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: SMARCD2 |
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Mutation Data (+)
# Cell Line/Tumor sample Tissue of Origin cDNA change Protein change Source FATHMM Prediction PolyPhen2 Prediction 1 587220 LARGE INTESTINE c.659G>A p.R220Q COSMIC NP NP 2 587220 LARGE INTESTINE c.956T>C p.M319T COSMIC NP NP 3 587284 LARGE INTESTINE c.700C>T p.R234W COSMIC NP NP 4 587288 LARGE INTESTINE c.293C>T p.P98L COSMIC NP NP 5 587338 LARGE INTESTINE c.530G>A p.R177Q COSMIC CANCER Probably Damaging 6 587342 LARGE INTESTINE c.964G>A p.A322T COSMIC NP NP 7 LUAD-F00282 LUNG c.491G>A p.G164E COSMIC NP NP 8 LUAD-S01405 LUNG c.1191G>C p.Q397H COSMIC NP NP 9 MD-286 CENTRAL NERVOUS SYSTEM c.143G>T p.R48L COSMIC NP NP 10 TCGA-49-6767-01 LUNG c.185G>A p.R62H COSMIC NP NP 11 TCGA-78-7155-01 LUNG c.1072G>A p.D358N COSMIC NP NP 12 TCGA-99-8025-01 LUNG c.301C>T p.Q101* COSMIC NP NP 13 TCGA-A5-A0VQ-01 ENDOMETRIUM c.938G>A p.R313H COSMIC NP NP 14 TCGA-A6-5666-01 LARGE INTESTINE c.1298delC p.P433fs*19 COSMIC NP NP 15 TCGA-A6-6780-01 LARGE INTESTINE c.1249C>T p.R417C COSMIC NP NP 16 TCGA-A6-6781-01 LARGE INTESTINE c.107delC p.P36fs*20 COSMIC NP NP 17 TCGA-AP-A051-01 ENDOMETRIUM c.685G>A p.G229S COSMIC NP Probably Damaging 18 TCGA-AP-A0LM-01 ENDOMETRIUM c.204G>A p.A68A COSMIC NP NP 19 TCGA-AU-6004-01 LARGE INTESTINE c.1312C>T p.R438* COSMIC NP NP 20 TCGA-AX-A05Y-01 ENDOMETRIUM c.931C>T p.R311* COSMIC NP NP 21 TCGA-AY-4071-01 LARGE INTESTINE c.1132G>A p.A378T COSMIC PASSENGER/OTHER Benign 22 TCGA-AZ-6601-01 LARGE INTESTINE c.146C>A p.P49H COSMIC NP NP 23 TCGA-B0-5698-01 KIDNEY c.931C>T p.R311* COSMIC NP NP 24 TCGA-B5-A0JY-01 ENDOMETRIUM c.143G>A p.R48Q COSMIC NP NP 25 TCGA-B5-A0JY-01 ENDOMETRIUM c.415C>T p.R139W COSMIC NP NP 26 TCGA-B5-A0K9-01 ENDOMETRIUM c.1323C>G p.F441L COSMIC NP NP 27 TCGA-BG-A0MQ-01 ENDOMETRIUM c.1217C>T p.T406I COSMIC NP NP 28 TCGA-CK-5913-01 LARGE INTESTINE c.1126_1128delGAG p.E376delE COSMIC NP NP 29 ccRCC-23 KIDNEY c.331C>T p.R111W 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 SMARCD2 SMARCD2 SMARCD2 ENSP00000318451 Q92925 QuickGO HGNC Ensembl Genome Browser TreeFam UniProt Q92925 SMARCD2 ENSP00000318451 SMARCD2 Q92925 Expression Atlas Protein Atlas OMIM IntAct PharmGKB SMARCD2 ENSP00000318451 601736 Q92925 PA35957
