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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for DOLK |
Basic gene info. | Gene symbol | DOLK |
Gene name | dolichol kinase | |
Synonyms | CDG1M|DK|DK1|SEC59|TMEM15 | |
Cytomap | UCSC genome browser: 9q34.11 | |
Genomic location | chr9 :131707808-131710012 | |
Type of gene | protein-coding | |
RefGenes | NM_014908.3, | |
Ensembl id | ENSG00000175283 | |
Description | SEC59 homologdolichol kinase 1transmembrane protein 15 | |
Modification date | 20141219 | |
dbXrefs | MIM : 610746 | |
HGNC : HGNC | ||
Ensembl : ENSG00000175283 | ||
HPRD : 15525 | ||
Vega : OTTHUMG00000020765 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_DOLK | |
BioGPS: 22845 | ||
Gene Expression Atlas: ENSG00000175283 | ||
The Human Protein Atlas: ENSG00000175283 | ||
Pathway | NCI Pathway Interaction Database: DOLK | |
KEGG: DOLK | ||
REACTOME: DOLK | ||
ConsensusPathDB | ||
Pathway Commons: DOLK | ||
Metabolism | MetaCyc: DOLK | |
HUMANCyc: DOLK | ||
Regulation | Ensembl's Regulation: ENSG00000175283 | |
miRBase: chr9 :131,707,808-131,710,012 | ||
TargetScan: NM_014908 | ||
cisRED: ENSG00000175283 | ||
Context | iHOP: DOLK | |
cancer metabolism search in PubMed: DOLK | ||
UCL Cancer Institute: DOLK | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for DOLK(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: DOLK |
Familial Cancer Database: DOLK |
* This gene is included in those cancer gene databases. |
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Oncogene 1 | Significant driver gene in |
cf) number; DB name 1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long, 2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/, 3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html, 4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long, 5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php, 1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/ |
Metabolic Pathway Description | |
REACTOME_METABOLISM_OF_PROTEINS |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: DOLK |
MedGen: DOLK (Human Medical Genetics with Condition) | |
ClinVar: DOLK | |
Phenotype | MGI: DOLK (International Mouse Phenotyping Consortium) |
PhenomicDB: DOLK |
Mutations for DOLK |
* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site. |
Structural Variants in COSMIC: go to COSMIC mutation histogram |
- Statistics for Tissue and Mutation type | Top |
- For Inter-chromosomal Variations |
There's no inter-chromosomal structural variation. |
- For Intra-chromosomal Variations |
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'. |
Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
ovary | DOLK | chr9 | 131707865 | 131707885 | chr9 | 131682887 | 131682907 |
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract) |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows DOLK related fusion information. |
ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
There's no copy number variation information in COSMIC data for this gene. |
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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=39) | (# total SNVs=8) |
(# total SNVs=1) | (# total SNVs=0) |
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Top 10 SNVs Having the Most Samples in COSMIC data |
* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID. |
GRCh37 position | Mutation(aa) | Unique sampleID count |
chr9:131708694-131708694 | p.R297C | 3 |
chr9:131709575-131709575 | p.R3Q | 2 |
chr9:131708450-131708450 | p.Y378C | 2 |
chr9:131708138-131708138 | p.A482V | 2 |
chr9:131708141-131708141 | p.F481C | 2 |
chr9:131708119-131708119 | p.A488A | 1 |
chr9:131708838-131708838 | p.D249N | 1 |
chr9:131708405-131708405 | p.S393F | 1 |
chr9:131709243-131709243 | p.V114M | 1 |
chr9:131708619-131708619 | p.R322W | 1 |
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SNV Counts per Each Loci in TCGA data |
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Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
# sample | 1 | 2 |   | 6 |   |   | 1 |   |   |   |   | 3 | 1 | 2 |   |   | 2 | 5 | 1 | 7 |
# mutation | 1 | 2 |   | 6 |   |   | 1 |   |   |   |   | 3 | 1 | 2 |   |   | 2 | 6 | 1 | 8 |
nonsynonymous SNV |   | 2 |   | 5 |   |   | 1 |   |   |   |   | 1 |   | 2 |   |   | 1 | 5 |   | 4 |
synonymous SNV | 1 |   |   | 1 |   |   |   |   |   |   |   | 2 | 1 |   |   |   | 1 | 1 | 1 | 4 |
cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma]) |
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Top 10 SNVs Having the Most Samples in TCGA data |
* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID. |
Genomic Position | Mutation(aa) | Unique sampleID count |
chr9:131708450 | p.Y378C | 2 |
chr9:131708126 | p.T476I | 1 |
chr9:131708478 | p.T296T | 1 |
chr9:131709023 | p.A442A | 1 |
chr9:131708138 | p.L291I | 1 |
chr9:131708488 | p.P440S | 1 |
chr9:131709240 | p.I257I | 1 |
chr9:131708156 | p.Q428H | 1 |
chr9:131708573 | p.Q207P | 1 |
chr9:131709243 | p.P418P | 1 |
Other DBs for Point Mutations |
Copy Number for DOLK in TCGA |
* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene. |
cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma] |
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Gene Expression for DOLK |
Gene Expression in Cancer Cell-lines (CCLE) |
* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
Differential Gene Expression in Primary Tumors (TCGA) |
* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis. (t test, adjusted p<0.05 (using Benjamini-Hochberg FDR)) |
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CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
Co-Expressed gene's network Plot |
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown. Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene |
CACFD1,COQ4,DOLK,DOLPP1,DPM2,FBP1,MFSD5, NDUFA8,ORMDL2,PPP2R4,SLC27A4,SURF1,TMEM141,TMEM203, TOR1A,TOR1B,TOR2A,TRUB2,URM1,ZDHHC12,ZER1 | ATOX1,LAMTOR1,SLC35F6,CAPNS1,CD63,CLPTM1L,DOLK, FAM32A,GNAI2,MSRA,PGAM1,POLR2L,POP4,PSMB1, PSMB4,RNASEK,RNF181,SERF2,SNX17,TAF10,UROD |
ALG2,APTX,ARPC5L,C9orf114,RPP25L,C9orf69,DOLK, DPM2,EXOSC2,MED27,POLE3,PSMB7,SDCCAG3,SIGMAR1, SSNA1,TMEM203,TOR1A,UCK1,WDR34,ZDHHC12,ZMYND19 | AEN,ALDH1B1,C14orf169,LURAP1L,CCDC86,CDK5RAP1,DOLK, ECD,FDX1L,G6PC3,GNB1L,GRWD1,HSPBP1,NDUFV3, PUF60,RNH1,RRP1,SLC25A19,SRM,TIMM44,TRIM16 |
Co-Expressed gene's Protein-protein interaction Network Plot |
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown. Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for DOLK |
There's no related Drug. |
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Cross referenced IDs for DOLK |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
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