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: HDAC1 |
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Mutation Data (+)
# Cell Line/Tumor sample Tissue of Origin cDNA change Protein change Source FATHMM Prediction PolyPhen2 Prediction 1 BICR18 UPPER AERODIGESTIVE TRACT c.81C>G p.G27G CCLE NP NP 2 BICR18 UPPER AERODIGESTIVE TRACT c.87A>C p.P29P CCLE NP NP 3 CL34 LARGE INTESTINE c.1323G>T p.K441N CCLE PASSENGER/OTHER Possibly Damaging 4 CMLT1 HAEMATOPOIETIC AND LYMPHOID TISSUE c.907T>C p.Y303H CCLE PASSENGER/OTHER Probably Damaging 5 DND41 HAEMATOPOIETIC AND LYMPHOID TISSUE c.495_splice p.K165_splice CCLE NP NP 6 GP2D LARGE INTESTINE c.1397_1399delAGG p.E468del CCLE NP NP 7 GP2D LARGE INTESTINE c.199T>C p.Y67H CCLE PASSENGER/OTHER Probably Damaging 8 HEC151 ENDOMETRIUM c.1397_1399delAGG p.E468del CCLE NP NP 9 HEC6 ENDOMETRIUM c.235A>G p.I79V CCLE PASSENGER/OTHER Probably Damaging 10 HT HAEMATOPOIETIC AND LYMPHOID TISSUE c.629A>G p.D210G CCLE PASSENGER/OTHER Probably Damaging 11 ISHIKAWAHERAKLIO02ER ENDOMETRIUM c.1360_1362delGAG p.E455del CCLE NP NP 12 JHH5 LIVER c.607G>A p.E203K CCLE PASSENGER/OTHER Possibly Damaging 13 KM12 LARGE INTESTINE c.1381G>A p.E461K CCLE PASSENGER/OTHER Benign 14 LNCAPCLONEFGC PROSTATE c.1360_1362delGAG p.E455del CCLE NP NP 15 MOLT16 HAEMATOPOIETIC AND LYMPHOID TISSUE c.1292G>A p.R431H CCLE PASSENGER/OTHER Probably Damaging 16 SKMEL28 SKIN c.1426A>C p.K476Q CCLE PASSENGER/OTHER Possibly Damaging 17 SNU1040 LARGE INTESTINE c.748G>A p.E250K CCLE PASSENGER/OTHER Possibly Damaging 18 SNU175 LARGE INTESTINE c.1264G>A p.D422N CCLE PASSENGER/OTHER Probably Damaging 19 SNU81 LARGE INTESTINE c.1381G>A p.E461K CCLE PASSENGER/OTHER Benign 20 SW48 LARGE INTESTINE c.232T>C p.S78P CCLE PASSENGER/OTHER Probably Damaging 21 SW48 LARGE INTESTINE c.844G>A p.A282T CCLE PASSENGER/OTHER Possibly Damaging 22 TEN ENDOMETRIUM c.356_splice p.A119_splice CCLE NP NP 23 107094 BREAST c.1094G>A p.R365Q COSMIC PASSENGER/OTHER Probably Damaging 24 112140 LUNG c.1291C>T p.R431C COSMIC PASSENGER/OTHER Probably Damaging 25 CRC-6 LARGE INTESTINE c.1292G>A p.R431H COSMIC PASSENGER/OTHER Probably Damaging 26 H322T LUNG c.229C>T p.R77C COSMIC PASSENGER/OTHER Probably Damaging 27 HCC128T LIVER c.183T>A p.A61A COSMIC NP NP 28 ME009T SKIN c.1363G>A p.E455K COSMIC PASSENGER/OTHER Possibly Damaging 29 NCI-H322M LUNG c.229C>T p.R77C COSMIC PASSENGER/OTHER Probably Damaging 30 PD4076a BREAST c.1192G>A p.E398K COSMIC PASSENGER/OTHER Benign 31 PD4601a NS c.468C>T p.I156I COSMIC NP NP 32 SA218 BREAST c.418C>T p.H140Y COSMIC CANCER Probably Damaging 33 TCGA-23-1122-01 OVARY c.74G>C p.G25A COSMIC PASSENGER/OTHER Probably Damaging 34 TCGA-60-2721-01 LUNG c.1188G>C p.E396D COSMIC PASSENGER/OTHER Benign 35 TCGA-70-6722-01 LUNG c.917G>T p.R306L COSMIC PASSENGER/OTHER Possibly Damaging 36 TCGA-73-4666-01 LUNG c.895G>T p.G299* COSMIC NP NP 37 TCGA-A3-3346-01 KIDNEY c.921C>T p.N307N COSMIC NP NP 38 TCGA-A3-3373-01 KIDNEY c.1162G>A p.A388T COSMIC PASSENGER/OTHER Benign 39 TCGA-A6-5661-01 LARGE INTESTINE c.74G>A p.G25E COSMIC PASSENGER/OTHER Probably Damaging 40 TCGA-A6-6780-01 LARGE INTESTINE c.1397_1399delAGG p.E468delE COSMIC NP NP 41 TCGA-AA-A01Q-01 LARGE INTESTINE c.1192G>A p.E398K COSMIC PASSENGER/OTHER Benign 42 TCGA-AA-A02K-01 LARGE INTESTINE c.1397_1399delAGG p.E468delE COSMIC NP NP 43 TCGA-AN-A0FJ-01 BREAST c.1135G>T p.V379F COSMIC PASSENGER/OTHER Probably Damaging 44 TCGA-AP-A051-01 ENDOMETRIUM c.767C>T p.A256V COSMIC PASSENGER/OTHER Possibly Damaging 45 TCGA-AP-A059-01 ENDOMETRIUM c.932G>A p.C311Y COSMIC PASSENGER/OTHER Probably Damaging 46 TCGA-AX-A0J0-01 ENDOMETRIUM c.1191C>T p.D397D COSMIC NP NP 47 TCGA-B0-5707-01 KIDNEY c.258G>C p.E86D COSMIC PASSENGER/OTHER Benign 48 TCGA-BH-A208-01 BREAST c.504G>A p.Q168Q COSMIC NP NP 49 TCGA-BK-A0C9-01 ENDOMETRIUM c.206G>A p.S69N COSMIC PASSENGER/OTHER Benign 50 TCGA-BS-A0U8-01 ENDOMETRIUM c.1360_1362delGAG p.E455delE COSMIC NP NP 51 TCGA-BS-A0U8-01 ENDOMETRIUM c.1397_1399delAGG p.E468delE COSMIC NP NP 52 TCGA-C8-A12X-01 BREAST c.1422G>A p.G474G COSMIC NP NP 53 TCGA-CM-4746-01 LARGE INTESTINE c.570G>A p.T190T COSMIC NP NP 54 TCGA-D1-A103-01 ENDOMETRIUM c.240T>C p.R80R COSMIC NP NP 55 TCGA-D1-A17Q-01 ENDOMETRIUM c.101G>A p.R34Q COSMIC PASSENGER/OTHER Possibly Damaging 56 TCGA-D5-6535-01 LARGE INTESTINE c.74G>A p.G25E COSMIC PASSENGER/OTHER Probably Damaging 57 TCGA-D8-A1JM-01 BREAST c.966G>T p.T322T COSMIC NP NP 58 TCGA-E9-A22G-01 BREAST c.1335_1336delAG p.E446fs*2 COSMIC NP NP 59 TCGA-G2-A2EK-01 URINARY TRACT c.1090C>T p.Q364* COSMIC NP NP 60 cSCCP6 SKIN c.1108C>T p.L370F 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 (+)
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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 HDAC1 HDAC1 HDAC1 ENSP00000362649 Q13547 QuickGO HGNC Ensembl Genome Browser TreeFam UniProt Q13547 HDAC1 ENSP00000362649 HDAC1 Q13547 Expression Atlas Protein Atlas OMIM IntAct PharmGKB HDAC1 ENSP00000362649 601241 Q13547 PA29226
