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 TPO
Basic gene info.Gene symbolTPO
Gene namethyroid peroxidase
SynonymsMSA|TDH2A|TPX
CytomapUCSC genome browser: 2p25
Genomic locationchr2 :1417232-1546499
Type of geneprotein-coding
RefGenesNM_000547.5,
NM_001206744.1,NM_001206745.1,NM_175719.3,NM_175721.3,
NM_175722.3,NM_175720.1,
Ensembl idENSG00000115705
Descriptionthyroid microsomal antigenthyroperoxidase
Modification date20141222
dbXrefs MIM : 606765
HGNC : HGNC
Ensembl : ENSG00000115705
HPRD : 06000
Vega : OTTHUMG00000090271
ProteinUniProt: P07202
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_TPO
BioGPS: 7173
Gene Expression Atlas: ENSG00000115705
The Human Protein Atlas: ENSG00000115705
PathwayNCI Pathway Interaction Database: TPO
KEGG: TPO
REACTOME: TPO
ConsensusPathDB
Pathway Commons: TPO
MetabolismMetaCyc: TPO
HUMANCyc: TPO
RegulationEnsembl's Regulation: ENSG00000115705
miRBase: chr2 :1,417,232-1,546,499
TargetScan: NM_000547
cisRED: ENSG00000115705
ContextiHOP: TPO
cancer metabolism search in PubMed: TPO
UCL Cancer Institute: TPO
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of TPO in cancer cell metabolism1. Cipollini M, Pastor S, Gemignani F, Castell J, Garritano S, et al. (2013) TPO genetic variants and risk of differentiated thyroid carcinoma in two European populations. International Journal of Cancer 133: 2843-2851. go to article
2. Schulten H-J, Alotibi R, Al-Ahmadi A, Ata M, Karim S, et al. (2015) Effect of BRAF mutational status on expression profiles in conventional papillary thyroid carcinomas. BMC genomics 16: S6. go to article

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

check002.gifOthers
OMIM 274500; phenotype.
274500; phenotype.
606765; gene.
606765; gene.
Orphanet 95716; Familial thyroid dyshormonogenesis.
95716; Familial thyroid dyshormonogenesis.
DiseaseKEGG Disease: TPO
MedGen: TPO (Human Medical Genetics with Condition)
ClinVar: TPO
PhenotypeMGI: TPO (International Mouse Phenotyping Consortium)
PhenomicDB: TPO

Mutations for TPO
* 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
ovaryTPOchr214639151463935chr24272400642724026
ovaryTPOchr214684011468421chr21261578412615804
ovaryTPOchr215223341522354TPOchr215172371517257
pancreasTPOchr214291111429311TPOchr214286821428882
pancreasTPOchr214481331448333TPOchr214488271449027
pancreasTPOchr214735111473531DPY30chr23225750132257521
pancreasTPOchr215283671528387TPOchr215290051529025
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 TPO related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BI004881TPO39173215444621546295RAB11FIP317331716546060546204
BG990924TPO15239214975811497812TPO237316214883881488467

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               
GAIN (# sample)                 
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=8

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=187)
Stat. for Synonymous SNVs
(# total SNVs=58)
Stat. for Deletions
(# total SNVs=4)
Stat. for Insertions
(# total SNVs=2)

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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
chr2:1499899-1499899p.P715P5
chr2:1481155-1481155p.A373S4
chr2:1507809-1507809p.A826T4
chr2:1481231-1481231p.S398T4
chr2:1520676-1520676p.V847A4
chr2:1544469-1544469p.R908W4
chr2:1544423-1544423p.P892P3
chr2:1546234-1546234p.P930P3
chr2:1507739-1507739p.D802D3
chr2:1459909-1459909p.R225H3

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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
# sample841315 12 41131125 14022 18
# mutation841265 12 41132125 15625 21
nonsynonymous SNV741224 9 31124114 13816 14
synonymous SNV1  41 3 1  811  189 7
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
chr2:1507809p.A653T,TPO4
chr2:1544469p.D258H,TPO3
chr2:1491665p.N384S,TPO3
chr2:1460007p.R864W,TPO3
chr2:1488383p.D279N,TPO2
chr2:1544475p.S807F,TPO2
chr2:1488505p.K63K,TPO2
chr2:1426879p.A403E,TPO2
chr2:1491722p.D629E,TPO2
chr2:1488506p.S841L,TPO2

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 TPO 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 TPO

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

ADCY4,ARHGEF15,AVPR2,BMX,BTNL9,CCM2L,CCL14,
CXorf36,ACKR1,GPIHBP1,GPR146,FAM110D,KANK3,LRRC70,
MMRN2,PDE2A,S1PR1,SDPR,TPO,TSPAN7,USHBP1
ADCY4,APOL3,CXorf36,ERG,GATA2,HLA-E,MAP3K3,
MCF2L,MMRN2,NEURL1B,NOD1,NOS3,PLVAP,RAMP3,
RAPGEF3,RPS6KA2,SCARF1,SH2D3C,SLCO4A1,TPO,USHBP1

ABCC9,C2orf40,CCL14,CDON,CHRDL2,CNTNAP1,CPEB1,
ACKR1,FILIP1,GDF5,HAND2,KIAA2022,LONRF2,MASP1,
OGN,PDE2A,SDPR,SPARCL1,TLL1,TMOD1,TPO
MCEMP1,C4BPB,CLCA3P,ERP27,IFITM2,IFITM3,IL13RA2,
IL19,IL22,INSL4,LYPD5,MKX,MMP1,MMP3,
PLA2G2A,PRSS22,PRSS27,RIMS1,RTP1,SLC6A14,TPO
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 TPO
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryChEMBL CHEMBL1839; -.
ChemistryGuidetoPHARMACOLOGY 2526; -.
ChemistryChEMBL CHEMBL1839; -.
ChemistryGuidetoPHARMACOLOGY 2526; -.
Organism-specific databasesPharmGKB PA36694; -.
Organism-specific databasesPharmGKB PA36694; -.
Organism-specific databasesCTD 7173; -.
Organism-specific databasesCTD 7173; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00389thyroid peroxidaseapprovedCarbimazole
DB00509thyroid peroxidaseapprovedDextrothyroxine
DB00550thyroid peroxidaseapprovedPropylthiouracil
DB00763thyroid peroxidaseapprovedMethimazole


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Cross referenced IDs for TPO
* 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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