Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

Gene Summary

Phenotypic Information (metabolism pathway, cancer, disease, phenome)

Mutations: SVs, CNVs, SNVs

Gene expression: GE, Protein, DEGE, CNV vs GE

Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG

Pharmacological Information: Drug-Gene Network

Cross referenced IDs

Gene Summary for DCK
Basic gene info.Gene symbolDCK
Gene namedeoxycytidine kinase
Synonyms-
CytomapUCSC genome browser: 4q13.3-q21.1
Genomic locationchr4 :71859264-71896629
Type of geneprotein-coding
RefGenesNM_000788.2,
Ensembl idENSG00000156136
Descriptiondeoxynucleoside kinase
Modification date20141207
dbXrefs MIM : 125450
HGNC : HGNC
Ensembl : ENSG00000156136
HPRD : 00507
Vega : OTTHUMG00000129908
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_DCK
BioGPS: 1633
Gene Expression Atlas: ENSG00000156136
The Human Protein Atlas: ENSG00000156136
PathwayNCI Pathway Interaction Database: DCK
KEGG: DCK
REACTOME: DCK
ConsensusPathDB
Pathway Commons: DCK
MetabolismMetaCyc: DCK
HUMANCyc: DCK
RegulationEnsembl's Regulation: ENSG00000156136
miRBase: chr4 :71,859,264-71,896,629
TargetScan: NM_000788
cisRED: ENSG00000156136
ContextiHOP: DCK
cancer metabolism search in PubMed: DCK
UCL Cancer Institute: DCK
Assigned class in ccmGDBC

Top
Phenotypic Information for DCK(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: DCK
Familial Cancer Database: DCK
* This gene is included in those cancer gene databases.

.

Oncogene 1

Tumor Suppressor gene 2

Cancer Gene Census 3

CancerGenes 4

Network of Cancer Gene 5

Significant driver gene in

Therapeutic Vulnerabilities in Cancer1

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/

check002.gifMetabolic Pathway Description
KEGG_PURINE_METABOLISM
KEGG_PYRIMIDINE_METABOLISM
REACTOME_METABOLISM_OF_NUCLEOTIDES
REACTOME_PURINE_METABOLISM
REACTOME_PYRIMIDINE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: DCK
MedGen: DCK (Human Medical Genetics with Condition)
ClinVar: DCK
PhenotypeMGI: DCK (International Mouse Phenotyping Consortium)
PhenomicDB: DCK

Mutations for DCK
* 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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows DCK related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BG315007RAPGEF112659134454093134454357DCK26239847188812771888262

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

Top
check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample          1      
GAIN (# sample)          1      
LOSS (# sample)                 
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

Top
check002.gifSNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation

 : Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=4

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=24)
Stat. for Synonymous SNVs
(# total SNVs=7)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.There's no inserted snv.

Top
check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr4:71889409-71889409p.Q179K3
chr4:71888182-71888182p.L102L2
chr4:71892391-71892391p.F225F2
chr4:71888090-71888090p.T72S2
chr4:71888092-71888092p.T72T2
chr4:71889394-71889394p.G174R2
chr4:71891559-71891559p.R192R1
chr4:71888183-71888183p.S103G1
chr4:71891606-71891606p.L208R1
chr4:71888187-71888187p.R104Q1

Top
check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample2  61 2  1 413     5
# mutation2  51 2  1 413     5
nonsynonymous SNV1  31 2  1 311     4
synonymous SNV1  2       1 2     1
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])

Top
check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr4:71888090p.F225F2
chr4:71888092p.T72S2
chr4:71892391p.T72T2
chr4:71888183p.N164T1
chr4:71892401p.Q165Q1
chr4:71888189p.R192L1
chr4:71892453p.R192R1
chr4:71888254p.I26M1
chr4:71895091p.L208R1
chr4:71859630p.V61V1

check002.gifOther DBs for Point Mutations
Point Mutation Table of Ensembl: go to Ensembl variation table
Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

check002.gifCopy Number for DCK 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]

Top
Gene Expression for DCK

check002.gifGene 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.

check002.gifDifferential 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))
Top
check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


Top
Gene-Gene Network Information
check002.gifCo-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

: Open all plots for all cancer types

ANKRD17,CEP135,CNOT6L,DCK,ENOPH1,G3BP2,GNA13,
GRSF1,LIN54,MOB1B,NUP54,PAQR3,PDS5A,PPAT,
SDAD1,SRSF10,TMEM194A,TMEM33,UBA6,UBE2K,USO1
ANKRD13C,ANP32E,CGGBP1,DCK,DEK,GNA13,GOLT1B,
HSPA13,LRRC40,MIER1,NUS1,PAPD4,BLOC1S6,RAP2C,
RNGTT,SMNDC1,SPAST,TMX1,TRAM1,TROVE2,UFM1

C14orf142,CISD2,CNIH1,COMMD8,COPS4,COX18,DCK,
ENOPH1,LRRC40,MAD2L1,MED28,MTHFD2L,NUP54,PAQR3,
PRDX3,RCHY1,SELT,SEP15,SRP72,TMEM165,UBE2D3
BUB3,MZT1,C5orf28,DCK,E2F5,ERLEC1,FAM49B,
GABPB1,HAUS1,MRPS14,NIF3L1,PDCD2,PMS2P1,POLB,
PRKRIR,PRPSAP2,RBBP4,SLBP,TANK,TFAM,UNC50
check002.gifCo-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

: Open all plots for all cancer types

Top
check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top
Pharmacological Information for DCK
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB01073deoxycytidine kinaseapprovedFludarabine
DB02594deoxycytidine kinaseexperimental2'-Deoxycytidine
DB03431deoxycytidine kinaseexperimentalAdenosine-5'-Diphosphate
DB00709deoxycytidine kinaseapproved; investigationalLamivudine
DB00694deoxycytidine kinaseapprovedDaunorubicin
DB00773deoxycytidine kinaseapprovedEtoposide
DB00619deoxycytidine kinaseapprovedImatinib
DB01204deoxycytidine kinaseapproved; investigationalMitoxantrone
DB00541deoxycytidine kinaseapproved; investigationalVincristine
DB02745deoxycytidine kinaseexperimentalUridine
DB00987deoxycytidine kinaseapproved; investigationalCytarabine
DB00441deoxycytidine kinaseapprovedGemcitabine
DB00515deoxycytidine kinaseapprovedCisplatin


Top
Cross referenced IDs for DCK
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section

: Open all cross reference information



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas