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: HDAC5 |
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Mutation Data (+)
# Cell Line/Tumor sample Tissue of Origin cDNA change Protein change Source FATHMM Prediction PolyPhen2 Prediction 1 587234 LARGE INTESTINE c.1427G>A p.R476H COSMIC PASSENGER/OTHER Probably Damaging 2 587338 LARGE INTESTINE c.2935A>G p.T979A COSMIC CANCER Benign 3 587376 LARGE INTESTINE c.2947T>G p.F983V COSMIC PASSENGER/OTHER Probably Damaging 4 HCC142T LIVER c.1448C>T p.T483M COSMIC PASSENGER/OTHER Probably Damaging 5 HCT-15 LARGE INTESTINE c.3263C>T p.A1088V COSMIC CANCER Probably Damaging 6 LUAD-74TBW LUNG c.1074C>T p.P358P COSMIC NP NP 7 MB_Exm1017 CENTRAL NERVOUS SYSTEM c.2093G>A p.C698Y COSMIC CANCER Probably Damaging 8 ME100L SKIN c.1328C>T p.S443F COSMIC PASSENGER/OTHER Probably Damaging 9 P03-1426 PROSTATE c.850C>A p.R284S COSMIC CANCER Probably Damaging 10 PA285 PANCREAS c.1717_1718insC p.R573fs*8 COSMIC NP NP 11 PA285 PANCREAS c.3183G>A p.V1061V COSMIC NP NP 12 PR-04-3347 PROSTATE c.1013T>A p.V338D COSMIC PASSENGER/OTHER Probably Damaging 13 TCGA-05-4244-01 LUNG c.918G>T p.G306G COSMIC NP NP 14 TCGA-13-2057-01 OVARY c.51G>A p.L17L COSMIC NP NP 15 TCGA-18-3415-01 LUNG c.2161A>G p.T721A COSMIC CANCER Benign 16 TCGA-24-0979-01 OVARY c.1747C>G p.Q583E COSMIC PASSENGER/OTHER Benign 17 TCGA-44-4112-01 LUNG c.1322A>T p.H441L COSMIC PASSENGER/OTHER Probably Damaging 18 TCGA-50-5930-01 LUNG c.846G>A p.L282L COSMIC NP NP 19 TCGA-50-5946-01 LUNG c.1038C>T p.L346L COSMIC NP NP 20 TCGA-50-5946-02 LUNG c.1038C>T p.L346L COSMIC NP NP 21 TCGA-50-5946-02 LUNG c.2220C>G p.I740M COSMIC CANCER Possibly Damaging 22 TCGA-50-5946-02 LUNG c.2234C>G p.S745C COSMIC CANCER Benign 23 TCGA-A8-A07C-01 BREAST c.622C>T p.P208S COSMIC PASSENGER/OTHER Benign 24 TCGA-AA-3492-01 LARGE INTESTINE c.1722G>T p.E574D COSMIC PASSENGER/OTHER Benign 25 TCGA-AA-3492-01 LARGE INTESTINE c.2594T>C p.L865P COSMIC CANCER Probably Damaging 26 TCGA-AA-3811-01 LARGE INTESTINE c.2079G>A p.K693K COSMIC NP NP 27 TCGA-AA-A01R-01 LARGE INTESTINE c.3127G>A p.A1043T COSMIC CANCER Probably Damaging 28 TCGA-AD-6964-01 LARGE INTESTINE c.924G>A p.S308S COSMIC NP NP 29 TCGA-AG-3726-01 LARGE INTESTINE c.1140C>A p.V380V COSMIC NP NP 30 TCGA-AG-A002-01 LARGE INTESTINE c.3127G>A p.A1043T COSMIC CANCER Probably Damaging 31 TCGA-AP-A056-01 ENDOMETRIUM c.3028G>A p.A1010T COSMIC PASSENGER/OTHER Possibly Damaging 32 TCGA-AP-A059-01 ENDOMETRIUM c.178C>T p.R60W COSMIC PASSENGER/OTHER Probably Damaging 33 TCGA-AP-A059-01 ENDOMETRIUM c.2142C>A p.I714I COSMIC NP NP 34 TCGA-AP-A059-01 ENDOMETRIUM c.2501C>T p.A834V COSMIC CANCER Probably Damaging 35 TCGA-AP-A059-01 ENDOMETRIUM c.588G>T p.K196N COSMIC PASSENGER/OTHER Probably Damaging 36 TCGA-AX-A0J1-01 ENDOMETRIUM c.2639C>T p.A880V COSMIC PASSENGER/OTHER Possibly Damaging 37 TCGA-AY-6197-01 LARGE INTESTINE c.370C>T p.L124L COSMIC NP NP 38 TCGA-AZ-5403-01 LARGE INTESTINE c.1748A>G p.Q583R COSMIC PASSENGER/OTHER Benign 39 TCGA-AZ-6598-01 LARGE INTESTINE c.1871C>A p.A624D COSMIC PASSENGER/OTHER Benign 40 TCGA-AZ-6601-01 LARGE INTESTINE c.1749G>T p.Q583H COSMIC PASSENGER/OTHER Benign 41 TCGA-AZ-6601-01 LARGE INTESTINE c.2793delC p.I932fs*14 COSMIC NP NP 42 TCGA-B5-A11E-01 ENDOMETRIUM c.2330C>T p.A777V COSMIC PASSENGER/OTHER Benign 43 TCGA-BG-A0MQ-01 ENDOMETRIUM c.420G>A p.E140E COSMIC NP NP 44 TCGA-BH-A0W7-01 BREAST c.1700G>A p.G567E COSMIC PASSENGER/OTHER Benign 45 TCGA-BS-A0UA-01 ENDOMETRIUM c.2796T>C p.I932I COSMIC NP NP 46 TCGA-BS-A0UM-01 ENDOMETRIUM c.604G>A p.G202S COSMIC PASSENGER/OTHER Possibly Damaging 47 TCGA-BS-A0UV-01 ENDOMETRIUM c.1181C>T p.S394L COSMIC PASSENGER/OTHER Benign 48 TCGA-BS-A0UV-01 ENDOMETRIUM c.3154G>A p.E1052K COSMIC CANCER Benign 49 TCGA-CF-A3MG-01 URINARY TRACT c.1402C>T p.Q468* COSMIC NP NP 50 TCGA-CK-5916-01 LARGE INTESTINE c.1696_1697insG p.E566fs*15 COSMIC NP NP 51 TCGA-CM-5860-01 LARGE INTESTINE c.1748A>G p.Q583R COSMIC PASSENGER/OTHER Benign 52 TCGA-D1-A0ZZ-01 ENDOMETRIUM c.1444C>T p.R482W COSMIC PASSENGER/OTHER Probably Damaging 53 TCGA-D1-A167-01 ENDOMETRIUM c.927C>T p.S309S COSMIC NP NP 54 TCGA-D1-A16X-01 ENDOMETRIUM c.2129G>A p.R710Q COSMIC CANCER Probably Damaging 55 TCGA-D1-A17Q-01 ENDOMETRIUM c.1686C>A p.V562V COSMIC NP NP 56 TCGA-D5-6930-01 LARGE INTESTINE c.1748A>G p.Q583R COSMIC PASSENGER/OTHER Benign 57 TCGA-D8-A1XJ-01 BREAST c.1265C>T p.S422F COSMIC PASSENGER/OTHER Probably Damaging 58 TCGA-E6-A1LZ-01 ENDOMETRIUM c.1479G>A p.L493L COSMIC NP NP 59 TCGA-F4-6703-01 LARGE INTESTINE c.1838C>T p.A613V COSMIC PASSENGER/OTHER Benign 60 TCGA-F4-6856-01 LARGE INTESTINE c.2763C>T p.N921N COSMIC NP NP 61 TCGA-F4-6856-01 LARGE INTESTINE c.923C>T p.S308L COSMIC PASSENGER/OTHER Probably Damaging 62 TCGA-G4-6309-01 LARGE INTESTINE c.3132G>A p.V1044V COSMIC NP NP 63 TCGA-G4-6315-01 LARGE INTESTINE c.1748A>G p.Q583R COSMIC PASSENGER/OTHER Benign 64 YURTHE SKIN c.1789G>A p.E597K COSMIC PASSENGER/OTHER Benign
*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. Variants are not present in 1000 Genomes!!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 HDAC5 HDAC5 HDAC5 ENSP00000225983 Q9UQL6 QuickGO HGNC Ensembl Genome Browser TreeFam UniProt Q9UQL6 HDAC5 ENSP00000225983 HDAC5 Q9UQL6 Expression Atlas Protein Atlas OMIM IntAct PharmGKB HDAC5 ENSP00000225983 605315 Q9UQL6 PA29230
