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: SMARCD1 |
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Mutation Data (+)
# Cell Line/Tumor sample Tissue of Origin cDNA change Protein change Source FATHMM Prediction PolyPhen2 Prediction 1 1604875 UPPER AERODIGESTIVE TRACT c.631G>A p.G211R COSMIC NP NP 2 587228 LARGE INTESTINE c.703C>T p.R235W COSMIC NP NP 3 587342 LARGE INTESTINE c.537T>G p.D179E COSMIC NP NP 4 587376 LARGE INTESTINE c.431G>A p.R144Q COSMIC NP NP 5 HCC136T LIVER c.225G>A p.Q75Q COSMIC NP NP 6 LC_S4 LUNG c.413A>G p.K138R COSMIC NP Possibly Damaging 7 PCSI_0108_Pa_P NS c.1241A>G p.N414S COSMIC NP NP 8 PD4125a BREAST c.958C>T p.Q320* COSMIC NP NP 9 PD4937a BREAST c.1054G>C p.D352H COSMIC NP NP 10 TCGA-23-1021-01 OVARY c.1351G>A p.A451T COSMIC NP NP 11 TCGA-38-4625-01 LUNG c.1203C>T p.F401F COSMIC NP NP 12 TCGA-44-5644-01 LUNG c.462T>C p.A154A COSMIC NP NP 13 TCGA-55-6970-01 LUNG c.1315C>T p.R439* COSMIC NP NP 14 TCGA-55-6970-01 LUNG c.86G>T p.R29L COSMIC NP NP 15 TCGA-60-2698-01 LUNG c.610G>A p.E204K COSMIC NP NP 16 TCGA-73-7498-01 LUNG c.524G>A p.R175Q COSMIC NP NP 17 TCGA-75-5126-01 LUNG c.1368C>G p.F456L COSMIC NP Possibly Damaging 18 TCGA-95-7947-01 LUNG c.722T>A p.V241E COSMIC CANCER Probably Damaging 19 TCGA-A5-A0VP-01 ENDOMETRIUM c.790C>T p.R264* COSMIC NP NP 20 TCGA-AA-3518-01 LARGE INTESTINE c.708G>A p.P236P COSMIC NP NP 21 TCGA-AA-3554-01 LARGE INTESTINE c.1360C>T p.R454* COSMIC NP NP 22 TCGA-AA-3672-01 LARGE INTESTINE c.911T>C p.L304P COSMIC PASSENGER/OTHER Probably Damaging 23 TCGA-AA-3950-01 LARGE INTESTINE c.915G>A p.Q305Q COSMIC NP NP 24 TCGA-AA-3977-01 LARGE INTESTINE c.582C>A p.F194L COSMIC NP NP 25 TCGA-AG-A002-01 LARGE INTESTINE c.331C>A p.L111I COSMIC NP NP 26 TCGA-AG-A002-01 LARGE INTESTINE c.431G>A p.R144Q COSMIC NP NP 27 TCGA-AP-A056-01 ENDOMETRIUM c.582C>A p.F194L COSMIC NP NP 28 TCGA-AX-A05Z-01 ENDOMETRIUM c.261G>T p.K87N COSMIC NP NP 29 TCGA-BG-A0MQ-01 ENDOMETRIUM c.974T>C p.L325S COSMIC NP NP 30 TCGA-BK-A0C9-01 ENDOMETRIUM c.599C>T p.S200F COSMIC NP NP 31 TCGA-BS-A0UF-01 ENDOMETRIUM c.1396G>T p.E466* COSMIC NP NP 32 TCGA-D1-A103-01 ENDOMETRIUM c.80G>A p.G27D COSMIC NP NP 33 TCGA-D1-A16Y-01 ENDOMETRIUM c.431G>T p.R144L COSMIC NP NP 34 TCGA-D5-6529-01 LARGE INTESTINE c.879C>T p.H293H COSMIC NP NP 35 TCGA-E9-A1NH-01 BREAST c.409A>G p.I137V COSMIC PASSENGER/OTHER Benign
*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 SMARCD1 SMARCD1 SMARCD1 ENSP00000370924 Q96GM5 QuickGO HGNC Ensembl Genome Browser TreeFam UniProt Q96GM5 SMARCD1 ENSP00000370924 SMARCD1 Q96GM5 Expression Atlas Protein Atlas OMIM IntAct PharmGKB SMARCD1 ENSP00000370924 601735 Q96GM5 PA35956
