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 TYRP1
Basic gene info.Gene symbolTYRP1
Gene nametyrosinase-related protein 1
SynonymsCAS2|CATB|GP75|OCA3|TRP|TRP1|TYRP|b-PROTEIN
CytomapUCSC genome browser: 9p23
Genomic locationchr9 :12693385-12710266
Type of geneprotein-coding
RefGenesNM_000550.2,
Ensembl idENSG00000107165
Description5,6-dihydroxyindole-2-carboxylic acid oxidaseDHICA oxidasecatalase Bglycoprotein 75melanoma antigen gp75
Modification date20141207
dbXrefs MIM : 115501
HGNC : HGNC
Ensembl : ENSG00000107165
HPRD : 00283
Vega : OTTHUMG00000021034
ProteinUniProt: P17643
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_TYRP1
BioGPS: 7306
Gene Expression Atlas: ENSG00000107165
The Human Protein Atlas: ENSG00000107165
PathwayNCI Pathway Interaction Database: TYRP1
KEGG: TYRP1
REACTOME: TYRP1
ConsensusPathDB
Pathway Commons: TYRP1
MetabolismMetaCyc: TYRP1
HUMANCyc: TYRP1
RegulationEnsembl's Regulation: ENSG00000107165
miRBase: chr9 :12,693,385-12,710,266
TargetScan: NM_000550
cisRED: ENSG00000107165
ContextiHOP: TYRP1
cancer metabolism search in PubMed: TYRP1
UCL Cancer Institute: TYRP1
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for TYRP1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: TYRP1
Familial Cancer Database: TYRP1
* 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 115501; gene.
203290; phenotype.
612271; phenotype.
Orphanet 79433; Oculocutaneous albinism type 3.
DiseaseKEGG Disease: TYRP1
MedGen: TYRP1 (Human Medical Genetics with Condition)
ClinVar: TYRP1
PhenotypeMGI: TYRP1 (International Mouse Phenotyping Consortium)
PhenomicDB: TYRP1

Mutations for TYRP1
* 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 TYRP1 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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample     1    1   1  
GAIN (# sample)          1   1  
LOSS (# sample)     1           
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)

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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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=51)
Stat. for Synonymous SNVs
(# total SNVs=24)
Stat. for Deletions
(# total SNVs=5)
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
chr9:12702411-12702414p.N353fs*315
chr9:12694057-12694057p.Q21*3
chr9:12698645-12698645p.T301T2
chr9:12694160-12694160p.R55H2
chr9:12698513-12698513p.V257V2
chr9:12695518-12695518p.R130M2
chr9:12709118-12709118p.D517V2
chr9:12694066-12694066p.A24S2
chr9:12695817-12695817p.R230S2
chr9:12695618-12695618p.T163T1

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 218  1 22 431  8318
# mutation 217  1 22 431  83111
nonsynonymous SNV 214  1 12 42   8216
synonymous SNV   3    1   11   1 5
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
chr9:12694121p.C42Y2
chr9:12698513p.V257V2
chr9:12698633p.R130M1
chr9:12694240p.S292F1
chr9:12708029p.I466T1
chr9:12695714p.L136L1
chr9:12702354p.Y296D1
chr9:12694303p.Q467K1
chr9:12708083p.S137N1
chr9:12695729p.D297D1

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 TYRP1 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 TYRP1

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

LURAP1L,CT45A1,CT45A3,DHRS2,FRG2B,GABPB1,HGC6.3,
LOC643008,MAGEA8,MAGEB18,NAP1L6,RGS5,RPL3L,SPPL2A,
SUMO2,TYRP1,UGT2B10,UGT2B15,USP29,USP8,ZIM3
ACTC1,ALDH1B1,C20orf166-AS1,CAMK2G,CASQ2,FYCO1,INPP5A,
ITIH4,LGI1,LOC401093,LRRC7,MN1,MUSTN1,PDE4C,
PDE4D,PLN,SGCD,SRRM4,SYNPO2,TYRP1,UNC13C

ADCY2,NREP,CST5,DAAM2,ELN,FOXF1,GJD2,
GPBAR1,LRRC10,LSAMP,LTBP1,MFAP2,NKX2-3,OSBPL6,
PCDH18,RCAN2,RGMA,RIMS1,SLC24A3,TCF21,TYRP1
ABCC12,AMBN,ANO4,CALML5,CAPNS2,CCDC63,CLDN19,
LOC100133920,MUCL1,NKX6-1,OR4A16,OR6B2,OR7E24,OR8D2,
PGK2,SCGB2A2,SNORA13,SNORA58,TCF23,TYRP1,WFDC8
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 TYRP1


There's no related Drug.
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Cross referenced IDs for TYRP1
* 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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