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: KDM5D |
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Mutation Data (+)
# Cell Line/Tumor sample Tissue of Origin cDNA change Protein change Source FATHMM Prediction PolyPhen2 Prediction 1 002 KIDNEY c.2434G>T p.V812L COSMIC PASSENGER/OTHER Benign 2 587228 LARGE INTESTINE c.476G>A p.R159H COSMIC PASSENGER/OTHER Probably Damaging 3 587332 LARGE INTESTINE c.4177C>T p.L1393F COSMIC PASSENGER/OTHER Probably Damaging 4 587350 LARGE INTESTINE c.4235C>A p.P1412H COSMIC PASSENGER/OTHER Possibly Damaging 5 CLL168 HAEMATOPOIETIC AND LYMPHOID TISSUE c.1513A>G p.I505V COSMIC PASSENGER/OTHER Possibly Damaging 6 CP66-MEL SKIN c.469T>A p.Y157N COSMIC PASSENGER/OTHER Probably Damaging 7 LUAD-NYU1195 LUNG c.1577G>T p.G526V COSMIC PASSENGER/OTHER Probably Damaging 8 LUAD-S01302 LUNG c.379G>T p.A127S COSMIC PASSENGER/OTHER Benign 9 PD6354a NS c.2374C>T p.R792C COSMIC PASSENGER/OTHER Probably Damaging 10 S01366 LUNG c.3997A>G p.K1333E COSMIC PASSENGER/OTHER Benign 11 SK-MEL-2 SKIN c.2905C>T p.R969C COSMIC PASSENGER/OTHER Benign 12 TCGA-18-3409-01 LUNG c.4042G>T p.E1348* COSMIC NP NP 13 TCGA-18-3417-01 LUNG c.550G>T p.E184* COSMIC NP NP 14 TCGA-38-4629-01 LUNG c.3864G>A p.V1288V COSMIC NP NP 15 TCGA-39-5022-01 LUNG c.4299G>C p.R1433R COSMIC NP NP 16 TCGA-55-8089-01 LUNG c.2694G>T p.L898L COSMIC NP NP 17 TCGA-55-8089-01 LUNG c.3206G>T p.R1069I COSMIC PASSENGER/OTHER Probably Damaging 18 TCGA-78-7633-01 LUNG c.3052G>C p.A1018P COSMIC PASSENGER/OTHER Probably Damaging 19 TCGA-95-7944-01 LUNG c.1363G>A p.E455K COSMIC PASSENGER/OTHER Probably Damaging 20 TCGA-97-7937-01 LUNG c.1508G>T p.W503L COSMIC PASSENGER/OTHER Probably Damaging 21 TCGA-AA-A00A-01 LARGE INTESTINE c.3492A>G p.P1164P COSMIC NP NP 22 TCGA-AA-A00E-01 LARGE INTESTINE c.1734G>A p.Q578Q COSMIC NP NP 23 TCGA-AA-A00J-01 LARGE INTESTINE c.341G>A p.S114N COSMIC PASSENGER/OTHER Possibly Damaging 24 TCGA-AA-A01I-01 LARGE INTESTINE c.2302C>T p.R768* COSMIC NP NP 25 TCGA-AG-A002-01 LARGE INTESTINE c.3229C>A p.L1077I COSMIC PASSENGER/OTHER Probably Damaging 26 TCGA-AY-6197-01 LARGE INTESTINE c.4325G>A p.R1442Q COSMIC PASSENGER/OTHER Probably Damaging 27 TCGA-AZ-4315-01 LARGE INTESTINE c.1380G>A p.A460A COSMIC NP NP 28 TCGA-AZ-4315-01 LARGE INTESTINE c.4255C>T p.R1419C COSMIC PASSENGER/OTHER Benign 29 TCGA-AZ-6601-01 LARGE INTESTINE c.3903G>A p.Q1301Q COSMIC NP NP 30 TCGA-CJ-6030-01 KIDNEY c.376G>A p.E126K COSMIC PASSENGER/OTHER Probably Damaging 31 TCGA-D5-6930-01 LARGE INTESTINE c.3009G>A p.L1003L COSMIC NP NP 32 TCGA-D5-6930-01 LARGE INTESTINE c.800delC p.P267fs*5 COSMIC NP NP 33 YURIDA SKIN c.2165C>T p.S722F COSMIC PASSENGER/OTHER Benign 34 pfg029T STOMACH c.3585G>C p.W1195C COSMIC CANCER Probably Damaging
*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 (+)
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Structure Domains (+)
1. PFAM Domains:Domain ID Domain Name Start Site End Site E-value PF02375 JmjN 15 48 3e-15 PF01388 ARID 77 165 8.8e-24 PF00628 PHD 316 362 4.3e-12 PB006766 Pfam-B_6766 330 365 1.9e-06 PF02373 JmjC 491 607 8.6e-43 PF02928 zf-C5HC2 697 750 2e-16 PF08429 PLU-1 761 1087 5.3e-93 PF00628 PHD 1174 1236 7.8e-07 PB000113 Pfam-B_113 1193 1304 2.7e-36 PB012821 Pfam-B_12821 1401 1466 1.3e-29 2. Superfamily Domains:Domain ID Start Site End Site E-value 0047105 440 645 1.92e-35 0046063 60 183 7.33e-32 0050474 301 368 5.54e-17 0050473 1169 1241 1.06e-11 -
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 KDM5D KDM5D KDM5D ENSP00000322408 Q9BY66 QuickGO HGNC Ensembl Genome Browser TreeFam UniProt Q9BY66 KDM5D ENSP00000322408 KDM5D Q9BY66 Expression Atlas Protein Atlas OMIM IntAct PharmGKB KDM5D ENSP00000322408 426000 Q9BY66 PA35965
