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: HDAC3 |
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Mutation Data (+)
# Cell Line/Tumor sample Tissue of Origin cDNA change Protein change Source FATHMM Prediction PolyPhen2 Prediction 1 CW2 LARGE INTESTINE c.901C>T p.R301* CCLE NP NP 2 DMS53 LUNG c.362A>C p.K121T CCLE PASSENGER/OTHER Possibly Damaging 3 EBC1 LUNG c.1006G>T p.A336S CCLE NP NP 4 EN ENDOMETRIUM c.1075A>G p.N359D CCLE NP NP 5 HCC1428 BREAST c.748_757delATCCTGAGGG p.I250fs CCLE NP NP 6 HDLM2 HAEMATOPOIETIC AND LYMPHOID TISSUE c.68C>G p.P23R CCLE PASSENGER/OTHER Probably Damaging 7 HEC251 ENDOMETRIUM c.1075A>G p.N359D CCLE NP NP 8 HEC251 ENDOMETRIUM c.608T>C p.V203A CCLE NP NP 9 HEC59 ENDOMETRIUM c.1075A>G p.N359D CCLE NP NP 10 HEC6 ENDOMETRIUM c.1199C>A p.P400H CCLE PASSENGER/OTHER Benign 11 HRT18 LARGE INTESTINE c.571T>C p.S191P CCLE CANCER Probably Damaging 12 HT115 LARGE INTESTINE c.1261G>T p.D421Y CCLE PASSENGER/OTHER Probably Damaging 13 KYSE70 OESOPHAGUS c.838G>A p.V280I CCLE PASSENGER/OTHER Probably Damaging 14 LMSU STOMACH c.1075A>G p.N359D CCLE NP NP 15 LS411N LARGE INTESTINE c.1060_splice p.Y354_splice CCLE NP NP 16 NCIH2291 LUNG c.804_804delC p.S268fs CCLE NP NP 17 NCIH650 LUNG c.1150C>T p.L384F CCLE PASSENGER/OTHER Possibly Damaging 18 OVMANA OVARY c.328G>A p.A110T CCLE PASSENGER/OTHER Probably Damaging 19 PL21 HAEMATOPOIETIC AND LYMPHOID TISSUE c.1075A>G p.N359D CCLE NP NP 20 RKO LARGE INTESTINE c.746G>T p.R249L CCLE NP NP 21 SHP77 LUNG c.1170_1171TG>CA p.D391N CCLE PASSENGER/OTHER Possibly Damaging 22 SKLU1 LUNG c.1033C>T p.R345C CCLE PASSENGER/OTHER Probably Damaging 23 SKMEL24 SKIN c.610G>A p.E204K CCLE NP NP 24 SNU1040 LARGE INTESTINE c.1027A>G p.K343E CCLE NP NP 25 SNU175 LARGE INTESTINE c.571T>C p.S191P CCLE CANCER Probably Damaging 26 SNU46 UPPER AERODIGESTIVE TRACT c.1189G>T p.E397* CCLE NP NP 27 SNU668 STOMACH c.1010C>G p.A337G CCLE NP NP 28 TUHR10TKB KIDNEY c.7A>G p.K3E CCLE PASSENGER/OTHER Benign 29 UMUC3 URINARY TRACT c.704G>T p.R235L CCLE NP Probably Damaging 30 587226 LARGE INTESTINE c.71T>C p.M24T COSMIC PASSENGER/OTHER Probably Damaging 31 HN_62860 UPPER AERODIGESTIVE TRACT c.902G>T p.R301L COSMIC PASSENGER/OTHER Probably Damaging 32 LAU63 SKIN c.793C>T p.R265* COSMIC NP NP 33 LAU63 SKIN c.820C>T p.R274* COSMIC NP NP 34 LUAD-NYU315 LUNG c.334C>T p.L112L COSMIC NP NP 35 ME009T SKIN c.272G>A p.G91D COSMIC PASSENGER/OTHER Probably Damaging 36 PR-09-5702 PROSTATE c.277G>A p.D93N COSMIC PASSENGER/OTHER Possibly Damaging 37 S00936 LUNG c.313T>C p.S105P COSMIC PASSENGER/OTHER Probably Damaging 38 TCGA-24-1469-01 OVARY c.526G>C p.G176R COSMIC CANCER Probably Damaging 39 TCGA-33-4586-01 LUNG c.949G>T p.E317* COSMIC NP NP 40 TCGA-A5-A0GP-01 ENDOMETRIUM c.1041G>T p.E347D COSMIC PASSENGER/OTHER Benign 41 TCGA-A7-A0CE-01 BREAST c.1232A>G p.N411S COSMIC PASSENGER/OTHER Possibly Damaging 42 TCGA-AA-3521-01 LARGE INTESTINE c.316C>T p.R106C COSMIC PASSENGER/OTHER Probably Damaging 43 TCGA-AA-3947-01 LARGE INTESTINE c.1168A>G p.T390A COSMIC PASSENGER/OTHER Benign 44 TCGA-AB-2819-03 HAEMATOPOIETIC AND LYMPHOID TISSUE c.443A>G p.N148S COSMIC PASSENGER/OTHER Probably Damaging 45 TCGA-AP-A056-01 ENDOMETRIUM c.328G>A p.A110T COSMIC PASSENGER/OTHER Probably Damaging 46 TCGA-AP-A059-01 ENDOMETRIUM c.915C>G p.R305R COSMIC NP NP 47 TCGA-AP-A0LM-01 ENDOMETRIUM c.132G>T p.K44N COSMIC PASSENGER/OTHER Probably Damaging 48 TCGA-AP-A0LM-01 ENDOMETRIUM c.155A>G p.Q52R COSMIC PASSENGER/OTHER Benign 49 TCGA-AP-A0LM-01 ENDOMETRIUM c.988G>A p.E330K COSMIC PASSENGER/OTHER Probably Damaging 50 TCGA-AX-A0J1-01 ENDOMETRIUM c.510C>T p.D170D COSMIC NP NP 51 TCGA-AX-A0J1-01 ENDOMETRIUM c.750G>A p.T250T COSMIC NP NP 52 TCGA-B5-A11E-01 ENDOMETRIUM c.268G>A p.V90I COSMIC PASSENGER/OTHER Benign 53 TCGA-B5-A11E-01 ENDOMETRIUM c.328G>A p.A110T COSMIC PASSENGER/OTHER Probably Damaging 54 TCGA-B5-A11N-01 ENDOMETRIUM c.295G>A p.G99R COSMIC PASSENGER/OTHER Probably Damaging 55 TCGA-BS-A0UV-01 ENDOMETRIUM c.295G>A p.G99R COSMIC PASSENGER/OTHER Probably Damaging 56 TCGA-D1-A17D-01 ENDOMETRIUM c.643C>T p.R215C COSMIC PASSENGER/OTHER Probably Damaging 57 TCGA-D1-A17Q-01 ENDOMETRIUM c.221G>A p.S74N COSMIC PASSENGER/OTHER Benign 58 TCGA-D5-6927-01 LARGE INTESTINE c.838G>A p.V280I COSMIC PASSENGER/OTHER Probably Damaging 59 TCGA-E2-A155-01 BREAST c.1012C>T p.L338F COSMIC PASSENGER/OTHER Probably Damaging 60 TCGA-FD-A3B3-01 URINARY TRACT c.567G>A p.T189T COSMIC NP NP 61 YUGOE SKIN c.793C>T p.R265* COSMIC NP NP 62 YULAN SKIN c.314C>T p.S105L COSMIC PASSENGER/OTHER Possibly Damaging 63 pfg001T STOMACH c.273C>T p.G91G 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 (+)
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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. Sequence alignment with CCLE mutants:
Click on button to get Sequence alignment with Coverage, Consensus and Quality 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 HDAC3 HDAC3 HDAC3 ENSP00000302967 O15379 QuickGO HGNC Ensembl Genome Browser TreeFam UniProt O15379 HDAC3 ENSP00000302967 HDAC3 O15379 Expression Atlas Protein Atlas OMIM IntAct PharmGKB HDAC3 ENSP00000302967 605166 O15379 PA29228
