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 TRIM29

Gene summary

Basic gene Info.	Gene symbol	TRIM29
	Gene name	tripartite motif containing 29
	Synonyms	ATDC
	Cytomap	UCSC genome browser: 11q23.3
	Type of gene	protein-coding
	RefGenes	NM_012101.3, NM_058193.1,
	Description	ataxia telangiectasia group D-associated proteinataxia-telangiectasia group D-associated proteintripartite motif protein TRIM29tripartite motif-containing 29tripartite motif-containing protein 29
	Modification date	20141207
dbXrefs	MIM : 610658
	HGNC : HGNC
	Ensembl : ENSG00000137699
	HPRD : 10280
	Vega : OTTHUMG00000140377
Protein	UniProt: Q14134 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_TRIM29
	BioGPS: 23650
Pathway	NCI Pathway Interaction Database: TRIM29
	KEGG: TRIM29
	REACTOME: TRIM29
	Pathway Commons: TRIM29
Context	iHOP: TRIM29
	ligand binding site mutation search in PubMed: TRIM29
	UCL Cancer Institute: TRIM29
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 TRIM29

Cancer type specific mutLBS sorted by frequency

LBS	AAchange of nsSNV	Cancer type	# samples
C236	F235C	BRCA	1
C236	C236Y	COAD	1
H255	T257I	LUAD	1
C247	L246F	SKCM	1
C225	R223H	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 TRIM29

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
C225	R223H	-1.6152926
C236	C236Y	-1.059891
C247	L246F	-0.95813136
H255	T257I	-0.8152281
C236	F235C	-0.79816483

(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 TRIM29 from PDB

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Differential gene expression and gene-gene network for TRIM29

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 TRIM29 and the right PPI network was created from samples without mutations in the LBS of TRIM29. 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 TRIM29

Gene level disease information (DisGeNet)

Disease ID

Disease name

# PubMed

Association type

Mutation level pathogenic information (ClinVar annotation)

Allele ID

AA change

Clinical significance

Origin

Phenotype IDs

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Pharmacological information for TRIM29

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.