS: 9618
Pathway	NCI Pathway Interaction Database: TRAF4
	KEGG: TRAF4
	REACTOME: TRAF4
	Pathway Commons: TRAF4
Context	iHOP: TRAF4
	ligand binding site mutation search in PubMed: TRAF4
	UCL Cancer Institute: TRAF4
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
GO:0045860	positive regulation of protein kinase activity	16157600
GO:0046330	positive regulation of JNK cascade	16157600
GO:0090073	positive regulation of protein homodimerization activity	16157600

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Ligand binding site mutations for TRAF4

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
C134	P135L	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 TRAF4

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
C134	P135L	-0.86267546

(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 TRAF4 from PDB

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Differential gene expression and gene-gene network for TRAF4

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 TRAF4 and the right PPI network was created from samples without mutations in the LBS of TRAF4. 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 TRAF4

Gene level disease information (DisGeNet)

Disease ID	Disease name	# PubMed	Association type
umls:C0270611	Brain Injuries	1	Biomarker

Mutation level pathogenic information (ClinVar annotation)

Allele ID

AA change

Clinical significance

Origin

Phenotype IDs

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Pharmacological information for TRAF4

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.