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: CHD4 |
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Mutation Data (+)
# Cell Line/Tumor sample Tissue of Origin cDNA change Protein change Source FATHMM Prediction PolyPhen2 Prediction 1 31231321 STOMACH c.4698A>G p.I1566M COSMIC PASSENGER/OTHER Benign 2 Br27P CENTRAL NERVOUS SYSTEM c.1935G>A p.R645R COSMIC NP NP 3 Br27P CENTRAL NERVOUS SYSTEM c.4601G>A p.G1534E COSMIC PASSENGER/OTHER Benign 4 ESO-085 OESOPHAGUS c.5402G>A p.R1801Q COSMIC CANCER Probably Damaging 5 ESO-117 OESOPHAGUS c.3119A>G p.Y1040C COSMIC PASSENGER/OTHER Probably Damaging 6 ESO-175 OESOPHAGUS c.5339A>C p.K1780T COSMIC CANCER Probably Damaging 7 HCC30T LIVER c.687G>T p.A229A COSMIC NP NP 8 HCC33T LIVER c.2288T>G p.V763G COSMIC PASSENGER/OTHER Probably Damaging 9 HCC39T LIVER c.5084G>A p.R1695H COSMIC PASSENGER/OTHER Probably Damaging 10 HCC58T LIVER c.4375T>C p.Y1459H COSMIC CANCER Probably Damaging 11 HCC60T LIVER c.3709_3725del17 p.D1237fs*2 COSMIC NP NP 12 HCT-116 LARGE INTESTINE c.3484C>T p.R1162W COSMIC CANCER Probably Damaging 13 ICGC_MB40 CENTRAL NERVOUS SYSTEM c.340_358>16 p.K119delK COSMIC NP NP 14 KM12 LARGE INTESTINE c.3250G>A p.D1084N COSMIC CANCER Probably Damaging 15 MN-1041 MENINGES c.2867G>A p.R956Q COSMIC CANCER Probably Damaging 16 MOLT-4 HAEMATOPOIETIC AND LYMPHOID TISSUE c.2554T>C p.Y852H COSMIC CANCER Probably Damaging 17 RK062_C01 LIVER c.1702C>T p.Q568* COSMIC NP NP 18 RK177_C01 LIVER c.3696T>A p.T1232T COSMIC NP NP 19 TCGA-05-4390-01 LUNG c.2448C>G p.I816M COSMIC PASSENGER/OTHER Probably Damaging 20 TCGA-05-4396-01 LUNG c.4905C>A p.P1635P COSMIC NP NP 21 TCGA-05-4424-01 LUNG c.1096G>C p.E366Q COSMIC CANCER Probably Damaging 22 TCGA-05-5428-01 LUNG c.1625A>C p.Q542P COSMIC PASSENGER/OTHER Possibly Damaging 23 TCGA-09-1674-01 OVARY c.846T>C p.D282D COSMIC NP NP 24 TCGA-18-3414-01 LUNG c.3659A>G p.K1220R COSMIC PASSENGER/OTHER Benign 25 TCGA-18-3417-01 LUNG c.1821G>A p.E607E COSMIC NP NP 26 TCGA-34-5928-01 LUNG c.3775G>C p.D1259H COSMIC PASSENGER/OTHER Possibly Damaging 27 TCGA-38-4625-01 LUNG c.1804G>T p.D602Y COSMIC PASSENGER/OTHER Probably Damaging 28 TCGA-39-5019-01 LUNG c.3319G>C p.E1107Q COSMIC PASSENGER/OTHER Probably Damaging 29 TCGA-43-5668-01 LUNG c.2280G>C p.Q760H COSMIC PASSENGER/OTHER Probably Damaging 30 TCGA-44-2668-01 LUNG c.3559G>C p.V1187L COSMIC CANCER Benign 31 TCGA-44-4112-01 LUNG c.1314G>T p.G438G COSMIC NP NP 32 TCGA-44-8119-01 LUNG c.2335C>T p.L779L COSMIC NP NP 33 TCGA-55-6968-01 LUNG c.637A>G p.S213G COSMIC PASSENGER/OTHER Probably Damaging 34 TCGA-61-1741-01 OVARY c.2924G>A p.R975H COSMIC PASSENGER/OTHER Probably Damaging 35 TCGA-63-5131-01 LUNG c.2197G>T p.G733C COSMIC PASSENGER/OTHER Probably Damaging 36 TCGA-66-2777-01 LUNG c.4615A>G p.K1539E COSMIC PASSENGER/OTHER Benign 37 TCGA-75-5125-01 LUNG c.4804_4805TC>CT p.S1602L COSMIC PASSENGER/OTHER Benign 38 TCGA-78-7152-01 LUNG c.3482A>G p.H1161R COSMIC PASSENGER/OTHER Benign 39 TCGA-A2-A04W-01 BREAST c.4933G>T p.E1645* COSMIC NP NP 40 TCGA-A6-3809-01 LARGE INTESTINE c.1536G>A p.Q512Q COSMIC NP NP 41 TCGA-A6-5665-01 LARGE INTESTINE c.417G>T p.E139D COSMIC PASSENGER/OTHER Benign 42 TCGA-A6-6781-01 LARGE INTESTINE c.1039C>T p.R347* COSMIC NP NP 43 TCGA-A8-A07O-01 BREAST c.2574C>T p.D858D COSMIC NP NP 44 TCGA-A8-A07R-01 BREAST c.1863G>A p.W621* COSMIC NP NP 45 TCGA-AA-3713-01 LARGE INTESTINE c.699G>A p.A233A COSMIC NP NP 46 TCGA-AA-3815-01 LARGE INTESTINE c.5635C>G p.P1879A COSMIC PASSENGER/OTHER Probably Damaging 47 TCGA-AA-A02K-01 LARGE INTESTINE c.3334T>C p.F1112L COSMIC CANCER Probably Damaging 48 TCGA-AB-2878-03 HAEMATOPOIETIC AND LYMPHOID TISSUE c.3517C>T p.R1173W COSMIC CANCER Probably Damaging 49 TCGA-AB-2949-03 HAEMATOPOIETIC AND LYMPHOID TISSUE c.2924G>A p.R975H COSMIC PASSENGER/OTHER Probably Damaging 50 TCGA-AD-5900-01 LARGE INTESTINE c.4214C>T p.A1405V COSMIC PASSENGER/OTHER Possibly Damaging 51 TCGA-AH-6643-01 LARGE INTESTINE c.4602G>A p.G1534G COSMIC NP NP 52 TCGA-AO-A12E-01 BREAST c.2710C>A p.P904T COSMIC CANCER Probably Damaging 53 TCGA-AP-A051-01 ENDOMETRIUM c.3803C>T p.T1268I COSMIC PASSENGER/OTHER Benign 54 TCGA-AP-A056-01 ENDOMETRIUM c.4013G>T p.R1338I COSMIC CANCER Probably Damaging 55 TCGA-AP-A059-01 ENDOMETRIUM c.151C>A p.L51I COSMIC PASSENGER/OTHER Benign 56 TCGA-AP-A059-01 ENDOMETRIUM c.3672G>T p.E1224D COSMIC CANCER Benign 57 TCGA-AP-A059-01 ENDOMETRIUM c.4467C>A p.R1489R COSMIC NP NP 58 TCGA-AP-A059-01 ENDOMETRIUM c.4866G>T p.E1622D COSMIC PASSENGER/OTHER Benign 59 TCGA-AP-A059-01 ENDOMETRIUM c.783G>T p.K261N COSMIC PASSENGER/OTHER Probably Damaging 60 TCGA-AQ-A1H3-01 BREAST c.2630G>A p.R877Q COSMIC PASSENGER/OTHER Probably Damaging 61 TCGA-AX-A06L-01 ENDOMETRIUM c.2630G>A p.R877Q COSMIC PASSENGER/OTHER Probably Damaging 62 TCGA-AX-A0J0-01 ENDOMETRIUM c.423T>G p.D141E COSMIC PASSENGER/OTHER Benign 63 TCGA-AX-A0J1-01 ENDOMETRIUM c.5441C>A p.P1814H COSMIC PASSENGER/OTHER Probably Damaging 64 TCGA-AZ-4315-01 LARGE INTESTINE c.1429A>G p.N477D COSMIC PASSENGER/OTHER Probably Damaging 65 TCGA-AZ-6599-01 LARGE INTESTINE c.1933C>T p.R645W COSMIC PASSENGER/OTHER Probably Damaging 66 TCGA-AZ-6601-01 LARGE INTESTINE c.4409C>T p.P1470L COSMIC PASSENGER/OTHER Probably Damaging 67 TCGA-B0-5077-01 KIDNEY c.2911G>C p.E971Q COSMIC PASSENGER/OTHER Probably Damaging 68 TCGA-B0-5098-01 KIDNEY c.529A>G p.N177D COSMIC PASSENGER/OTHER Probably Damaging 69 TCGA-B0-5121-01 KIDNEY c.4703A>C p.E1568A COSMIC PASSENGER/OTHER Benign 70 TCGA-B5-A0JY-01 ENDOMETRIUM c.2655C>A p.F885L COSMIC PASSENGER/OTHER Probably Damaging 71 TCGA-B5-A11E-01 ENDOMETRIUM c.325G>A p.D109N COSMIC PASSENGER/OTHER Probably Damaging 72 TCGA-B5-A11E-01 ENDOMETRIUM c.5422T>C p.S1808P COSMIC PASSENGER/OTHER Possibly Damaging 73 TCGA-B5-A11E-01 ENDOMETRIUM c.913C>T p.R305C COSMIC PASSENGER/OTHER Probably Damaging 74 TCGA-B5-A11N-01 ENDOMETRIUM c.3644T>G p.L1215R COSMIC PASSENGER/OTHER Possibly Damaging 75 TCGA-B6-A0RS-01 BREAST c.888C>G p.I296M COSMIC PASSENGER/OTHER Probably Damaging 76 TCGA-B8-4153-01 KIDNEY c.512A>C p.D171A COSMIC CANCER Possibly Damaging 77 TCGA-BG-A2AE-01 ENDOMETRIUM c.3570_3572delGAA p.K1191delK COSMIC NP NP 78 TCGA-BH-A0DD-01 BREAST c.484G>A p.D162N COSMIC CANCER Benign 79 TCGA-BH-A0E1-01 BREAST c.2629C>T p.R877W COSMIC PASSENGER/OTHER Probably Damaging 80 TCGA-BH-A0HY-01 BREAST c.3390C>T p.G1130G COSMIC NP NP 81 TCGA-BK-A13C-01 ENDOMETRIUM c.3475A>G p.R1159G COSMIC CANCER Possibly Damaging 82 TCGA-BP-4976-01 KIDNEY c.4669G>A p.V1557I COSMIC PASSENGER/OTHER Benign 83 TCGA-BP-4989-01 KIDNEY c.4952A>C p.D1651A COSMIC PASSENGER/OTHER Benign 84 TCGA-BP-5001-01 KIDNEY c.2873T>A p.L958H COSMIC PASSENGER/OTHER Probably Damaging 85 TCGA-BS-A0TC-01 ENDOMETRIUM c.2618A>G p.D873G COSMIC CANCER Probably Damaging 86 TCGA-BS-A0TC-01 ENDOMETRIUM c.830G>A p.S277N COSMIC PASSENGER/OTHER Benign 87 TCGA-BS-A0UA-01 ENDOMETRIUM c.915T>C p.R305R COSMIC NP NP 88 TCGA-BS-A0UV-01 ENDOMETRIUM c.2140C>T p.R714* COSMIC NP NP 89 TCGA-BS-A0UV-01 ENDOMETRIUM c.2212C>T p.R738C COSMIC PASSENGER/OTHER Probably Damaging 90 TCGA-BS-A0UV-01 ENDOMETRIUM c.2953T>C p.Y985H COSMIC PASSENGER/OTHER Probably Damaging 91 TCGA-C8-A27B-01 BREAST c.269C>A p.P90Q COSMIC PASSENGER/OTHER Benign 92 TCGA-C8-A27B-01 BREAST c.703G>C p.A235P COSMIC PASSENGER/OTHER Benign 93 TCGA-CA-6717-01 LARGE INTESTINE c.1715G>A p.R572Q COSMIC PASSENGER/OTHER Probably Damaging 94 TCGA-CJ-4923-01 KIDNEY c.2108C>T p.T703M COSMIC PASSENGER/OTHER Probably Damaging 95 TCGA-CK-5912-01 LARGE INTESTINE c.4216C>G p.R1406G COSMIC PASSENGER/OTHER Probably Damaging 96 TCGA-CK-6746-01 LARGE INTESTINE c.4706delA p.N1569fs*9 COSMIC NP NP 97 TCGA-CK-6746-01 LARGE INTESTINE c.5645C>T p.A1882V COSMIC CANCER Probably Damaging 98 TCGA-CM-5861-01 LARGE INTESTINE c.3822T>C p.N1274N COSMIC NP NP 99 TCGA-CM-6170-01 LARGE INTESTINE c.1971G>A p.E657E COSMIC NP NP 100 TCGA-D1-A103-01 ENDOMETRIUM c.4013G>T p.R1338I COSMIC CANCER Probably Damaging 101 TCGA-D1-A17Q-01 ENDOMETRIUM c.1040G>A p.R347Q COSMIC CANCER Benign 102 TCGA-D8-A1JN-01 BREAST c.2965A>T p.I989F COSMIC PASSENGER/OTHER Probably Damaging 103 TCGA-DK-A2I1-01 URINARY TRACT c.3895G>C p.E1299Q COSMIC CANCER Benign 104 TCGA-DK-A2I1-01 URINARY TRACT c.4111G>C p.E1371Q COSMIC PASSENGER/OTHER Probably Damaging 105 TCGA-DM-A1D9-01 LARGE INTESTINE c.4600G>T p.G1534W COSMIC PASSENGER/OTHER Possibly Damaging 106 TCGA-E2-A1B6-01 BREAST c.4812T>C p.D1604D COSMIC NP NP 107 TCGA-E9-A1NG-01 BREAST c.3484C>T p.R1162W COSMIC CANCER Probably Damaging 108 TCGA-E9-A1NI-01 BREAST c.355_357delAAG p.K119delK COSMIC NP NP 109 TCGA-F4-6570-01 LARGE INTESTINE c.4393C>T p.R1465W COSMIC PASSENGER/OTHER Probably Damaging 110 TCGA-F4-6856-01 LARGE INTESTINE c.4543C>T p.R1515C COSMIC PASSENGER/OTHER Probably Damaging 111 TCGA-FD-A3NA-01 URINARY TRACT c.1902G>C p.K634N COSMIC PASSENGER/OTHER Probably Damaging 112 TCGA-FD-A3NA-01 URINARY TRACT c.1923G>C p.L641F COSMIC PASSENGER/OTHER Probably Damaging 113 TCGA-G2-A2EC-01 URINARY TRACT c.4405G>C p.E1469Q COSMIC CANCER Probably Damaging 114 TCGA-G2-A2EJ-01 URINARY TRACT c.3997C>G p.L1333V COSMIC CANCER Probably Damaging 115 TCGA-G2-A2EJ-01 URINARY TRACT c.4621C>G p.P1541A COSMIC PASSENGER/OTHER Possibly Damaging 116 TCGA-G4-6309-01 LARGE INTESTINE c.1412A>G p.Y471C COSMIC PASSENGER/OTHER Probably Damaging 117 TCGA-G4-6309-01 LARGE INTESTINE c.218delA p.K73fs*129 COSMIC NP NP 118 TCGA-G4-6588-01 LARGE INTESTINE c.2835delA p.K945fs*28 COSMIC NP NP 119 TCGA-G9-6356-01 PROSTATE c.3778C>T p.R1260C COSMIC PASSENGER/OTHER Probably Damaging 120 TCGA-GV-A3QH-01 URINARY TRACT c.1618G>A p.E540K COSMIC PASSENGER/OTHER Possibly Damaging 121 YUDEDE SKIN c.772C>T p.R258C COSMIC PASSENGER/OTHER Probably Damaging 122 YUFOLD SKIN c.4091C>T p.S1364F COSMIC PASSENGER/OTHER Probably Damaging 123 YUFOLD SKIN c.4262G>A p.R1421Q COSMIC CANCER Possibly Damaging 124 YUGOE SKIN c.517C>T p.R173* COSMIC NP NP 125 YUKLAB SKIN c.848C>T p.A283V COSMIC PASSENGER/OTHER Benign 126 YUPER SKIN c.4622C>T p.P1541L COSMIC PASSENGER/OTHER Probably Damaging 127 YUPROST SKIN c.2170G>T p.G724* COSMIC NP NP 128 ccRCC-41 KIDNEY c.1448T>A p.I483N COSMIC PASSENGER/OTHER Probably Damaging 129 pfg008T STOMACH c.5190T>C p.H1730H COSMIC NP NP 130 pfg008T STOMACH c.5217C>T p.A1739A COSMIC NP NP 131 pfg017T STOMACH c.3380G>A p.R1127Q 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 (+)
1. PFAM Domains:Domain ID Domain Name Start Site End Site E-value PF08073 CHDNT 163 217 1.3e-31 PF00628 PHD 372 416 4.6e-11 PF00628 PHD 451 495 9.2e-11 PB011224 Pfam-B_11224 462 495 7.2e-08 PF00385 Chromo 540 574 3.8e-05 PF00385 Chromo 624 670 1.5e-12 PF00176 SNF2_N 729 1025 4.5e-66 PB015666 Pfam-B_15666 1047 1159 2.5e-05 PB014180 Pfam-B_14180 1048 1082 0.0001 PB018422 Pfam-B_18422 1049 1075 0.00013 PF00271 Helicase_C 1085 1164 2.4e-17 PB008129 Pfam-B_8129 1093 1261 1.8e-25 PF06465 DUF1087 1290 1352 1.7e-26 PF06461 DUF1086 1378 1522 5.8e-69 PF08074 CHDCT2 1724 1896 3.2e-95 -
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 CHD4 CHD4 CHD4 ENSP00000349508 Q14839 QuickGO HGNC Ensembl Genome Browser TreeFam UniProt Q14839 CHD4 ENSP00000349508 CHD4 Q14839 Expression Atlas Protein Atlas OMIM IntAct PharmGKB CHD4 ENSP00000349508 603277 Q14839 PA26455
