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 TRIM28
Gene summary
Basic gene Info.Gene symbolTRIM28
Gene nametripartite motif containing 28
CytomapUCSC genome browser: 19q13.4
Type of geneprotein-coding
DescriptionE3 SUMO-protein ligase TRIM28KAP-1KRAB [Kruppel-associated box domain]-associated protein 1KRAB-associated protein 1KRAB-interacting protein 1KRIP-1RING finger protein 96TIF1-betanuclear corepressor KAP-1protein phosphatase 1, regulatory subunit
Modification date20141207
dbXrefs MIM : 601742
Ensembl : ENSG00000130726
HPRD : 03445
Vega : OTTHUMG00000183546
ProteinUniProt: Q13263
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_TRIM28
BioGPS: 10155
PathwayNCI Pathway Interaction Database: TRIM28
Pathway Commons: TRIM28
ContextiHOP: TRIM28
ligand binding site mutation search in PubMed: TRIM28
UCL Cancer Institute: TRIM28
Assigned class in mutLBSgeneDBB: This gene belongs to targetable_mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO:0006281DNA repair17178852
GO:0016567protein ubiquitination18082607
GO:0016925protein sumoylation18082607
GO:0042993positive regulation of transcription factor import into nucleus23665872
GO:0045087innate immune response18248090
GO:0045739positive regulation of DNA repair17178852
GO:0045892negative regulation of transcription, DNA-templated9016654
GO:0051259protein oligomerization17512541
GO:1902187negative regulation of viral release from host cell18248090

Ligand binding site mutations for TRIM28

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 TRIM28
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 TRIM28 from PDB

Differential gene expression and gene-gene network for TRIM28
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 TRIM28 and the right PPI network was created from samples without mutations in the LBS of TRIM28. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for TRIM28
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type

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

Pharmacological information for TRIM28
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 TRIM28 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS

Conservation information for LBS of TRIM28
Multiple alignments for Q13263 in multiple species
LBSAA sequence# speciesSpecies
C209ERTVYCNVHKH3Homo sapiens, Mus musculus, Rattus norvegicus
C221PLVLFCESCDT3Homo sapiens, Mus musculus, Rattus norvegicus
C224LFCESCDTLTC3Homo sapiens, Mus musculus, Rattus norvegicus
C229CDTLTCRDCQL3Homo sapiens, Mus musculus, Rattus norvegicus
C232LTCRDCQLNAH3Homo sapiens, Mus musculus, Rattus norvegicus
C628DSATICRVCQK3Homo sapiens, Mus musculus, Rattus norvegicus
C631TICRVCQKPGD3Homo sapiens, Mus musculus, Rattus norvegicus
C640GDLVMCNQCEF3Homo sapiens, Mus musculus, Rattus norvegicus
C643VMCNQCEFCFH3Homo sapiens, Mus musculus, Rattus norvegicus
C651CFHLDCHLPAL2Homo sapiens, Mus musculus
C651CFHLDCHLPSL1Rattus norvegicus
C666GEEWSCSLCHV3Homo sapiens, Mus musculus, Rattus norvegicus
C669WSCSLCHVLPD3Homo sapiens, Mus musculus, Rattus norvegicus
H212VYCNVHKHEPL3Homo sapiens, Mus musculus, Rattus norvegicus
H237CQLNAHKDHQY3Homo sapiens, Mus musculus, Rattus norvegicus
H240NAHKDHQYQFL3Homo sapiens, Mus musculus, Rattus norvegicus
H648CEFCFHLDCHL3Homo sapiens, Mus musculus, Rattus norvegicus
V630ATICRVCQKPG3Homo sapiens, Mus musculus, Rattus norvegicus

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