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: SMYD4 |
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Mutation Data (+)
# Cell Line/Tumor sample Tissue of Origin cDNA change Protein change Source FATHMM Prediction PolyPhen2 Prediction 1 24T SKIN c.189G>C p.K63N COSMIC PASSENGER/OTHER Probably Damaging 2 24T SKIN c.190G>A p.D64N COSMIC PASSENGER/OTHER Probably Damaging 3 24T SKIN c.2370C>T p.S790S COSMIC NP NP 4 585260 LUNG c.1346C>T p.A449V COSMIC PASSENGER/OTHER Benign 5 587278 LARGE INTESTINE c.608G>A p.S203N COSMIC PASSENGER/OTHER Benign 6 587382 LARGE INTESTINE c.1108C>T p.L370F COSMIC PASSENGER/OTHER Benign 7 CLL137 HAEMATOPOIETIC AND LYMPHOID TISSUE c.676G>C p.E226Q COSMIC PASSENGER/OTHER Benign 8 ESO-859 OESOPHAGUS c.1047C>T p.H349H COSMIC NP NP 9 GC7_T STOMACH c.1294A>T p.T432S COSMIC PASSENGER/OTHER Possibly Damaging 10 KM12 LARGE INTESTINE c.290A>G p.H97R COSMIC PASSENGER/OTHER Probably Damaging 11 LAU63 SKIN c.1597C>T p.P533S COSMIC PASSENGER/OTHER Probably Damaging 12 P03-1334 PROSTATE c.1120A>G p.I374V COSMIC PASSENGER/OTHER Benign 13 PD2127a KIDNEY c.1801G>C p.A601P COSMIC PASSENGER/OTHER Benign 14 PD2198a KIDNEY c.1134C>T p.D378D COSMIC NP NP 15 PD4119a BREAST c.577C>T p.R193C COSMIC PASSENGER/OTHER Probably Damaging 16 PD4120a BREAST c.612C>T p.L204L COSMIC NP NP 17 S01366 LUNG c.982delG p.E328fs*25 COSMIC NP NP 18 SA224 BREAST c.1891G>A p.D631N COSMIC PASSENGER/OTHER Benign 19 TCGA-18-3419-01 LUNG c.1929C>T p.S643S COSMIC NP NP 20 TCGA-23-1120-01 OVARY c.2390C>A p.P797H COSMIC PASSENGER/OTHER Probably Damaging 21 TCGA-37-3789-01 LUNG c.722C>A p.P241H COSMIC PASSENGER/OTHER Probably Damaging 22 TCGA-55-7283-01 LUNG c.742G>A p.V248I COSMIC PASSENGER/OTHER Benign 23 TCGA-55-7727-01 LUNG c.2209A>G p.S737G COSMIC PASSENGER/OTHER Probably Damaging 24 TCGA-69-7973-01 LUNG c.2338G>C p.D780H COSMIC PASSENGER/OTHER Benign 25 TCGA-A2-A25A-01 BREAST c.702C>A p.S234S COSMIC NP NP 26 TCGA-A6-6780-01 LARGE INTESTINE c.72G>T p.Q24H COSMIC PASSENGER/OTHER Possibly Damaging 27 TCGA-AA-3554-01 LARGE INTESTINE c.831G>A p.P277P COSMIC NP NP 28 TCGA-AD-5900-01 LARGE INTESTINE c.742G>A p.V248I COSMIC PASSENGER/OTHER Benign 29 TCGA-AP-A056-01 ENDOMETRIUM c.1275C>A p.V425V COSMIC NP NP 30 TCGA-AP-A0LP-01 ENDOMETRIUM c.957C>T p.S319S COSMIC NP NP 31 TCGA-AX-A05Z-01 ENDOMETRIUM c.338C>T p.S113L COSMIC PASSENGER/OTHER Probably Damaging 32 TCGA-AX-A0J1-01 ENDOMETRIUM c.1451A>G p.D484G COSMIC PASSENGER/OTHER Possibly Damaging 33 TCGA-B5-A11E-01 ENDOMETRIUM c.442C>T p.R148C COSMIC PASSENGER/OTHER Probably Damaging 34 TCGA-BH-A0AW-01 BREAST c.1473G>A p.A491A COSMIC NP NP 35 TCGA-BH-A0C0-01 BREAST c.832C>G p.H278D COSMIC PASSENGER/OTHER Possibly Damaging 36 TCGA-BL-A3JM-01 URINARY TRACT c.2064G>C p.E688D COSMIC PASSENGER/OTHER Benign 37 TCGA-BS-A0UV-01 ENDOMETRIUM c.1577G>A p.R526H COSMIC PASSENGER/OTHER Probably Damaging 38 TCGA-CM-4743-01 LARGE INTESTINE c.874G>A p.G292R COSMIC PASSENGER/OTHER Probably Damaging 39 TCGA-CM-6170-01 LARGE INTESTINE c.2326G>C p.G776R COSMIC PASSENGER/OTHER Probably Damaging 40 TCGA-D1-A15X-01 ENDOMETRIUM c.2119C>T p.R707W COSMIC PASSENGER/OTHER Probably Damaging 41 TCGA-D5-6928-01 LARGE INTESTINE c.1672C>T p.R558W COSMIC PASSENGER/OTHER Probably Damaging 42 TCGA-D8-A1JD-01 BREAST c.359G>A p.G120D COSMIC PASSENGER/OTHER Possibly Damaging 43 TCGA-DS-A0VK-01 CERVIX c.2364G>T p.M788I COSMIC PASSENGER/OTHER Probably Damaging 44 TCGA-G2-A2EF-01 URINARY TRACT c.1335C>G p.L445L COSMIC NP NP 45 TCGA-GV-A3JZ-01 URINARY TRACT c.1642G>C p.V548L COSMIC PASSENGER/OTHER Benign 46 YUBOO SKIN c.923C>T p.P308L COSMIC CANCER Probably Damaging 47 YUMOYA SKIN c.2309T>C p.V770A COSMIC PASSENGER/OTHER Possibly Damaging 48 cSCCP6 SKIN c.142G>A p.D48N COSMIC PASSENGER/OTHER Probably Damaging 49 pfg019T STOMACH c.1212C>T p.I404I 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 (+)
Users must enabled the Java in their browser to see structure.
Users can also download Java from here.Modelled Structure Structures available in PDB Structure is not available in PDB -
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. 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 SMYD4 SMYD4 SMYD4 ENSP00000304360 Q8IYR2 QuickGO HGNC Ensembl Genome Browser TreeFam UniProt Q8IYR2 SMYD4 ENSP00000304360 SMYD4 Q8IYR2 Expression Atlas Protein Atlas OMIM IntAct PharmGKB SMYD4 ENSP00000304360 NA Q8IYR2 PA134925431
