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: JMJD4 |
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Mutation Data (+)
# Cell Line/Tumor sample Tissue of Origin cDNA change Protein change Source FATHMM Prediction PolyPhen2 Prediction 1 019 HAEMATOPOIETIC AND LYMPHOID TISSUE c.1351C>T p.Q451* COSMIC NP NP 2 019-0047-01TD HAEMATOPOIETIC AND LYMPHOID TISSUE c.1351C>T p.Q451* COSMIC NP NP 3 112T THYROID c.529A>G p.R177G COSMIC PASSENGER/OTHER Benign 4 BN13T LIVER c.638A>G p.D213G COSMIC PASSENGER/OTHER Possibly Damaging 5 BN49T LIVER c.1029G>A p.L343L COSMIC NP NP 6 ESO-601 OESOPHAGUS c.1021C>T p.R341C COSMIC PASSENGER/OTHER Benign 7 HCC47T LIVER c.240G>C p.S80S COSMIC NP NP 8 HCC47T LIVER c.242A>G p.E81G COSMIC PASSENGER/OTHER Benign 9 LC_S46 LUNG c.293A>G p.N98S COSMIC PASSENGER/OTHER Probably Damaging 10 LUAD-RT-S01777 LUNG c.277G>T p.G93C COSMIC PASSENGER/OTHER Possibly Damaging 11 ME044T SKIN c.100G>A p.E34K COSMIC PASSENGER/OTHER Benign 12 OPM2 HAEMATOPOIETIC AND LYMPHOID TISSUE c.1030C>G p.Q344E COSMIC PASSENGER/OTHER Benign 13 RK041_C01 LIVER c.1295C>T p.P432L COSMIC PASSENGER/OTHER Benign 14 RK055_C01 LIVER c.719G>T p.R240L COSMIC PASSENGER/OTHER Possibly Damaging 15 TCGA-05-4432-01 LUNG c.499G>T p.E167* COSMIC NP NP 16 TCGA-44-3919-01 LUNG c.843C>G p.L281L COSMIC NP NP 17 TCGA-55-1592-01 LUNG c.1289C>T p.A430V COSMIC PASSENGER/OTHER Benign 18 TCGA-61-2110-01 OVARY c.750G>C p.G250G COSMIC NP NP 19 TCGA-A6-6780-01 LARGE INTESTINE c.1258C>T p.R420C COSMIC PASSENGER/OTHER Benign 20 TCGA-AG-3609-01 LARGE INTESTINE c.546C>T p.L182L COSMIC NP NP 21 TCGA-AP-A0LM-01 ENDOMETRIUM c.674C>T p.A225V COSMIC PASSENGER/OTHER Benign 22 TCGA-AP-A0LM-01 ENDOMETRIUM c.714C>A p.I238I COSMIC NP NP 23 TCGA-AX-A064-01 ENDOMETRIUM c.1172C>T p.A391V COSMIC PASSENGER/OTHER Possibly Damaging 24 TCGA-B5-A0K2-01 ENDOMETRIUM c.1032G>C p.Q344H COSMIC PASSENGER/OTHER Benign 25 TCGA-B5-A11E-01 ENDOMETRIUM c.1183C>T p.L395F COSMIC PASSENGER/OTHER Possibly Damaging 26 TCGA-CW-5581-01 KIDNEY c.621G>A p.W207* COSMIC NP NP 27 TCGA-EI-6507-01 LARGE INTESTINE c.1276G>A p.A426T COSMIC PASSENGER/OTHER Benign 28 TCGA-G9-6363-01 PROSTATE c.1136A>C p.N379T 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 Structure is not available in PDB -
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 JMJD4 JMJD4 JMJD4 ENSP00000355720 Q9H9V9 QuickGO HGNC Ensembl Genome Browser TreeFam UniProt Q9H9V9 JMJD4 ENSP00000355720 JMJD4 Q9H9V9 Expression Atlas Protein Atlas OMIM IntAct PharmGKB JMJD4 ENSP00000355720 NA Q9H9V9 PA142671643
