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: KDM4D |
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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.1451C>T p.S484L COSMIC PASSENGER/OTHER Benign 2 2334192 LUNG c.640G>T p.V214L COSMIC PASSENGER/OTHER Benign 3 587228 LARGE INTESTINE c.613C>T p.H205Y COSMIC PASSENGER/OTHER Probably Damaging 4 587238 LARGE INTESTINE c.386G>A p.R129H COSMIC PASSENGER/OTHER Possibly Damaging 5 CHC433T LIVER c.1010A>G p.K337R COSMIC PASSENGER/OTHER Possibly Damaging 6 ESO-0067 OESOPHAGUS c.1347C>A p.G449G COSMIC NP NP 7 ESO-1608 OESOPHAGUS c.673C>T p.R225C COSMIC PASSENGER/OTHER Benign 8 ESO-169 OESOPHAGUS c.868G>A p.A290T COSMIC PASSENGER/OTHER Probably Damaging 9 ESO-632 OESOPHAGUS c.95A>C p.D32A COSMIC PASSENGER/OTHER Benign 10 H1672 LUNG c.640G>T p.V214L COSMIC PASSENGER/OTHER Benign 11 HCT-15 LARGE INTESTINE c.386G>A p.R129H COSMIC PASSENGER/OTHER Possibly Damaging 12 HN_63080 UPPER AERODIGESTIVE TRACT c.1542T>A p.A514A COSMIC NP NP 13 LUAD-CHTN-3090346 LUNG c.79G>A p.E27K COSMIC PASSENGER/OTHER Probably Damaging 14 LUAD-E00897 LUNG c.473G>T p.G158V COSMIC PASSENGER/OTHER Probably Damaging 15 RK209_C01 LIVER c.12G>T p.M4I COSMIC PASSENGER/OTHER Benign 16 T155 ENDOMETRIUM c.355G>A p.E119K COSMIC PASSENGER/OTHER Benign 17 TCGA-05-4384-01 LUNG c.564G>C p.T188T COSMIC NP NP 18 TCGA-05-4410-01 LUNG c.951G>T p.V317V COSMIC NP NP 19 TCGA-18-3409-01 LUNG c.190G>A p.D64N COSMIC PASSENGER/OTHER Benign 20 TCGA-18-3416-01 LUNG c.708G>C p.R236R COSMIC NP NP 21 TCGA-22-4601-01 LUNG c.1181G>A p.G394E COSMIC PASSENGER/OTHER Benign 22 TCGA-23-1029-01 OVARY c.1289G>C p.S430T COSMIC PASSENGER/OTHER Benign 23 TCGA-30-1857-01 OVARY c.1130T>A p.L377H COSMIC PASSENGER/OTHER Benign 24 TCGA-39-5030-01 LUNG c.798G>A p.Q266Q COSMIC NP NP 25 TCGA-60-2711-01 LUNG c.1182G>C p.G394G COSMIC NP NP 26 TCGA-63-5128-01 LUNG c.681C>A p.A227A COSMIC NP NP 27 TCGA-64-5781-01 LUNG c.1178G>T p.S393I COSMIC PASSENGER/OTHER Benign 28 TCGA-66-2759-01 LUNG c.368G>C p.R123P COSMIC PASSENGER/OTHER Probably Damaging 29 TCGA-73-4670-01 LUNG c.1117G>T p.G373C COSMIC PASSENGER/OTHER Probably Damaging 30 TCGA-86-7701-01 LUNG c.358G>T p.D120Y COSMIC PASSENGER/OTHER Probably Damaging 31 TCGA-AA-3811-01 LARGE INTESTINE c.1012C>T p.R338C COSMIC PASSENGER/OTHER Benign 32 TCGA-AA-A00A-01 LARGE INTESTINE c.140G>A p.G47D COSMIC CANCER Probably Damaging 33 TCGA-AD-6889-01 LARGE INTESTINE c.271delA p.K93fs*4 COSMIC NP NP 34 TCGA-AK-3451-01 KIDNEY c.263A>G p.Q88R COSMIC PASSENGER/OTHER Probably Damaging 35 TCGA-AO-A12H-01 BREAST c.370A>T p.K124* COSMIC NP NP 36 TCGA-AP-A051-01 ENDOMETRIUM c.1175G>A p.R392H COSMIC PASSENGER/OTHER Possibly Damaging 37 TCGA-AP-A059-01 ENDOMETRIUM c.1378C>T p.L460L COSMIC NP NP 38 TCGA-AP-A0LT-01 ENDOMETRIUM c.304C>T p.R102C COSMIC PASSENGER/OTHER Benign 39 TCGA-AX-A0J0-01 ENDOMETRIUM c.79G>T p.E27* COSMIC NP NP 40 TCGA-AY-6197-01 LARGE INTESTINE c.271delA p.K93fs*4 COSMIC NP NP 41 TCGA-AZ-6598-01 LARGE INTESTINE c.271delA p.K93fs*4 COSMIC NP NP 42 TCGA-B5-A0JV-01 ENDOMETRIUM c.995G>A p.R332H COSMIC PASSENGER/OTHER Probably Damaging 43 TCGA-B5-A0K2-01 ENDOMETRIUM c.244C>T p.R82W COSMIC PASSENGER/OTHER Probably Damaging 44 TCGA-BP-5186-01 KIDNEY c.1449T>A p.A483A COSMIC NP NP 45 TCGA-BS-A0UF-01 ENDOMETRIUM c.1124G>T p.R375I COSMIC PASSENGER/OTHER Possibly Damaging 46 TCGA-C4-A0F6-01 URINARY TRACT c.1459G>A p.E487K COSMIC PASSENGER/OTHER Benign 47 TCGA-CA-6717-01 LARGE INTESTINE c.771T>G p.N257K COSMIC PASSENGER/OTHER Probably Damaging 48 TCGA-CK-4950-01 LARGE INTESTINE c.186C>T p.T62T COSMIC NP NP 49 TCGA-CM-5861-01 LARGE INTESTINE c.271delA p.K93fs*4 COSMIC NP NP 50 TCGA-D1-A103-01 ENDOMETRIUM c.1048C>T p.P350S COSMIC PASSENGER/OTHER Possibly Damaging 51 TCGA-D1-A174-01 ENDOMETRIUM c.367C>T p.R123* COSMIC NP NP 52 TCGA-D5-6927-01 LARGE INTESTINE c.271delA p.K93fs*4 COSMIC NP NP 53 TCGA-G4-6628-01 LARGE INTESTINE c.271delA p.K93fs*4 COSMIC NP NP 54 cSCCP7 SKIN c.827C>T p.P276L COSMIC PASSENGER/OTHER 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 (+)
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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 KDM4D KDM4D KDM4D ENSP00000334181 Q6B0I6 QuickGO HGNC Ensembl Genome Browser TreeFam UniProt Q6B0I6 KDM4D ENSP00000334181 KDM4D Q6B0I6 Expression Atlas Protein Atlas OMIM IntAct PharmGKB KDM4D ENSP00000334181 609766 Q6B0I6 PA164721552
