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: KDM1A |
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Mutation Data (+)
# Cell Line/Tumor sample Tissue of Origin cDNA change Protein change Source FATHMM Prediction PolyPhen2 Prediction 1 BN28T LIVER c.1874A>C p.E625A COSMIC NP NP 2 BN45T LIVER c.21G>T p.A7A COSMIC NP NP 3 ESO-0176 OESOPHAGUS c.812G>T p.R271L COSMIC NP NP 4 HN_62854 UPPER AERODIGESTIVE TRACT c.1176C>T p.V392V COSMIC NP NP 5 LC_C8 LUNG c.34G>T p.A12S COSMIC PASSENGER/OTHER Possibly Damaging 6 LC_C8 LUNG c.35C>T p.A12V COSMIC PASSENGER/OTHER Probably Damaging 7 LPJ108 HAEMATOPOIETIC AND LYMPHOID TISSUE c.1658T>C p.L553P COSMIC NP NP 8 LPJ108 HAEMATOPOIETIC AND LYMPHOID TISSUE c.1665G>T p.W555C COSMIC NP NP 9 LUAD-RT-S01777 LUNG c.1981G>A p.V661I COSMIC NP NP 10 MB_Exm1017 CENTRAL NERVOUS SYSTEM c.1207G>A p.E403K COSMIC NP NP 11 MHH-CALL-2 HAEMATOPOIETIC AND LYMPHOID TISSUE c.2537C>T p.A846V COSMIC PASSENGER/OTHER Benign 12 P05-3852 PROSTATE c.2317T>G p.S773A COSMIC NP NP 13 PD4004a BREAST c.775G>A p.E259K COSMIC NP NP 14 SA106 BREAST c.1045C>G p.L349V COSMIC NP Benign 15 SJMB011 CENTRAL NERVOUS SYSTEM c.1207G>A p.E403K COSMIC NP NP 16 SK-MEL-2 SKIN c.2513C>T p.A838V COSMIC NP NP 17 TCGA-13-1488-01 OVARY c.454C>A p.P152T COSMIC PASSENGER/OTHER Probably Damaging 18 TCGA-39-5035-01 LUNG c.1399G>T p.E467* COSMIC NP NP 19 TCGA-49-4487-01 LUNG c.959T>G p.F320C COSMIC PASSENGER/OTHER Probably Damaging 20 TCGA-55-6968-01 LUNG c.754G>C p.E252Q COSMIC NP NP 21 TCGA-60-2719-01 LUNG c.1522C>G p.H508D COSMIC NP NP 22 TCGA-91-6831-01 LUNG c.2471G>A p.G824E COSMIC NP NP 23 TCGA-97-7937-01 LUNG c.2031G>A p.R677R COSMIC NP NP 24 TCGA-AA-3492-01 LARGE INTESTINE c.1251T>C p.S417S COSMIC NP NP 25 TCGA-AA-3864-01 LARGE INTESTINE c.1610C>T p.A537V COSMIC NP NP 26 TCGA-AA-3984-01 LARGE INTESTINE c.902T>G p.V301G COSMIC NP Probably Damaging 27 TCGA-AA-A00R-01 LARGE INTESTINE c.928G>T p.G310C COSMIC NP NP 28 TCGA-AB-2842-03 HAEMATOPOIETIC AND LYMPHOID TISSUE c.1995A>G p.P665P COSMIC NP NP 29 TCGA-AG-3731-01 LARGE INTESTINE c.1272C>T p.V424V COSMIC NP NP 30 TCGA-AG-3892-01 LARGE INTESTINE c.515C>T p.S172L COSMIC CANCER Possibly Damaging 31 TCGA-AG-A002-01 LARGE INTESTINE c.852C>T p.F284F COSMIC NP NP 32 TCGA-AP-A0LM-01 ENDOMETRIUM c.1501G>A p.E501K COSMIC NP NP 33 TCGA-AX-A05S-01 ENDOMETRIUM c.2584C>T p.R862C COSMIC NP NP 34 TCGA-AX-A0J1-01 ENDOMETRIUM c.1926C>T p.C642C COSMIC NP NP 35 TCGA-B5-A0JY-01 ENDOMETRIUM c.2106C>T p.F702F COSMIC NP NP 36 TCGA-B5-A0K6-01 ENDOMETRIUM c.2409A>G p.P803P COSMIC NP NP 37 TCGA-B5-A11E-01 ENDOMETRIUM c.2455C>T p.R819* COSMIC NP NP 38 TCGA-BG-A0M4-01 ENDOMETRIUM c.847A>G p.N283D COSMIC NP NP 39 TCGA-BS-A0UJ-01 ENDOMETRIUM c.1433A>G p.K478R COSMIC NP NP 40 TCGA-CA-6717-01 LARGE INTESTINE c.2427G>A p.S809S COSMIC NP NP 41 TCGA-CM-6166-01 LARGE INTESTINE c.1846C>T p.Q616* COSMIC NP NP 42 TCGA-CM-6171-01 LARGE INTESTINE c.251A>G p.Q84R COSMIC PASSENGER/OTHER Benign 43 TCGA-D1-A17Q-01 ENDOMETRIUM c.852C>T p.F284F COSMIC NP NP 44 TCGA-DK-A1AD-01 URINARY TRACT c.926C>G p.S309* COSMIC NP NP 45 TCGA-DK-A3IT-01 URINARY TRACT c.1266C>T p.F422F COSMIC NP NP 46 TCGA-EI-6507-01 LARGE INTESTINE c.1088C>A p.A363D COSMIC NP NP 47 TCGA-G2-A3IE-01 URINARY TRACT c.599A>G p.Q200R COSMIC NP NP 48 TCGA-GD-A2C5-01 URINARY TRACT c.2410A>G p.I804V 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 (+)
Users must enabled the Java in their browser to see structure.
Users can also download Java from here.Modelled Structure Structures available in PDB 2COM, 2DW4, 2EJR, 2H94, 2HKO, 2IW5, 2L3D, 2UXN, 2UXX, 2V1D, 2X0L, 2XAF, 2XAG, 2XAH, 2XAJ, 2XAQ, 2XAS, 2Y48, 2Z3Y, 2Z5U, 3ABT, 3ABU, 3ZMS, 3ZMT, 3ZMU, 3ZMV, 3ZMZ, 3ZN0, 3ZN1, 4BAY, 4CZZ, 4KUM, 4UV8, 4UV9, 4UVA, 4UVB, 4UVC, -
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 KDM1A KDM1A KDM1A ENSP00000349049 O60341 QuickGO HGNC Ensembl Genome Browser TreeFam UniProt O60341 KDM1A ENSP00000349049 KDM1A O60341 Expression Atlas Protein Atlas OMIM IntAct PharmGKB KDM1A ENSP00000349049 609132 O60341 PA165751392
