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: KDM1B |
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Mutation Data (+)
# Cell Line/Tumor sample Tissue of Origin cDNA change Protein change Source FATHMM Prediction PolyPhen2 Prediction 1 24T SKIN c.470T>C p.I157T COSMIC PASSENGER/OTHER Benign 2 587238 LARGE INTESTINE c.1459G>A p.A487T COSMIC NP NP 3 587270 LARGE INTESTINE c.89C>A p.A30E COSMIC PASSENGER/OTHER Benign 4 CCRF-CEM HAEMATOPOIETIC AND LYMPHOID TISSUE c.862C>T p.R288* COSMIC NP NP 5 ESO-874 OESOPHAGUS c.371A>C p.E124A COSMIC PASSENGER/OTHER Probably Damaging 6 HN_62756 UPPER AERODIGESTIVE TRACT c.1614G>A p.V538V COSMIC NP NP 7 LAU165 SKIN c.1559A>G p.Y520C COSMIC NP NP 8 LC_C24 LUNG c.953T>C p.M318T COSMIC NP NP 9 LUAD-B00416 LUNG c.1075G>A p.D359N COSMIC NP NP 10 LUAD-B02515 LUNG c.1447G>A p.G483R COSMIC NP NP 11 PD4137a BREAST c.1458C>T p.V486V COSMIC NP NP 12 SA093 BREAST c.466G>A p.E156K COSMIC PASSENGER/OTHER Benign 13 SWE-21 PROSTATE c.287T>G p.F96C COSMIC PASSENGER/OTHER Probably Damaging 14 TCGA-05-4432-01 LUNG c.417G>T p.W139C COSMIC PASSENGER/OTHER Probably Damaging 15 TCGA-22-1011-01 LUNG c.1064C>T p.A355V COSMIC NP NP 16 TCGA-50-5933-01 LUNG c.1065A>G p.A355A COSMIC NP NP 17 TCGA-55-7574-01 LUNG c.1765G>A p.A589T COSMIC NP NP 18 TCGA-66-2755-01 LUNG c.1203G>T p.Q401H COSMIC NP NP 19 TCGA-A5-A0VP-01 ENDOMETRIUM c.1728A>G p.A576A COSMIC NP NP 20 TCGA-A6-2676-01 LARGE INTESTINE c.185G>C p.C62S COSMIC PASSENGER/OTHER Benign 21 TCGA-AA-3713-01 LARGE INTESTINE c.34G>T p.A12S COSMIC PASSENGER/OTHER Benign 22 TCGA-AA-3811-01 LARGE INTESTINE c.230G>A p.G77D COSMIC PASSENGER/OTHER Probably Damaging 23 TCGA-AA-3984-01 LARGE INTESTINE c.1740C>T p.G580G COSMIC NP NP 24 TCGA-AA-3984-01 LARGE INTESTINE c.863G>A p.R288Q COSMIC NP NP 25 TCGA-AA-A00A-01 LARGE INTESTINE c.543C>T p.T181T COSMIC NP NP 26 TCGA-AA-A00R-01 LARGE INTESTINE c.54G>A p.P18P COSMIC NP NP 27 TCGA-AP-A051-01 ENDOMETRIUM c.312G>T p.K104N COSMIC PASSENGER/OTHER Probably Damaging 28 TCGA-AP-A051-01 ENDOMETRIUM c.507C>T p.C169C COSMIC NP NP 29 TCGA-AP-A054-01 ENDOMETRIUM c.1639T>C p.Y547H COSMIC NP NP 30 TCGA-AP-A056-01 ENDOMETRIUM c.996C>A p.F332L COSMIC NP NP 31 TCGA-AP-A059-01 ENDOMETRIUM c.996C>A p.F332L COSMIC NP NP 32 TCGA-AP-A05H-01 ENDOMETRIUM c.1638C>A p.A546A COSMIC NP NP 33 TCGA-AP-A0LM-01 ENDOMETRIUM c.1376G>A p.R459Q COSMIC NP NP 34 TCGA-AX-A0IS-01 ENDOMETRIUM c.639C>T p.C213C COSMIC NP NP 35 TCGA-AX-A0J1-01 ENDOMETRIUM c.617G>T p.R206L COSMIC NP NP 36 TCGA-B5-A11J-01 ENDOMETRIUM c.1426G>A p.V476M COSMIC NP NP 37 TCGA-BG-A0M4-01 ENDOMETRIUM c.861C>T p.G287G COSMIC NP NP 38 TCGA-BS-A0UV-01 ENDOMETRIUM c.996C>A p.F332L COSMIC NP NP 39 TCGA-D1-A15X-01 ENDOMETRIUM c.369C>T p.T123T COSMIC NP NP 40 TCGA-D1-A165-01 ENDOMETRIUM c.120G>A p.E40E COSMIC NP NP 41 TCGA-D1-A17M-01 ENDOMETRIUM c.640G>A p.V214I COSMIC NP NP 42 TCGA-D1-A17Q-01 ENDOMETRIUM c.502C>T p.R168* COSMIC NP NP 43 TCGA-DK-A1AD-01 URINARY TRACT c.1242G>A p.K414K COSMIC NP NP 44 TCGA-DK-A3IK-01 URINARY TRACT c.1233G>A p.L411L COSMIC NP NP 45 TCGA-EY-A1GS-01 ENDOMETRIUM c.1166A>C p.Q389P COSMIC NP NP 46 TCGA-F4-6570-01 LARGE INTESTINE c.682G>T p.G228C COSMIC NP NP 47 TCGA-GV-A3QI-01 URINARY TRACT c.1720A>G p.T574A COSMIC NP NP 48 YUAKER SKIN c.1631G>A p.G544E COSMIC NP Probably Damaging 49 YUKLAB SKIN c.562C>T p.P188S COSMIC PASSENGER/OTHER Possibly Damaging 50 YULAPE SKIN c.409C>T p.P137S COSMIC PASSENGER/OTHER Probably Damaging 51 cSCCP8 SKIN c.1322G>T p.S441I 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 (+)
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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. Sequence alignment with 1000 genome variations:
Click on button to get Sequence alignment with Coverage, Consensus and Quality 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 KDM1B KDM1B KDM1B ENSP00000297792 Q8NB78 QuickGO HGNC Ensembl Genome Browser TreeFam UniProt Q8NB78 KDM1B ENSP00000297792 KDM1B Q8NB78 Expression Atlas Protein Atlas OMIM IntAct PharmGKB KDM1B ENSP00000297792 613081 Q8NB78 PA165617946
