Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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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 TYR
Basic gene info.Gene symbolTYR
Gene nametyrosinase
SynonymsATN|CMM8|OCA1|OCA1A|OCAIA|SHEP3
CytomapUCSC genome browser: 11q14.3
Genomic locationchr11 :88911039-89028927
Type of geneprotein-coding
RefGenesNM_000372.4,
Ensembl idENSG00000077498
DescriptionLB24-ABSK29-ABmonophenol monooxygenaseoculocutaneous albinism IAtumor rejection antigen AB
Modification date20141219
dbXrefs MIM : 606933
HGNC : HGNC
Ensembl : ENSG00000077498
HPRD : 06086
Vega : OTTHUMG00000167294
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_TYR
BioGPS: 7299
Gene Expression Atlas: ENSG00000077498
The Human Protein Atlas: ENSG00000077498
PathwayNCI Pathway Interaction Database: TYR
KEGG: TYR
REACTOME: TYR
ConsensusPathDB
Pathway Commons: TYR
MetabolismMetaCyc: TYR
HUMANCyc: TYR
RegulationEnsembl's Regulation: ENSG00000077498
miRBase: chr11 :88,911,039-89,028,927
TargetScan: NM_000372
cisRED: ENSG00000077498
ContextiHOP: TYR
cancer metabolism search in PubMed: TYR
UCL Cancer Institute: TYR
Assigned class in ccmGDBC

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

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

Mutations for TYR
* 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 TYR 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 # sample1       1        
GAIN (# sample)1       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)

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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=8

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=116)
Stat. for Synonymous SNVs
(# total SNVs=25)
Stat. for Deletions
(# total SNVs=2)
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
chr11:88911358-88911358p.S79S6
chr11:88924500-88924500p.D317G4
chr11:88911234-88911234p.P38L3
chr11:88911329-88911329p.P70S3
chr11:88961040-88961040p.M362I2
chr11:88911220-88911220p.K33N2
chr11:88924522-88924522p.L324F2
chr11:88924442-88924442p.R298W2
chr11:89017961-89017961p.R402Q2
chr11:88911312-88911312p.P64Q2

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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=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample381161 4 1  2093  412110
# mutation381131 4 1  2293  412114
nonsynonymous SNV36 81 2 1  2091  49 11
synonymous SNV 215  2    2 2   313
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
chr11:88924500p.D317G4
chr11:88911358p.S79S2
chr11:88911234p.G254R2
chr11:88911881p.N261K2
chr11:88911904p.P38L2
chr11:88911554p.I145V1
chr11:88961003p.D240Y1
chr11:89028447p.P350L1
chr11:88911731p.R434T1
chr11:88961116p.R501R1

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 TYR 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 TYR

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 TYR
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
DB00157tyrosinaseapproved; nutraceuticalNADH
DB00548tyrosinaseapprovedAzelaic Acid
DB00600tyrosinaseapprovedMonobenzone
DB01055tyrosinaseapprovedMimosine


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Cross referenced IDs for TYR
* 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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