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: HDAC8 |
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Mutation Data (+)
# Cell Line/Tumor sample Tissue of Origin cDNA change Protein change Source FATHMM Prediction PolyPhen2 Prediction 1 639V URINARY TRACT c.86A>T p.D29V CCLE PASSENGER/OTHER Probably Damaging 2 BICR18 UPPER AERODIGESTIVE TRACT c.456T>C p.F152F CCLE NP NP 3 DMS114 LUNG c.407A>G p.N136S CCLE PASSENGER/OTHER Probably Damaging 4 DU145 PROSTATE c.669_669delG p.R223fs CCLE NP NP 5 HCC1954 BREAST c.516T>A p.I172I CCLE NP NP 6 HPBALL HAEMATOPOIETIC AND LYMPHOID TISSUE c.592G>A p.V198M CCLE PASSENGER/OTHER Probably Damaging 7 IGROV1 OVARY c.384C>T p.D128D CCLE NP NP 8 K562 HAEMATOPOIETIC AND LYMPHOID TISSUE c.480G>T p.L160L CCLE NP NP 9 LS411N LARGE INTESTINE c.91C>T p.L31L CCLE NP NP 10 NCIH1573 LUNG c.259G>T p.D87Y CCLE PASSENGER/OTHER Probably Damaging 11 NCIH596 LUNG c.492A>C p.R164R CCLE NP NP 12 SW1271 LUNG c.551_splice p.G184_splice CCLE NP NP 13 LUAD-F00368 LUNG c.132G>T p.L44F COSMIC PASSENGER/OTHER Probably Damaging 14 S00833 LUNG c.817C>A p.P273T COSMIC PASSENGER/OTHER Probably Damaging 15 TCGA-05-4397-01 LUNG c.118A>G p.M40V COSMIC PASSENGER/OTHER Benign 16 TCGA-22-5492-01 LUNG c.733G>T p.E245* COSMIC NP NP 17 TCGA-61-2611-02 OVARY c.146C>T p.A49V COSMIC PASSENGER/OTHER Benign 18 TCGA-A2-A0YF-01 BREAST c.1106T>A p.I369N COSMIC PASSENGER/OTHER Probably Damaging 19 TCGA-A2-A0YK-01 BREAST c.463C>G p.L155V COSMIC PASSENGER/OTHER Benign 20 TCGA-A6-3809-01 LARGE INTESTINE c.67G>T p.E23* COSMIC NP NP 21 TCGA-A8-A09I-01 BREAST c.932C>T p.T311M COSMIC PASSENGER/OTHER Probably Damaging 22 TCGA-AP-A056-01 ENDOMETRIUM c.522C>T p.Y174Y COSMIC NP NP 23 TCGA-AP-A059-01 ENDOMETRIUM c.1047G>A p.T349T COSMIC NP NP 24 TCGA-B5-A0JV-01 ENDOMETRIUM c.1057C>T p.R353W COSMIC PASSENGER/OTHER Probably Damaging 25 TCGA-BI-A0VR-01 CERVIX c.567C>G p.F189L COSMIC PASSENGER/OTHER Probably Damaging 26 TCGA-CA-6717-01 LARGE INTESTINE c.506T>G p.F169C COSMIC PASSENGER/OTHER Probably Damaging 27 TCGA-CH-5790-01 PROSTATE c.431C>G p.A144G COSMIC PASSENGER/OTHER Possibly Damaging 28 TCGA-CM-5864-01 LARGE INTESTINE c.304T>C p.C102R COSMIC PASSENGER/OTHER Probably Damaging 29 TCGA-D1-A167-01 ENDOMETRIUM c.667C>T p.R223W COSMIC PASSENGER/OTHER Probably Damaging 30 TCGA-E9-A1R3-01 BREAST c.937C>T p.R313* 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 1T64, 1T67, 1T69, 1VKG, 1W22, 2V5W, 2V5X, 3EW8, 3EWF, 3EZP, 3EZT, 3F06, 3F07, 3F0R, 3MZ3, 3MZ4, 3MZ6, 3MZ7, 3RQD, 3SFF, 3SFH, 4QA0, 4QA1, 4QA2, 4QA3, 4QA4, 4QA5, 4QA6, 4QA7, -
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. Sequence alignment with CCLE mutants:
Click on button to get Sequence alignment with Coverage, Consensus and Quality 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 HDAC8 HDAC8 HDAC8 ENSP00000362655 Q9BY41 QuickGO HGNC Ensembl Genome Browser TreeFam UniProt Q9BY41 HDAC8 ENSP00000362655 HDAC8 Q9BY41 Expression Atlas Protein Atlas OMIM IntAct PharmGKB HDAC8 ENSP00000362655 300269 Q9BY41 PA37766
