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 TPH1
Basic gene info.Gene symbolTPH1
Gene nametryptophan hydroxylase 1
SynonymsTPRH|TRPH
CytomapUCSC genome browser: 11p15.3-p14
Genomic locationchr11 :18042083-18062335
Type of geneprotein-coding
RefGenesNM_004179.2,
Ensembl idENSG00000129167
DescriptionL-tryptophan hydroxylaseindoleacetic acid-5-hydroxylasetryptophan 5-hydroxylase 1tryptophan 5-monooxygenase 1tryptophan hydroxylase (tryptophan 5-monooxygenase)
Modification date20141207
dbXrefs MIM : 191060
HGNC : HGNC
HPRD : 01846
ProteinUniProt: P17752
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_TPH1
BioGPS: 7166
Gene Expression Atlas: ENSG00000129167
The Human Protein Atlas: ENSG00000129167
PathwayNCI Pathway Interaction Database: TPH1
KEGG: TPH1
REACTOME: TPH1
ConsensusPathDB
Pathway Commons: TPH1
MetabolismMetaCyc: TPH1
HUMANCyc: TPH1
RegulationEnsembl's Regulation: ENSG00000129167
miRBase: chr11 :18,042,083-18,062,335
TargetScan: NM_004179
cisRED: ENSG00000129167
ContextiHOP: TPH1
cancer metabolism search in PubMed: TPH1
UCL Cancer Institute: TPH1
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of TPH1 in cancer cell metabolism1. Juhász C, Nahleh Z, Zitron I, Chugani DC, Janabi MZ, et al. (2012) Tryptophan metabolism in breast cancers: molecular imaging and immunohistochemistry studies. Nuclear medicine and biology 39: 926-932. go to article

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Phenotypic Information for TPH1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: TPH1
Familial Cancer Database: TPH1
* 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_TRYPTOPHAN_METABOLISM
REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

check002.gifOthers
OMIM 191060; gene.
Orphanet
DiseaseKEGG Disease: TPH1
MedGen: TPH1 (Human Medical Genetics with Condition)
ClinVar: TPH1
PhenotypeMGI: TPH1 (International Mouse Phenotyping Consortium)
PhenomicDB: TPH1

Mutations for TPH1
* 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
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
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 TPH1 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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=35)
Stat. for Synonymous SNVs
(# total SNVs=10)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.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
chr11:18047154-18047154p.A300T2
chr11:18048097-18048097p.R248Q2
chr11:18051095-18051095p.R145Q2
chr11:18042711-18042711p.E388*2
chr11:18054916-18054916p.E103*2
chr11:18048081-18048081p.T253T1
chr11:18062244-18062244p.F22L1
chr11:18042689-18042689p.R395H1
chr11:18050857-18050858p.W174F1
chr11:18047146-18047146p.E302D1

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample2  52 2 4  102  173 7
# mutation2  52 2 4  122  194 8
nonsynonymous SNV   42 2 3  92  183 6
synonymous SNV2  1    1  3    11 2
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
chr11:18051095p.R145Q2
chr11:18051104p.D324Y1
chr11:18042699p.K25N1
chr11:18057644p.A300T1
chr11:18048061p.R142R1
chr11:18062276p.S23S1
chr11:18051105p.G299G1
chr11:18044361p.R142H1
chr11:18057663p.F22L1
chr11:18048081p.G294C1

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 TPH1 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 TPH1

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

ABI3BP,CC2D2A,CDHR2,CHRM4,AMER3,IGSF1,INSC,
MEP1A,MIXL1,MYOC,NEUROD4,RALYL,RNF133,RNF148,
SEC14L5,SEZ6L,SLC18A1,SLC9C1,TKTL1,TNFAIP8L3,TPH1
C4BPA,CETN1,CYP7B1,GCC2,GK5,GPRIN3,HIVEP3,
KNDC1,LCN15,LIPM,LRRC8B,NAA11,OR2A4,OSMR,
RNF24,SLC25A37,SLC28A3,TPH1,UBTFL1,UTP20,YTHDC2

ADAM2,AGXT,C2CD4B,CCDC33,DLL1,FAM133A,FGL1,
GIF,GP9,IL19,LCN8,MYO3B,PAGE1,PCCA,
PPP4R4,RFX6,RTBDN,SSX4,TPH1,WFDC2,ZG16
AVPR1B,CFC1B,CRH,CYP2W1,GABRA6,INSL5,KLK3,
KRTAP3-3,LMX1A,MYBPC1,NEUROD1,NKX2-2,PF4V1,RFX6,
RIMS4,SLC38A11,SST,TBX4,TNNC1,TPH1,TTR
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 TPH1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P17752; -.
ChemistryChEMBL CHEMBL5689; -.
ChemistryGuidetoPHARMACOLOGY 1241; -.
Organism-specific databasesPharmGKB PA355; -.
Organism-specific databasesCTD 7166; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00360tryptophan hydroxylase 1approved; investigationalTetrahydrobiopterin
DB03271tryptophan hydroxylase 1experimental7,8-Dihydro-L-Biopterin
DB00715tryptophan hydroxylase 1approved; investigationalParoxetine
DB00176tryptophan hydroxylase 1approved; investigationalFluvoxamine


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Cross referenced IDs for TPH1
* 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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