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: KDM4A |
| Expand All | Collapse All |
-
Mutation Data (+)
# Cell Line/Tumor sample Tissue of Origin cDNA change Protein change Source FATHMM Prediction PolyPhen2 Prediction 1 18T SKIN c.454C>T p.R152W COSMIC PASSENGER/OTHER Probably Damaging 2 585208 LUNG c.1903G>T p.A635S COSMIC PASSENGER/OTHER Benign 3 587228 LARGE INTESTINE c.1873A>G p.T625A COSMIC PASSENGER/OTHER Benign 4 587376 LARGE INTESTINE c.2516G>T p.R839I COSMIC PASSENGER/OTHER Benign 5 BN36T LIVER c.3030T>C p.L1010L COSMIC NP NP 6 ESOSCC162T OESOPHAGUS c.1684A>T p.R562W COSMIC PASSENGER/OTHER Possibly Damaging 7 H1703 LUNG c.1529C>G p.S510C COSMIC PASSENGER/OTHER Benign 8 HCC102T LIVER c.2728A>G p.K910E COSMIC PASSENGER/OTHER Probably Damaging 9 HCC91T LIVER c.1258C>A p.L420M COSMIC PASSENGER/OTHER Possibly Damaging 10 HN_62237 UPPER AERODIGESTIVE TRACT c.337G>A p.E113K COSMIC PASSENGER/OTHER Benign 11 HN_62237 UPPER AERODIGESTIVE TRACT c.8C>T p.S3F COSMIC PASSENGER/OTHER Possibly Damaging 12 HN_62505 UPPER AERODIGESTIVE TRACT c.1626C>T p.L542L COSMIC NP NP 13 HN_62686 UPPER AERODIGESTIVE TRACT c.1984G>T p.A662S COSMIC PASSENGER/OTHER Benign 14 HOP-62 LUNG c.2035C>T p.Q679* COSMIC NP NP 15 LAU108 SKIN c.1944T>A p.P648P COSMIC NP NP 16 LC_S51 LUNG c.2308delG p.A770fs*2 COSMIC NP NP 17 LUAD-B01970 LUNG c.2231G>A p.R744Q COSMIC PASSENGER/OTHER Benign 18 M14 HAEMATOPOIETIC AND LYMPHOID TISSUE c.3041T>C p.V1014A COSMIC PASSENGER/OTHER Possibly Damaging 19 ME015T SKIN c.716G>A p.R239H COSMIC PASSENGER/OTHER Probably Damaging 20 PD4093a BREAST c.866C>T p.T289I COSMIC PASSENGER/OTHER Probably Damaging 21 PR-09-5702 PROSTATE c.2613C>A p.D871E COSMIC PASSENGER/OTHER Probably Damaging 22 RK019_C01 LIVER c.2362G>T p.A788S COSMIC PASSENGER/OTHER Possibly Damaging 23 RK019_C01 LIVER c.2363C>T p.A788V COSMIC PASSENGER/OTHER Possibly Damaging 24 S00936 LUNG c.1303G>A p.A435T COSMIC PASSENGER/OTHER Benign 25 S01563 LUNG c.1602A>T p.R534R COSMIC NP NP 26 SWE-12 PROSTATE c.412G>A p.G138S COSMIC PASSENGER/OTHER Possibly Damaging 27 TCGA-34-2600-01 LUNG c.352G>T p.E118* COSMIC NP NP 28 TCGA-34-5927-01 LUNG c.2843G>C p.S948T COSMIC PASSENGER/OTHER Possibly Damaging 29 TCGA-36-2530-01 OVARY c.1283C>T p.T428M COSMIC PASSENGER/OTHER Probably Damaging 30 TCGA-44-2656-01 LUNG c.1702G>A p.A568T COSMIC PASSENGER/OTHER Benign 31 TCGA-44-7670-01 LUNG c.520C>A p.P174T COSMIC PASSENGER/OTHER Probably Damaging 32 TCGA-50-5930-01 LUNG c.2570A>T p.H857L COSMIC CANCER Probably Damaging 33 TCGA-60-2713-01 LUNG c.1672G>C p.E558Q COSMIC PASSENGER/OTHER Probably Damaging 34 TCGA-70-6722-01 LUNG c.259A>G p.I87V COSMIC PASSENGER/OTHER Benign 35 TCGA-A5-A0G9-01 ENDOMETRIUM c.1429G>A p.E477K COSMIC PASSENGER/OTHER Benign 36 TCGA-A6-3809-01 LARGE INTESTINE c.157T>G p.W53G COSMIC PASSENGER/OTHER Possibly Damaging 37 TCGA-A6-5659-01 LARGE INTESTINE c.4G>A p.A2T COSMIC PASSENGER/OTHER Benign 38 TCGA-A8-A06O-01 BREAST c.1043C>T p.P348L COSMIC PASSENGER/OTHER Probably Damaging 39 TCGA-A8-A09I-01 BREAST c.1276G>A p.E426K COSMIC PASSENGER/OTHER Benign 40 TCGA-AA-3811-01 LARGE INTESTINE c.429G>A p.K143K COSMIC NP NP 41 TCGA-AA-3877-01 LARGE INTESTINE c.2733C>T p.N911N COSMIC NP NP 42 TCGA-AA-3947-01 LARGE INTESTINE c.352G>A p.E118K COSMIC PASSENGER/OTHER Probably Damaging 43 TCGA-AD-6548-01 LARGE INTESTINE c.3087T>A p.I1029I COSMIC NP NP 44 TCGA-AG-A002-01 LARGE INTESTINE c.3038G>T p.R1013I COSMIC PASSENGER/OTHER Probably Damaging 45 TCGA-AG-A025-01 LARGE INTESTINE c.328C>T p.R110C COSMIC PASSENGER/OTHER Probably Damaging 46 TCGA-AP-A051-01 ENDOMETRIUM c.1199G>A p.R400Q COSMIC PASSENGER/OTHER Probably Damaging 47 TCGA-AP-A051-01 ENDOMETRIUM c.3182C>T p.A1061V COSMIC PASSENGER/OTHER Probably Damaging 48 TCGA-AP-A0LM-01 ENDOMETRIUM c.3073C>T p.R1025C COSMIC PASSENGER/OTHER Probably Damaging 49 TCGA-AR-A1AX-01 BREAST c.1495C>T p.L499F COSMIC PASSENGER/OTHER Possibly Damaging 50 TCGA-AU-6004-01 LARGE INTESTINE c.676delT p.F227fs*16 COSMIC NP NP 51 TCGA-AX-A05Z-01 ENDOMETRIUM c.1790G>A p.R597H COSMIC PASSENGER/OTHER Probably Damaging 52 TCGA-AX-A05Z-01 ENDOMETRIUM c.3073C>T p.R1025C COSMIC PASSENGER/OTHER Probably Damaging 53 TCGA-AZ-4315-01 LARGE INTESTINE c.962T>C p.V321A COSMIC PASSENGER/OTHER Probably Damaging 54 TCGA-AZ-6601-01 LARGE INTESTINE c.2778C>A p.T926T COSMIC NP NP 55 TCGA-B2-4099-01 KIDNEY c.606T>C p.F202F COSMIC NP NP 56 TCGA-B5-A0JY-01 ENDOMETRIUM c.2138C>T p.S713L COSMIC PASSENGER/OTHER Benign 57 TCGA-B5-A11E-01 ENDOMETRIUM c.83G>A p.S28N COSMIC PASSENGER/OTHER Benign 58 TCGA-BH-A0DG-01 BREAST c.383A>G p.N128S COSMIC PASSENGER/OTHER Benign 59 TCGA-BP-4163-01 KIDNEY c.1935G>C p.Q645H COSMIC PASSENGER/OTHER Probably Damaging 60 TCGA-CL-5918-01 LARGE INTESTINE c.144T>C p.V48V COSMIC NP NP 61 TCGA-D1-A0ZS-01 ENDOMETRIUM c.955G>A p.V319M COSMIC PASSENGER/OTHER Probably Damaging 62 TCGA-D1-A103-01 ENDOMETRIUM c.1940G>A p.R647Q COSMIC PASSENGER/OTHER Probably Damaging 63 TCGA-D1-A17D-01 ENDOMETRIUM c.2474G>A p.R825H COSMIC PASSENGER/OTHER Probably Damaging 64 TCGA-D5-6930-01 LARGE INTESTINE c.1699G>A p.A567T COSMIC PASSENGER/OTHER Benign 65 TCGA-D5-6930-01 LARGE INTESTINE c.356G>A p.R119Q COSMIC PASSENGER/OTHER Probably Damaging 66 TCGA-DC-5337-01 LARGE INTESTINE c.795A>G p.G265G COSMIC NP NP 67 TCGA-DK-A1A5-01 URINARY TRACT c.3094G>A p.E1032K COSMIC PASSENGER/OTHER Probably Damaging 68 TCGA-DS-A0VN-01 CERVIX c.2294G>A p.R765Q COSMIC PASSENGER/OTHER Possibly Damaging 69 YUWAND SKIN c.2513A>G p.K838R COSMIC PASSENGER/OTHER Possibly Damaging
*NP: Not Predicted -
Copy number variation and expression profile (+)
-
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 2GF7, 2GFA, 2GP3, 2GP5, 2OQ6, 2OQ7, 2OS2, 2OT7, 2OX0, 2P5B, 2PXJ, 2Q8C, 2Q8D, 2Q8E, 2QQR, 2QQS, 2VD7, 2WWJ, 2YBK, 2YBP, 2YBS, 3NJY, 3PDQ, 3RVH, 3U4S, 4AI9, 4BIS, 4GD4, -
Structure Domains (+)
-
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 (+)
-
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 KDM4A KDM4A KDM4A ENSP00000361473 O75164 QuickGO HGNC Ensembl Genome Browser TreeFam UniProt O75164 KDM4A ENSP00000361473 KDM4A O75164 Expression Atlas Protein Atlas OMIM IntAct PharmGKB KDM4A ENSP00000361473 609764 O75164 PA164721403
