dbEM
A Database of Epigenetic Modifiers
Cite: Nanda JS, Kumar R, Raghava GP. (2016) dbEM: A database of epigenetic modifiers curated from cancerous and normal genomes. Sci Rep. 6:19340.
Protein: SIRT4 |
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Mutation Data (+)
# Cell Line/Tumor sample Tissue of Origin cDNA change Protein change Source FATHMM Prediction PolyPhen2 Prediction 1 146 HAEMATOPOIETIC AND LYMPHOID TISSUE c.466C>T p.R156C COSMIC PASSENGER/OTHER Possibly Damaging 2 146-01-5TD HAEMATOPOIETIC AND LYMPHOID TISSUE c.466C>T p.R156C COSMIC PASSENGER/OTHER Possibly Damaging 3 587220 LARGE INTESTINE c.311G>A p.R104Q COSMIC PASSENGER/OTHER Possibly Damaging 4 587234 LARGE INTESTINE c.694G>A p.V232I COSMIC PASSENGER/OTHER Possibly Damaging 5 LC_S8 LUNG c.718C>T p.P240S COSMIC PASSENGER/OTHER Benign 6 LUAD-E00934 LUNG c.68C>G p.P23R COSMIC PASSENGER/OTHER Benign 7 PD7299a BONE c.531C>T p.P177P COSMIC NP NP 8 SK-MEL-28 HAEMATOPOIETIC AND LYMPHOID TISSUE c.404G>T p.G135V COSMIC PASSENGER/OTHER Probably Damaging 9 SWE-10 PROSTATE c.18G>T p.A6A COSMIC NP NP 10 TCGA-22-5472-01 LUNG c.451A>G p.K151E COSMIC PASSENGER/OTHER Probably Damaging 11 TCGA-38-4632-01 LUNG c.488G>T p.C163F COSMIC PASSENGER/OTHER Probably Damaging 12 TCGA-A6-3809-01 LARGE INTESTINE c.42C>T p.G14G COSMIC NP NP 13 TCGA-AA-3864-01 LARGE INTESTINE c.259C>A p.R87S COSMIC PASSENGER/OTHER Possibly Damaging 14 TCGA-AA-3984-01 LARGE INTESTINE c.758C>T p.A253V COSMIC PASSENGER/OTHER Possibly Damaging 15 TCGA-AA-A00N-01 LARGE INTESTINE c.547G>T p.E183* COSMIC NP NP 16 TCGA-AG-A002-01 LARGE INTESTINE c.260G>A p.R87H COSMIC PASSENGER/OTHER Benign 17 TCGA-AP-A059-01 ENDOMETRIUM c.12C>T p.S4S COSMIC NP NP 18 TCGA-AX-A05Z-01 ENDOMETRIUM c.759C>T p.A253A COSMIC NP NP 19 TCGA-AX-A0J0-01 ENDOMETRIUM c.905C>A p.S302Y COSMIC PASSENGER/OTHER Benign 20 TCGA-AY-6197-01 LARGE INTESTINE c.656C>T p.T219I COSMIC PASSENGER/OTHER Benign 21 TCGA-AZ-6601-01 LARGE INTESTINE c.533delG p.V180fs*9 COSMIC NP NP 22 TCGA-B5-A0JY-01 ENDOMETRIUM c.146G>A p.R49H COSMIC PASSENGER/OTHER Benign 23 TCGA-BP-4968-01 KIDNEY c.239G>T p.G80V COSMIC PASSENGER/OTHER Probably Damaging 24 TCGA-BS-A0UV-01 ENDOMETRIUM c.843G>A p.P281P COSMIC NP NP 25 ccRCC-22 KIDNEY c.467G>A p.R156H COSMIC PASSENGER/OTHER Possibly Damaging 26 tumor_4163639 HAEMATOPOIETIC AND LYMPHOID TISSUE c.480C>T p.L160L COSMIC NP NP
*NP: Not Predicted -
Copy number variation and expression profile (+)
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Gene Essentiality Data (+)
Note: Lower the GARP score (more negative), higher the essentiality of the gene. P-value tells about the significane of GARP score.test -
Tertiary structure (+)
Users must enabled the Java in their browser to see structure.
Users can also download Java from here.Modelled Structure Structures available in PDB Structure is not available in PDB -
Structure Domains (+)
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Sequence Alignment (+)
Users must enabled the Java in their browser to see sequence alignments.
Users can also download Java from here.1. Variants are not present in 1000 Genomes!!2. Mutants are not present in CCLE!!3. Sequence alignment with COSMIC mutants:
Click on button to get Sequence alignment with Coverage, Consensus and Quality 4. Sequence alignment with homologus proteins:
Click on button to get Sequence alignment with Coverage, Consensus and Quality -
Sequence Profiles (+)
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Post Translational Modifications (+)
$x "); for($d=2;$d<$l777;$d++) { fwrite($FP6,$row6[$d]); fwrite($FP7,"$row6[$d] "); fwrite($FP6,"\t"); } fwrite($FP6,"\n"); fwrite($FP7,""); } fclose($FP6); echo""; } else{echo"
"; ##### table ##### $ptm_tr=file_get_contents("$dir/ptm"); if($ptm_tr != '') { echo"S. No. Position Amino acid Type Post translational modifications are not found!!";} ?> -
Other Databases Link (+)
Proteomics DB COSMIC Gene Atlas STRING PIR SIRT4 SIRT4 SIRT4 ENSP00000202967 Q9Y6E7 QuickGO HGNC Ensembl Genome Browser TreeFam UniProt Q9Y6E7 SIRT4 ENSP00000202967 SIRT4 Q9Y6E7 Expression Atlas Protein Atlas OMIM IntAct PharmGKB SIRT4 ENSP00000202967 604482 Q9Y6E7 PA37937
