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: KDM4B |
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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.3170C>A p.A1057D COSMIC PASSENGER/OTHER Probably Damaging 2 587220 LARGE INTESTINE c.1523T>C p.V508A COSMIC PASSENGER/OTHER Possibly Damaging 3 587222 LARGE INTESTINE c.1046C>T p.A349V COSMIC PASSENGER/OTHER Probably Damaging 4 587226 LARGE INTESTINE c.1001A>C p.K334T COSMIC PASSENGER/OTHER Benign 5 587238 LARGE INTESTINE c.2077T>C p.Y693H COSMIC PASSENGER/OTHER Probably Damaging 6 587278 LARGE INTESTINE c.2557G>A p.V853M COSMIC PASSENGER/OTHER Probably Damaging 7 587284 LARGE INTESTINE c.877G>A p.A293T COSMIC PASSENGER/OTHER Probably Damaging 8 587342 LARGE INTESTINE c.2053G>A p.A685T COSMIC PASSENGER/OTHER Probably Damaging 9 BN01T LIVER c.2889T>C p.P963P COSMIC NP NP 10 BN43T LIVER c.2889T>C p.P963P COSMIC NP NP 11 CA1 LARGE INTESTINE c.1631A>G p.H544R COSMIC PASSENGER/OTHER Benign 12 ESO-1481 OESOPHAGUS c.874T>G p.F292V COSMIC PASSENGER/OTHER Probably Damaging 13 ESO-H01 OESOPHAGUS c.240G>A p.S80S COSMIC NP NP 14 H1155 LUNG c.886C>T p.R296W COSMIC PASSENGER/OTHER Probably Damaging 15 H23 LUNG c.2957G>T p.R986L COSMIC PASSENGER/OTHER Possibly Damaging 16 HCC13T LIVER c.254A>G p.Q85R COSMIC PASSENGER/OTHER Possibly Damaging 17 HCC19T LIVER c.73T>C p.F25L COSMIC PASSENGER/OTHER Probably Damaging 18 HCC33T LIVER c.537C>G p.F179L COSMIC PASSENGER/OTHER Probably Damaging 19 HCC67T LIVER c.1656G>T p.E552D COSMIC PASSENGER/OTHER Possibly Damaging 20 HCC87T LIVER c.1074G>T p.W358C COSMIC PASSENGER/OTHER Probably Damaging 21 LC_C8 LUNG c.1768C>T p.R590W COSMIC PASSENGER/OTHER Probably Damaging 22 LUAD-B02594 LUNG c.1036C>T p.R346W COSMIC PASSENGER/OTHER Probably Damaging 23 ME002T SKIN c.1171C>T p.P391S COSMIC PASSENGER/OTHER Benign 24 ME016T SKIN c.1960C>T p.P654S COSMIC PASSENGER/OTHER Benign 25 NCI-H128 LUNG c.2221G>A p.E741K COSMIC PASSENGER/OTHER Probably Damaging 26 NCI-H23 LUNG c.2957G>T p.R986L COSMIC PASSENGER/OTHER Possibly Damaging 27 PD6754a NS c.736A>G p.I246V COSMIC PASSENGER/OTHER Benign 28 S00933 LUNG c.60A>T p.P20P COSMIC NP NP 29 S00936 LUNG c.1991C>T p.A664V COSMIC PASSENGER/OTHER Possibly Damaging 30 S00936 LUNG c.2225C>A p.P742Q COSMIC PASSENGER/OTHER Probably Damaging 31 SA065 BREAST c.3223A>G p.S1075G COSMIC PASSENGER/OTHER Benign 32 SA067 BREAST c.343T>G p.F115V COSMIC PASSENGER/OTHER Benign 33 T154 ENDOMETRIUM c.2138C>T p.P713L COSMIC PASSENGER/OTHER Benign 34 TCGA-18-3409-01 LUNG c.2933C>T p.S978F COSMIC PASSENGER/OTHER Benign 35 TCGA-21-1076-01 LUNG c.689G>T p.G230V COSMIC PASSENGER/OTHER Possibly Damaging 36 TCGA-33-4532-01 LUNG c.1625A>T p.Q542L COSMIC PASSENGER/OTHER Benign 37 TCGA-33-4532-01 LUNG c.1626G>T p.Q542H COSMIC PASSENGER/OTHER Benign 38 TCGA-36-2543-01 OVARY c.192C>T p.D64D COSMIC NP NP 39 TCGA-51-4079-01 LUNG c.768C>T p.I256I COSMIC NP NP 40 TCGA-60-2724-01 LUNG c.1950C>T p.D650D COSMIC NP NP 41 TCGA-66-2770-01 LUNG c.1715G>T p.G572V COSMIC PASSENGER/OTHER Benign 42 TCGA-A6-5660-01 LARGE INTESTINE c.1059C>A p.P353P COSMIC NP NP 43 TCGA-A6-5665-01 LARGE INTESTINE c.1903G>A p.E635K COSMIC PASSENGER/OTHER Probably Damaging 44 TCGA-A6-6780-01 LARGE INTESTINE c.2208C>T p.G736G COSMIC NP NP 45 TCGA-A6-6781-01 LARGE INTESTINE c.1832G>A p.R611Q COSMIC PASSENGER/OTHER Probably Damaging 46 TCGA-AA-3663-01 LARGE INTESTINE c.2889T>C p.P963P COSMIC NP NP 47 TCGA-AA-3697-01 LARGE INTESTINE c.988T>C p.Y330H COSMIC PASSENGER/OTHER Possibly Damaging 48 TCGA-AA-3712-01 LARGE INTESTINE c.2889T>C p.P963P COSMIC NP NP 49 TCGA-AA-3864-01 LARGE INTESTINE c.705C>T p.C235C COSMIC NP NP 50 TCGA-AD-6889-01 LARGE INTESTINE c.1590C>T p.Y530Y COSMIC NP NP 51 TCGA-AP-A051-01 ENDOMETRIUM c.93C>T p.Y31Y COSMIC NP NP 52 TCGA-AP-A059-01 ENDOMETRIUM c.153G>A p.P51P COSMIC NP NP 53 TCGA-AP-A0LD-01 ENDOMETRIUM c.104T>A p.I35K COSMIC PASSENGER/OTHER Possibly Damaging 54 TCGA-AS-3778-01 KIDNEY c.161G>T p.W54L COSMIC PASSENGER/OTHER Probably Damaging 55 TCGA-AU-6004-01 LARGE INTESTINE c.2661C>T p.G887G COSMIC NP NP 56 TCGA-AX-A0J1-01 ENDOMETRIUM c.590G>A p.S197N COSMIC PASSENGER/OTHER Probably Damaging 57 TCGA-AY-6386-01 LARGE INTESTINE c.2889T>C p.P963P COSMIC NP NP 58 TCGA-AZ-6601-01 LARGE INTESTINE c.1712C>T p.T571M COSMIC PASSENGER/OTHER Probably Damaging 59 TCGA-B5-A0JY-01 ENDOMETRIUM c.210G>A p.A70A COSMIC NP NP 60 TCGA-B5-A11H-01 ENDOMETRIUM c.2556C>T p.C852C COSMIC NP NP 61 TCGA-B5-A11Y-01 ENDOMETRIUM c.1524C>T p.V508V COSMIC NP NP 62 TCGA-BG-A0VZ-01 ENDOMETRIUM c.392C>T p.P131L COSMIC PASSENGER/OTHER Probably Damaging 63 TCGA-BH-A0BP-01 BREAST c.1867C>A p.P623T COSMIC PASSENGER/OTHER Probably Damaging 64 TCGA-BS-A0U8-01 ENDOMETRIUM c.1125G>A p.R375R COSMIC NP NP 65 TCGA-BS-A0UF-01 ENDOMETRIUM c.709G>A p.A237T COSMIC PASSENGER/OTHER Probably Damaging 66 TCGA-BS-A0UJ-01 ENDOMETRIUM c.1302C>T p.A434A COSMIC NP NP 67 TCGA-D1-A103-01 ENDOMETRIUM c.2324G>A p.R775H COSMIC PASSENGER/OTHER Probably Damaging 68 TCGA-D1-A103-01 ENDOMETRIUM c.2374G>A p.A792T COSMIC PASSENGER/OTHER Probably Damaging 69 TCGA-D1-A163-01 ENDOMETRIUM c.1296G>A p.R432R COSMIC NP NP 70 TCGA-D1-A167-01 ENDOMETRIUM c.729G>A p.M243I COSMIC PASSENGER/OTHER Benign 71 TCGA-D1-A174-01 ENDOMETRIUM c.2661C>T p.G887G COSMIC NP NP 72 TCGA-D1-A17C-01 ENDOMETRIUM c.2680G>A p.D894N COSMIC PASSENGER/OTHER Probably Damaging 73 TCGA-D5-6540-01 LARGE INTESTINE c.1375T>G p.F459V COSMIC PASSENGER/OTHER Benign 74 TCGA-D5-6540-01 LARGE INTESTINE c.2655C>T p.A885A COSMIC NP NP 75 TCGA-D5-6930-01 LARGE INTESTINE c.1474C>A p.P492T COSMIC PASSENGER/OTHER Benign 76 TCGA-DC-6160-01 LARGE INTESTINE c.2889T>C p.P963P COSMIC NP NP 77 TCGA-DS-A0VL-01 CERVIX c.2240C>G p.S747C COSMIC PASSENGER/OTHER Probably Damaging 78 TCGA-DY-A1DC-01 LARGE INTESTINE c.1322G>A p.G441E COSMIC PASSENGER/OTHER Possibly Damaging 79 TCGA-DY-A1H8-01 LARGE INTESTINE c.489C>T p.R163R COSMIC NP NP 80 TCGA-F4-6856-01 LARGE INTESTINE c.1851G>C p.R617R COSMIC NP NP 81 TCGA-F5-6464-01 LARGE INTESTINE c.3125C>T p.T1042M COSMIC PASSENGER/OTHER Probably Damaging 82 TCGA-FD-A3NA-01 URINARY TRACT c.2204C>G p.S735C COSMIC PASSENGER/OTHER Probably Damaging 83 YUBER SKIN c.2201C>T p.T734I COSMIC PASSENGER/OTHER Possibly Damaging 84 YUGOE SKIN c.1172C>T p.P391L COSMIC PASSENGER/OTHER Benign 85 YUNACK SKIN c.2845G>A p.E949K COSMIC PASSENGER/OTHER Probably Damaging 86 cSCCP2 SKIN c.2933C>T p.S978F COSMIC PASSENGER/OTHER Benign 87 cSCCP7 SKIN c.1579C>T p.P527S 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 (+)
1. PFAM Domains:Domain ID Domain Name Start Site End Site E-value PF02375 JmjN 16 50 2.5e-15 PB008394 Pfam-B_8394 45 147 1.1e-74 PF02373 JmjC 176 292 6.6e-43 PB014467 Pfam-B_14467 604 696 3.3e-20 PF13831 PHD_2 754 789 7.1e-14 PF13832 zf-HC5HC2H_2 795 906 8.8e-37 PB005109 Pfam-B_5109 931 1039 4.2e-09 PB002825 Pfam-B_2825 1003 1057 6.8e-06 PB012059 Pfam-B_12059 1019 1093 3.8e-19 -
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 KDM4B KDM4B KDM4B ENSP00000159111 O94953 QuickGO HGNC Ensembl Genome Browser TreeFam UniProt O94953 KDM4B ENSP00000159111 KDM4B O94953 Expression Atlas Protein Atlas OMIM IntAct PharmGKB KDM4B ENSP00000159111 609765 O94953 PA164721452
