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mutLBSgeneDB |
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| Gene summary for TRIM28 |
 Gene summary |
| Basic gene Info. | Gene symbol | TRIM28 |
| Gene name | tripartite motif containing 28 | |
| Synonyms | KAP1|PPP1R157|RNF96|TF1B|TIF1B | |
| Cytomap | UCSC genome browser: 19q13.4 | |
| Type of gene | protein-coding | |
| RefGenes | NM_005762.2, | |
| Description | E3 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 date | 20141207 | |
| dbXrefs | MIM : 601742 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000130726 | ||
| HPRD : 03445 | ||
| Vega : OTTHUMG00000183546 | ||
| Protein | UniProt: Q13263 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_TRIM28 | |
| BioGPS: 10155 | ||
| Pathway | NCI Pathway Interaction Database: TRIM28 | |
| KEGG: TRIM28 | ||
| REACTOME: TRIM28 | ||
| Pathway Commons: TRIM28 | ||
| Context | iHOP: TRIM28 | |
| ligand binding site mutation search in PubMed: TRIM28 | ||
| UCL Cancer Institute: TRIM28 | ||
| 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:0006281 | DNA repair | 17178852 | GO:0016567 | protein ubiquitination | 18082607 | GO:0016925 | protein sumoylation | 18082607 | GO:0042993 | positive regulation of transcription factor import into nucleus | 23665872 | GO:0045087 | innate immune response | 18248090 | GO:0045739 | positive regulation of DNA repair | 17178852 | GO:0045892 | negative regulation of transcription, DNA-templated | 9016654 | GO:0051259 | protein oligomerization | 17512541 | GO:1902187 | negative regulation of viral release from host cell | 18248090 |
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| Ligand binding site mutations for TRIM28 |
| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | C628,V630 | R629H | STAD | 1 | C224 | D225N | 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 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 |
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| 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 | C628 | R629H | -1.4577953 | V630 | R629H | -1.4577953 | C224 | D225N | -0.38219871 |
| (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 |
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| 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) |
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| Phenotype information for TRIM28 |
| 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 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. |
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| Drug information targeting mutLBSgene (Approved drugs only) |
| Drug status | DrugBank ID | Name | Type | Drug structure |
| Gene-centered ligand-gene interaction network |
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| Ligands binding to mutated ligand binding site of TRIM28 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | ZN | ZINC(2+) | 2ro1 | A | C628 |
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| Conservation information for LBS of TRIM28 |
| Multiple alignments for Q13263 in multiple species |
| LBS | AA sequence | # species | Species | C209 | ERTVYCNVHKH | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | C221 | PLVLFCESCDT | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | C224 | LFCESCDTLTC | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | C229 | CDTLTCRDCQL | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | C232 | LTCRDCQLNAH | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | C628 | DSATICRVCQK | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | C631 | TICRVCQKPGD | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | C640 | GDLVMCNQCEF | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | C643 | VMCNQCEFCFH | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | C651 | CFHLDCHLPAL | 2 | Homo sapiens, Mus musculus | C651 | CFHLDCHLPSL | 1 | Rattus norvegicus | C666 | GEEWSCSLCHV | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | C669 | WSCSLCHVLPD | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | H212 | VYCNVHKHEPL | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | H237 | CQLNAHKDHQY | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | H240 | NAHKDHQYQFL | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | H648 | CEFCFHLDCHL | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | V630 | ATICRVCQKPG | 3 | Homo sapiens, Mus musculus, Rattus norvegicus |
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