Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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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 DCT
Basic gene info.Gene symbolDCT
Gene namedopachrome tautomerase
SynonymsTRP-2|TYRP2
CytomapUCSC genome browser: 13q32
Genomic locationchr13 :95091840-95131936
Type of geneprotein-coding
RefGenesNM_001129889.1,
NM_001922.3,
Ensembl idENSG00000080166
DescriptionDTL-dopachrome Delta-isomeraseL-dopachrome tautomeraseTRP2dopachrome delta-isomerasedopachrome tautomerase (dopachrome delta-isomerase, tyrosine-related protein 2)tyrosinase-related protein 2tyrosine-related protein 2
Modification date20141207
dbXrefs MIM : 191275
HGNC : HGNC
Ensembl : ENSG00000080166
HPRD : 01864
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_DCT
BioGPS: 1638
Gene Expression Atlas: ENSG00000080166
The Human Protein Atlas: ENSG00000080166
PathwayNCI Pathway Interaction Database: DCT
KEGG: DCT
REACTOME: DCT
ConsensusPathDB
Pathway Commons: DCT
MetabolismMetaCyc: DCT
HUMANCyc: DCT
RegulationEnsembl's Regulation: ENSG00000080166
miRBase: chr13 :95,091,840-95,131,936
TargetScan: NM_001129889
cisRED: ENSG00000080166
ContextiHOP: DCT
cancer metabolism search in PubMed: DCT
UCL Cancer Institute: DCT
Assigned class in ccmGDBC

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Phenotypic Information for DCT(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: DCT
Familial Cancer Database: DCT
* 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_TYROSINE_METABOLISM

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

Mutations for DCT
* 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

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
pancreasDCTchr139511900095119020CLDN10chr139612310496123124
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)

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

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

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check002.gifCopy 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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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=7

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=95)
Stat. for Synonymous SNVs
(# total SNVs=21)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

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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
chr13:95092216-95092216p.R499Q7
chr13:95131418-95131418p.T31M5
chr13:95092217-95092217p.R499*3
chr13:95121132-95121132p.D155N3
chr13:95092293-95092293p.L473L3
chr13:95131262-95131262p.R83H3
chr13:95131277-95131277p.R78Q3
chr13:95121089-95121089p.P169H2
chr13:95114343-95114343p.L322V2
chr13:95131420-95131420p.M30I2

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=5

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample41 201 2 5 11342  28113
# mutation41 211 2 5 11342  28112
nonsynonymous SNV21 171 2 4 1932  2719
synonymous SNV2  4    1  41    1 3
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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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
chr13:95092216p.R499Q,DCT5
chr13:95121132p.D155Y,DCT4
chr13:95131263p.G305G,DCT2
chr13:95131277p.R83C,DCT2
chr13:95118820p.R78Q,DCT2
chr13:95131316p.D230N,DCT2
chr13:95114392p.R65L,DCT2
chr13:95114393p.N37K,DCT1
chr13:95121279p.P470L,DCT1
chr13:95092274p.R326Q,DCT1

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 DCT 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 DCT

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

: Open all plots for all cancer types


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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

AGA,BBS12,C15orf57,WWC2-AS2,TRAPPC11,CAMLG,CBR4,
PRIMPOL,CDKN2AIP,CYP4V2,DCTD,EID1,FBXL5,FBXO8,
IRF2,CFAP97,LAMTOR3,OCIAD1,RWDD4,TMEM192,UFSP2
C6orf48,CDK4,CLTA,DCTD,EEF1A1,EEF1A1P9,ERGIC3,
KDELR1,LSM2,LYRM4,POLR2G,PPIA,PRELID1,RAB34,
SIGMAR1,SSR2,SSR4,TMEM179B,UBE2I,UFC1,YIPF3

ARFIP1,C4orf27,TRAPPC11,TMA16,CASP3,PRIMPOL,CDKN2AIP,
DCTD,ENOPH1,FRG1,CFAP97,MRPS18C,PIGY,PLRG1,
PPA2,PPID,RAP1GDS1,RWDD4,SPCS3,UBE2D3,UFSP2
ARMC10,BOD1,CINP,DCTD,DPH5,EEF1A1P9,EIF3E,
HSCB,MANEA,MRPS27,ICE2,PDCD2,PDCD2L,PRCP,
PRKRIR,RPS8,RSL1D1,SETMAR,TIMM9,TMEM5,ZNF22
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

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check002.gifInteracting Genes (from Pathway Commons)

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

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Pharmacological Information for DCT


There's no related Drug.
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Cross referenced IDs for DCT
* 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



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