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: HDAC4 |
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Mutation Data (+)
# Cell Line/Tumor sample Tissue of Origin cDNA change Protein change Source FATHMM Prediction PolyPhen2 Prediction 1 22RV1 PROSTATE c.1243C>T p.Q415* CCLE NP NP 2 22RV1 PROSTATE c.2703_2703delC p.P901fs CCLE NP NP 3 2313287 STOMACH c.2147C>T p.S716L CCLE CANCER Probably Damaging 4 AMO1 HAEMATOPOIETIC AND LYMPHOID TISSUE c.412C>T p.R138C CCLE PASSENGER/OTHER Probably Damaging 5 AN3CA ENDOMETRIUM c.3017A>G p.Q1006R CCLE PASSENGER/OTHER Benign 6 CADOES1 BONE c.3031G>A p.A1011T CCLE PASSENGER/OTHER Benign 7 CAL12T LUNG c.1555G>T p.E519* CCLE NP NP 8 CAL51 BREAST c.2272A>G p.S758G CCLE PASSENGER/OTHER Probably Damaging 9 COLO818 SKIN c.2800G>A p.D934N CCLE CANCER Probably Damaging 10 CW2 LARGE INTESTINE c.2150A>G p.E717G CCLE PASSENGER/OTHER Probably Damaging 11 EFM19 BREAST c.1534A>C p.S512R CCLE PASSENGER/OTHER Benign 12 EJM HAEMATOPOIETIC AND LYMPHOID TISSUE c.592G>A p.D198N CCLE PASSENGER/OTHER Probably Damaging 13 GAMG CENTRAL NERVOUS SYSTEM c.1199C>T p.S400L CCLE PASSENGER/OTHER Benign 14 GP2D LARGE INTESTINE c.2703_2703delC p.P901fs CCLE NP NP 15 HCC1143 BREAST c.3073_splice p.S1025_splice CCLE NP NP 16 HCT15 LARGE INTESTINE c.599G>A p.R200H CCLE PASSENGER/OTHER Probably Damaging 17 HEC108 ENDOMETRIUM c.2288A>G p.N763S CCLE PASSENGER/OTHER Probably Damaging 18 HEC108 ENDOMETRIUM c.2703_2703delC p.P901fs CCLE NP NP 19 HEC265 ENDOMETRIUM c.3031G>A p.A1011T CCLE PASSENGER/OTHER Benign 20 HEC59 ENDOMETRIUM c.1342C>T p.R448W CCLE PASSENGER/OTHER Probably Damaging 21 HEC59 ENDOMETRIUM c.2703_2703delC p.P901fs CCLE NP NP 22 HUG1N STOMACH c.1628G>T p.R543L CCLE PASSENGER/OTHER Possibly Damaging 23 IM95 STOMACH c.2177A>G p.N726S CCLE CANCER Benign 24 KELLY AUTONOMIC GANGLIA c.2950G>A p.A984T CCLE CANCER Probably Damaging 25 KM12 LARGE INTESTINE c.1118C>T p.A373V CCLE PASSENGER/OTHER Benign 26 KM12 LARGE INTESTINE c.2703_2703delC p.P901fs CCLE NP NP 27 KM12 LARGE INTESTINE c.500C>T p.A167V CCLE PASSENGER/OTHER Probably Damaging 28 LNCAPCLONEFGC PROSTATE c.2703_2703delC p.P901fs CCLE NP NP 29 LOVO LARGE INTESTINE c.2116G>A p.A706T CCLE CANCER Probably Damaging 30 LS513 LARGE INTESTINE c.373C>G p.Q125E CCLE PASSENGER/OTHER Benign 31 MEWO SKIN c.2180_2181CC>TT p.P727L CCLE CANCER Probably Damaging 32 MEWO SKIN c.2701C>T p.P901S CCLE CANCER Probably Damaging 33 MOLT13 HAEMATOPOIETIC AND LYMPHOID TISSUE c.395G>A p.R132Q CCLE PASSENGER/OTHER Possibly Damaging 34 NCIH1184 LUNG c.2689G>T p.G897C CCLE PASSENGER/OTHER Probably Damaging 35 NCIH1373 LUNG c.3037G>T p.A1013S CCLE PASSENGER/OTHER Probably Damaging 36 NCIH1915 LUNG c.2209A>C p.K737Q CCLE CANCER Possibly Damaging 37 NCIH2066 LUNG c.2664C>G p.F888L CCLE CANCER Probably Damaging 38 NCIH2286 LUNG c.659G>T p.G220V CCLE PASSENGER/OTHER Benign 39 NCIH650 LUNG c.2297A>T p.H766L CCLE CANCER Probably Damaging 40 RPMI7951 SKIN c.524T>G p.L175* CCLE NP NP 41 SNU175 LARGE INTESTINE c.2111G>A p.R704H CCLE PASSENGER/OTHER Probably Damaging 42 SNU324 PANCREAS c.2147C>T p.S716L CCLE CANCER Probably Damaging 43 SNU520 STOMACH c.2703_2703delC p.P901fs CCLE NP NP 44 SUDHL1 HAEMATOPOIETIC AND LYMPHOID TISSUE c.3064G>A p.E1022K CCLE PASSENGER/OTHER Benign 45 SW1783 CENTRAL NERVOUS SYSTEM c.602A>G p.Y201C CCLE PASSENGER/OTHER Probably Damaging 46 UBLC1 URINARY TRACT c.1612G>A p.E538K CCLE PASSENGER/OTHER Possibly Damaging 47 UMUC3 URINARY TRACT c.1544C>T p.A515V CCLE PASSENGER/OTHER Benign 48 585208 LUNG c.2635G>A p.E879K COSMIC CANCER Probably Damaging 49 585208 LUNG c.420G>T p.E140D COSMIC PASSENGER/OTHER Benign 50 585272 LUNG c.1495C>G p.Q499E COSMIC PASSENGER/OTHER Benign 51 587220 LARGE INTESTINE c.1867G>T p.G623C COSMIC PASSENGER/OTHER Probably Damaging 52 587238 LARGE INTESTINE c.703G>A p.A235T COSMIC PASSENGER/OTHER Benign 53 587278 LARGE INTESTINE c.1100C>T p.T367M COSMIC PASSENGER/OTHER Benign 54 587316 LARGE INTESTINE c.1654G>A p.A552T COSMIC PASSENGER/OTHER Benign 55 587342 LARGE INTESTINE c.1733C>T p.P578L COSMIC PASSENGER/OTHER Benign 56 587342 LARGE INTESTINE c.2191C>T p.Q731* COSMIC NP NP 57 587342 LARGE INTESTINE c.776A>G p.K259R COSMIC PASSENGER/OTHER Probably Damaging 58 587350 LARGE INTESTINE c.2703delC p.M902fs*55 COSMIC NP NP 59 B9 URINARY TRACT c.591C>T p.S197S COSMIC NP NP 60 BB27T BREAST c.2180C>G p.P727R COSMIC CANCER Probably Damaging 61 BN37T LIVER c.1144C>A p.Q382K COSMIC PASSENGER/OTHER Possibly Damaging 62 ESO-1096 OESOPHAGUS c.3038C>T p.A1013V COSMIC PASSENGER/OTHER Probably Damaging 63 ESO-116 OESOPHAGUS c.204G>A p.E68E COSMIC NP NP 64 ESO-1427 OESOPHAGUS c.2229C>T p.A743A COSMIC NP NP 65 ESO-143 OESOPHAGUS c.2083C>T p.R695W COSMIC CANCER Probably Damaging 66 HCC107T LIVER c.942C>T p.N314N COSMIC NP NP 67 HCC64T LIVER c.637C>T p.Q213* COSMIC NP NP 68 HN_62672 UPPER AERODIGESTIVE TRACT c.414C>T p.R138R COSMIC NP NP 69 HN_62741 UPPER AERODIGESTIVE TRACT c.2660G>T p.G887V COSMIC CANCER Probably Damaging 70 HX17T LIVER c.1751G>T p.S584I COSMIC PASSENGER/OTHER Benign 71 IPMN41 PANCREAS c.2801A>G p.D934G COSMIC CANCER Probably Damaging 72 KM12 LARGE INTESTINE c.500C>T p.A167V COSMIC PASSENGER/OTHER Probably Damaging 73 LUAD-B01970 LUNG c.876C>G p.C292W COSMIC PASSENGER/OTHER Probably Damaging 74 LUAD-E00934 LUNG c.2784G>T p.L928L COSMIC NP NP 75 LUAD-RT-S01703 LUNG c.481G>T p.G161C COSMIC PASSENGER/OTHER Benign 76 LUAD-RT-S01813 LUNG c.809G>T p.R270L COSMIC PASSENGER/OTHER Probably Damaging 77 LUAD-U6SJ7 LUNG c.2263G>T p.G755W COSMIC CANCER Probably Damaging 78 MZ7-mel SKIN c.346C>T p.Q116* COSMIC NP NP 79 MZ7-mel SKIN c.973G>A p.A325T COSMIC PASSENGER/OTHER Benign 80 NB-1110 AUTONOMIC GANGLIA c.2750C>T p.P917L COSMIC PASSENGER/OTHER Probably Damaging 81 PCSI_0101_Pa_P NS c.2110C>T p.R704C COSMIC PASSENGER/OTHER Probably Damaging 82 RK019_C01 LIVER c.541A>G p.N181D COSMIC PASSENGER/OTHER Probably Damaging 83 RK035_C01 LIVER c.1603C>A p.L535M COSMIC PASSENGER/OTHER Possibly Damaging 84 S01563 LUNG c.2577C>T p.Y859Y COSMIC NP NP 85 TCGA-05-4410-01 LUNG c.2751G>C p.P917P COSMIC NP NP 86 TCGA-05-4427-01 LUNG c.3238G>T p.E1080* COSMIC NP NP 87 TCGA-05-4432-01 LUNG c.3228G>T p.E1076D COSMIC PASSENGER/OTHER Probably Damaging 88 TCGA-10-0928-01 OVARY c.2106C>T p.R702R COSMIC NP NP 89 TCGA-10-0934-01 OVARY c.158_159TG>AT p.L53H COSMIC PASSENGER/OTHER Probably Damaging 90 TCGA-18-3409-01 LUNG c.721C>T p.L241F COSMIC PASSENGER/OTHER Probably Damaging 91 TCGA-22-4591-01 LUNG c.3165G>A p.T1055T COSMIC NP NP 92 TCGA-22-5473-01 LUNG c.2916C>T p.L972L COSMIC NP NP 93 TCGA-33-4566-01 LUNG c.2781G>T p.V927V COSMIC NP NP 94 TCGA-36-1575-01 OVARY c.578A>C p.H193P COSMIC PASSENGER/OTHER Possibly Damaging 95 TCGA-38-4626-01 LUNG c.3006A>T p.E1002D COSMIC PASSENGER/OTHER Benign 96 TCGA-38-7271-01 LUNG c.1548G>A p.R516R COSMIC NP NP 97 TCGA-44-2656-01 LUNG c.850C>T p.P284S COSMIC PASSENGER/OTHER Benign 98 TCGA-46-3769-01 LUNG c.2223G>A p.S741S COSMIC NP NP 99 TCGA-49-4488-01 LUNG c.2306G>T p.G769V COSMIC CANCER Benign 100 TCGA-50-5051-01 LUNG c.442C>G p.R148G COSMIC PASSENGER/OTHER Benign 101 TCGA-50-5933-01 LUNG c.553G>T p.A185S COSMIC PASSENGER/OTHER Probably Damaging 102 TCGA-55-8089-01 LUNG c.1671G>T p.Q557H COSMIC PASSENGER/OTHER Benign 103 TCGA-60-2726-01 LUNG c.319C>A p.Q107K COSMIC PASSENGER/OTHER Probably Damaging 104 TCGA-66-2785-01 LUNG c.2837A>G p.Y946C COSMIC PASSENGER/OTHER Probably Damaging 105 TCGA-66-2794-01 LUNG c.1237C>G p.L413V COSMIC PASSENGER/OTHER Probably Damaging 106 TCGA-70-6722-01 LUNG c.2042G>A p.R681K COSMIC CANCER Probably Damaging 107 TCGA-91-6828-01 LUNG c.2988G>T p.E996D COSMIC CANCER Benign 108 TCGA-99-8025-01 LUNG c.1641G>C p.Q547H COSMIC PASSENGER/OTHER Possibly Damaging 109 TCGA-A2-A25A-01 BREAST c.2238C>A p.F746L COSMIC PASSENGER/OTHER Benign 110 TCGA-A6-2676-01 LARGE INTESTINE c.2788T>A p.S930T COSMIC PASSENGER/OTHER Probably Damaging 111 TCGA-A6-6780-01 LARGE INTESTINE c.975G>T p.A325A COSMIC NP NP 112 TCGA-AA-3660-01 LARGE INTESTINE c.2106C>T p.R702R COSMIC NP NP 113 TCGA-AA-3812-01 LARGE INTESTINE c.516G>C p.K172N COSMIC PASSENGER/OTHER Probably Damaging 114 TCGA-AA-3815-01 LARGE INTESTINE c.1654G>A p.A552T COSMIC PASSENGER/OTHER Benign 115 TCGA-AA-A00J-01 LARGE INTESTINE c.2102_2103delTC p.I701fs*35 COSMIC NP NP 116 TCGA-AA-A00J-01 LARGE INTESTINE c.818A>G p.D273G COSMIC PASSENGER/OTHER Probably Damaging 117 TCGA-AA-A00U-01 LARGE INTESTINE c.705C>T p.A235A COSMIC NP NP 118 TCGA-AA-A022-01 LARGE INTESTINE c.590G>A p.S197N COSMIC PASSENGER/OTHER Benign 119 TCGA-AD-5900-01 LARGE INTESTINE c.2180C>A p.P727H COSMIC CANCER Probably Damaging 120 TCGA-AD-6889-01 LARGE INTESTINE c.155G>A p.R52H COSMIC PASSENGER/OTHER Probably Damaging 121 TCGA-AD-6964-01 LARGE INTESTINE c.883G>A p.A295T COSMIC PASSENGER/OTHER Probably Damaging 122 TCGA-AD-6964-01 LARGE INTESTINE c.992A>G p.H331R COSMIC PASSENGER/OTHER Benign 123 TCGA-AG-A002-01 LARGE INTESTINE c.882C>T p.S294S COSMIC NP NP 124 TCGA-AN-A0FS-01 BREAST c.2306G>A p.G769E COSMIC CANCER Benign 125 TCGA-AP-A051-01 ENDOMETRIUM c.847C>T p.R283C COSMIC CANCER Probably Damaging 126 TCGA-AP-A056-01 ENDOMETRIUM c.554C>T p.A185V COSMIC PASSENGER/OTHER Probably Damaging 127 TCGA-AP-A059-01 ENDOMETRIUM c.2451C>T p.S817S COSMIC NP NP 128 TCGA-AP-A059-01 ENDOMETRIUM c.3043C>T p.R1015C COSMIC PASSENGER/OTHER Benign 129 TCGA-AP-A0LD-01 ENDOMETRIUM c.2874G>T p.K958N COSMIC PASSENGER/OTHER Possibly Damaging 130 TCGA-AP-A0LM-01 ENDOMETRIUM c.2303C>T p.A768V COSMIC CANCER Possibly Damaging 131 TCGA-AP-A0LM-01 ENDOMETRIUM c.3043C>T p.R1015C COSMIC PASSENGER/OTHER Benign 132 TCGA-AU-6004-01 LARGE INTESTINE c.2106C>T p.R702R COSMIC NP NP 133 TCGA-AX-A05Z-01 ENDOMETRIUM c.1043C>T p.S348L COSMIC PASSENGER/OTHER Possibly Damaging 134 TCGA-AX-A060-01 ENDOMETRIUM c.1065G>A p.T355T COSMIC NP NP 135 TCGA-AX-A0J0-01 ENDOMETRIUM c.928G>A p.V310I COSMIC PASSENGER/OTHER Benign 136 TCGA-AX-A0J1-01 ENDOMETRIUM c.1512G>A p.M504I COSMIC PASSENGER/OTHER Benign 137 TCGA-AX-A0J1-01 ENDOMETRIUM c.657C>T p.S219S COSMIC NP NP 138 TCGA-B5-A11E-01 ENDOMETRIUM c.2450C>A p.S817Y COSMIC CANCER Probably Damaging 139 TCGA-B5-A11E-01 ENDOMETRIUM c.765G>A p.R255R COSMIC NP NP 140 TCGA-B5-A11E-01 ENDOMETRIUM c.851C>T p.P284L COSMIC PASSENGER/OTHER Probably Damaging 141 TCGA-BS-A0TA-01 ENDOMETRIUM c.2321C>T p.A774V COSMIC CANCER Probably Damaging 142 TCGA-BS-A0TJ-01 ENDOMETRIUM c.724A>G p.R242G COSMIC PASSENGER/OTHER Probably Damaging 143 TCGA-BS-A0UV-01 ENDOMETRIUM c.2613C>T p.F871F COSMIC NP NP 144 TCGA-BT-A0YX-01 URINARY TRACT c.936G>A p.A312A COSMIC NP NP 145 TCGA-BT-A20T-01 URINARY TRACT c.1759G>C p.E587Q COSMIC PASSENGER/OTHER Possibly Damaging 146 TCGA-CJ-6031-01 KIDNEY c.253C>G p.Q85E COSMIC PASSENGER/OTHER Probably Damaging 147 TCGA-CK-5913-01 LARGE INTESTINE c.1167delC p.G390fs*8 COSMIC NP NP 148 TCGA-CK-6746-01 LARGE INTESTINE c.802delC p.L268fs*13 COSMIC NP NP 149 TCGA-CM-5349-01 LARGE INTESTINE c.347A>G p.Q116R COSMIC PASSENGER/OTHER Possibly Damaging 150 TCGA-CM-5861-01 LARGE INTESTINE c.307C>T p.Q103* COSMIC NP NP 151 TCGA-CM-6162-01 LARGE INTESTINE c.312C>T p.H104H COSMIC NP NP 152 TCGA-D1-A103-01 ENDOMETRIUM c.1043C>T p.S348L COSMIC PASSENGER/OTHER Possibly Damaging 153 TCGA-D1-A103-01 ENDOMETRIUM c.2652C>T p.P884P COSMIC NP NP 154 TCGA-D1-A17H-01 ENDOMETRIUM c.503G>A p.S168N COSMIC PASSENGER/OTHER Probably Damaging 155 TCGA-D5-6540-01 LARGE INTESTINE c.1921G>A p.V641M COSMIC PASSENGER/OTHER Benign 156 TCGA-D5-6540-01 LARGE INTESTINE c.2703delC p.M902fs*55 COSMIC NP NP 157 TCGA-D5-6928-01 LARGE INTESTINE c.1868G>A p.G623D COSMIC PASSENGER/OTHER Possibly Damaging 158 TCGA-D5-6930-01 LARGE INTESTINE c.898C>T p.P300S COSMIC PASSENGER/OTHER Possibly Damaging 159 TCGA-DC-5337-01 LARGE INTESTINE c.2175G>A p.T725T COSMIC NP NP 160 TCGA-DK-A1A3-01 URINARY TRACT c.160G>A p.D54N COSMIC PASSENGER/OTHER Probably Damaging 161 TCGA-E9-A1NC-01 BREAST c.766C>T p.L256L COSMIC NP NP 162 TCGA-EI-6507-01 LARGE INTESTINE c.2106C>T p.R702R COSMIC NP NP 163 TCGA-G4-6315-01 LARGE INTESTINE c.2106C>T p.R702R COSMIC NP NP 164 W040 BILIARY TRACT c.1633C>T p.P545S COSMIC PASSENGER/OTHER Benign 165 YULAN SKIN c.851C>T p.P284L COSMIC PASSENGER/OTHER Probably Damaging 166 YULAXER SKIN c.2432G>T p.G811V COSMIC CANCER Probably Damaging 167 YUPEET SKIN c.2518G>A p.D840N COSMIC CANCER Probably Damaging 168 cSCCP6 SKIN c.1088C>T p.P363L COSMIC PASSENGER/OTHER Benign 169 ccRCC-60 KIDNEY c.2828T>C p.L943P COSMIC CANCER 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 HDAC4 HDAC4 HDAC4 ENSP00000264606 P56524 QuickGO HGNC Ensembl Genome Browser TreeFam UniProt P56524 HDAC4 ENSP00000264606 HDAC4 P56524 Expression Atlas Protein Atlas OMIM IntAct PharmGKB HDAC4 ENSP00000264606 605314 P56524 PA29229
