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: KDM5B |
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Mutation Data (+)
# Cell Line/Tumor sample Tissue of Origin cDNA change Protein change Source FATHMM Prediction PolyPhen2 Prediction 1 BB16T BREAST c.1993G>T p.E665* COSMIC NP NP 2 HCC2157 BREAST c.4715A>G p.K1572R COSMIC NP NP 3 J82 URINARY TRACT c.4658G>C p.R1553T COSMIC NP NP 4 TCGA-13-0755-01 OVARY c.2943_2944insG p.F982fs*32 COSMIC NP NP 5 TCGA-24-2290-01 OVARY c.2632C>A p.L878I COSMIC NP NP 6 cSCCP6 SKIN c.2321C>T p.A774V 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 (+)
1. PFAM Domains:Domain ID Domain Name Start Site End Site E-value PF02375 JmjN 33 66 5.1e-14 PF01388 ARID 95 183 1e-22 PF00628 PHD 311 357 2.4e-11 PB006766 Pfam-B_6766 325 360 4.7e-09 PF02373 JmjC 486 602 6.8e-44 PF02928 zf-C5HC2 692 745 3e-18 PF08429 PLU-1 756 1088 3e-94 PF00628 PHD 1178 1223 1.7e-08 PB000113 Pfam-B_113 1217 1270 1.9e-15 PB011260 Pfam-B_11260 1489 1537 7.5e-12 PF00628 PHD 1492 1537 9.7e-08 -
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 KDM5B KDM5B KDM5B ENSP00000356233 Q9UGL1 QuickGO HGNC Ensembl Genome Browser TreeFam UniProt Q9UGL1 KDM5B ENSP00000356233 KDM5B Q9UGL1 Expression Atlas Protein Atlas OMIM IntAct PharmGKB KDM5B ENSP00000356233 605393 Q9UGL1 PA164721626
