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: KDM2B |
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Mutation Data (+)
# Cell Line/Tumor sample Tissue of Origin cDNA change Protein change Source FATHMM Prediction PolyPhen2 Prediction 1 278 HAEMATOPOIETIC AND LYMPHOID TISSUE c.1313A>G p.H438R COSMIC NP NP 2 278-01-4TD HAEMATOPOIETIC AND LYMPHOID TISSUE c.1313A>G p.H438R COSMIC NP NP 3 51T SKIN c.401C>T p.T134I COSMIC NP NP 4 587228 LARGE INTESTINE c.1666G>A p.A556T COSMIC PASSENGER/OTHER Benign 5 587234 LARGE INTESTINE c.788G>A p.C263Y COSMIC NP NP 6 587268 LARGE INTESTINE c.1903C>T p.R635C COSMIC NP NP 7 587284 LARGE INTESTINE c.1114C>T p.R372C COSMIC NP NP 8 76629543 STOMACH c.1724G>A p.R575H COSMIC NP NP 9 ESO-859 OESOPHAGUS c.788G>A p.C263Y COSMIC NP NP 10 ESO-866 OESOPHAGUS c.2736C>A p.I912I COSMIC NP NP 11 HCC107T LIVER c.2362C>A p.P788T COSMIC NP NP 12 KM12 LARGE INTESTINE c.752G>A p.R251Q COSMIC NP NP 13 LC_S25 LUNG c.365C>G p.S122C COSMIC NP NP 14 LUAD-74TBW LUNG c.317G>A p.R106Q COSMIC NP NP 15 LUAD-VUMN6 LUNG c.1755G>C p.L585L COSMIC NP NP 16 LUAD_E00623 LUNG c.1704G>A p.E568E COSMIC NP NP 17 NCI-ADR-RES OVARY c.2305G>T p.D769Y COSMIC NP NP 18 OVCAR-5 OVARY c.1703_1705delAGA p.K571delK COSMIC NP NP 19 PA285 PANCREAS c.345G>A p.E115E COSMIC NP NP 20 PD6751a NS c.2400G>A p.W800* COSMIC NP NP 21 RK048_C01 LIVER c.967A>T p.M323L COSMIC NP Probably Damaging 22 TARGET-30-PARFWB AUTONOMIC GANGLIA c.1998A>G p.P666P COSMIC NP NP 23 TCGA-05-4424-01 LUNG c.2461T>A p.W821R COSMIC NP NP 24 TCGA-13-1497-01 OVARY c.2587G>T p.D863Y COSMIC NP NP 25 TCGA-18-3409-01 LUNG c.521C>T p.P174L COSMIC NP NP 26 TCGA-18-3419-01 LUNG c.2158G>C p.D720H COSMIC NP NP 27 TCGA-38-6178-01 LUNG c.1309G>A p.V437M COSMIC NP NP 28 TCGA-44-8119-01 LUNG c.39G>T p.V13V COSMIC NP NP 29 TCGA-55-6982-01 LUNG c.806G>A p.C269Y COSMIC NP NP 30 TCGA-64-1676-01 LUNG c.1150G>T p.G384C COSMIC NP NP 31 TCGA-66-2754-01 LUNG c.2746G>A p.D916N COSMIC NP NP 32 TCGA-97-7941-01 LUNG c.155A>T p.E52V COSMIC PASSENGER/OTHER Benign 33 TCGA-A2-A0YG-01 BREAST c.1576C>T p.R526W COSMIC NP NP 34 TCGA-A6-3809-01 LARGE INTESTINE c.980G>C p.C327S COSMIC NP NP 35 TCGA-A6-5665-01 LARGE INTESTINE c.1639G>A p.D547N COSMIC NP NP 36 TCGA-A7-A26E-01 BREAST c.2361G>T p.L787L COSMIC NP NP 37 TCGA-AA-3697-01 LARGE INTESTINE c.2609G>A p.R870Q COSMIC PASSENGER/OTHER Possibly Damaging 38 TCGA-AA-3715-01 LARGE INTESTINE c.285C>A p.A95A COSMIC NP NP 39 TCGA-AA-3864-01 LARGE INTESTINE c.204C>T p.G68G COSMIC NP NP 40 TCGA-AB-2803-03 HAEMATOPOIETIC AND LYMPHOID TISSUE c.1711_1713delAAG p.K571delK COSMIC NP NP 41 TCGA-AB-2806-03 HAEMATOPOIETIC AND LYMPHOID TISSUE c.1775A>G p.E592G COSMIC NP NP 42 TCGA-AG-A002-01 LARGE INTESTINE c.1376C>T p.S459L COSMIC NP NP 43 TCGA-AN-A0AR-01 BREAST c.2304C>A p.L768L COSMIC NP NP 44 TCGA-AP-A051-01 ENDOMETRIUM c.2391C>T p.G797G COSMIC NP NP 45 TCGA-AP-A051-01 ENDOMETRIUM c.2584C>A p.L862M COSMIC NP NP 46 TCGA-AP-A059-01 ENDOMETRIUM c.1810C>A p.L604M COSMIC NP NP 47 TCGA-AX-A0J1-01 ENDOMETRIUM c.1343C>T p.P448L COSMIC NP NP 48 TCGA-AX-A0J1-01 ENDOMETRIUM c.2131G>A p.A711T COSMIC NP NP 49 TCGA-AX-A0J1-01 ENDOMETRIUM c.329G>A p.R110K COSMIC NP NP 50 TCGA-AZ-6598-01 LARGE INTESTINE c.2170_2171delTG p.C724fs*14 COSMIC NP NP 51 TCGA-B5-A0JY-01 ENDOMETRIUM c.393G>T p.K131N COSMIC NP NP 52 TCGA-BS-A0UF-01 ENDOMETRIUM c.1557G>A p.A519A COSMIC NP NP 53 TCGA-BS-A0UV-01 ENDOMETRIUM c.2491C>T p.R831W COSMIC NP NP 54 TCGA-BS-A0UV-01 ENDOMETRIUM c.2857T>C p.F953L COSMIC NP NP 55 TCGA-BT-A0YX-01 URINARY TRACT c.1161C>G p.L387L COSMIC NP NP 56 TCGA-CF-A3MI-01 URINARY TRACT c.1027G>T p.E343* COSMIC NP NP 57 TCGA-CK-5913-01 LARGE INTESTINE c.2063G>T p.S688I COSMIC NP NP 58 TCGA-CK-5915-01 LARGE INTESTINE c.2777C>T p.S926F COSMIC NP NP 59 TCGA-CK-6746-01 LARGE INTESTINE c.814A>G p.M272V COSMIC NP NP 60 TCGA-DC-5869-01 LARGE INTESTINE c.1666G>A p.A556T COSMIC PASSENGER/OTHER Benign 61 TCGA-E2-A14S-01 BREAST c.1335C>T p.Y445Y COSMIC NP NP 62 TCGA-FD-A3N5-01 URINARY TRACT c.199G>T p.E67* COSMIC NP NP 63 WA33 PROSTATE c.450G>T p.E150D 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 (+)
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Structure Domains (+)
1. PFAM Domains:Domain ID Domain Name Start Site End Site E-value PF13621 Cupin_8 143 318 8.7e-07 PF02008 zf-CXXC 607 651 1.5e-14 PF00646 F-box 1051 1106 4.3e-12 PB009355 Pfam-B_9355 1117 1271 1.2e-20 PB006618 Pfam-B_6618 1123 1313 6.4e-82 PB001421 Pfam-B_1421 1224 1308 0.00047 2. Superfamily Domains:Domain ID Start Site End Site E-value 0047105 71 373 1.21e-56 0037738 1081 1313 6.28e-30 0050474 654 732 3.02e-08 -
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 KDM2B KDM2B KDM2B ENSP00000366269 Q8NHM5 QuickGO HGNC Ensembl Genome Browser TreeFam UniProt Q8NHM5 KDM2B ENSP00000366269 KDM2B Q8NHM5 Expression Atlas Protein Atlas OMIM IntAct PharmGKB KDM2B ENSP00000366269 609078 Q8NHM5 PA164721242
