Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

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 TPI1
Basic gene info.Gene symbolTPI1
Gene nametriosephosphate isomerase 1
SynonymsHEL-S-49|TIM|TPI|TPID
CytomapUCSC genome browser: 12p13
Genomic locationchr12 :6977277-6980110
Type of geneprotein-coding
RefGenesNM_000365.5,
NM_001159287.1,NM_001258026.1,
Ensembl idENSG00000268548
Descriptionepididymis secretory protein Li 49triose-phosphate isomerasetriosephosphate isomerase
Modification date20141207
dbXrefs MIM : 190450
HGNC : HGNC
Ensembl : ENSG00000111669
HPRD : 01833
Vega : OTTHUMG00000133767
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_TPI1
BioGPS: 7167
Gene Expression Atlas: ENSG00000268548
The Human Protein Atlas: ENSG00000268548
PathwayNCI Pathway Interaction Database: TPI1
KEGG: TPI1
REACTOME: TPI1
ConsensusPathDB
Pathway Commons: TPI1
MetabolismMetaCyc: TPI1
HUMANCyc: TPI1
RegulationEnsembl's Regulation: ENSG00000268548
miRBase: chr12 :6,977,277-6,980,110
TargetScan: NM_000365
cisRED: ENSG00000268548
ContextiHOP: TPI1
cancer metabolism search in PubMed: TPI1
UCL Cancer Institute: TPI1
Assigned class in ccmGDBC

Top
Phenotypic Information for TPI1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: TPI1
Familial Cancer Database: TPI1
* 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_GLYCOLYSIS_GLUCONEOGENESIS
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM
KEGG_INOSITOL_PHOSPHATE_METABOLISM
BIOCARTA_GLYCOLYSIS_PATHWAY
REACTOME_METABOLISM_OF_CARBOHYDRATES
REACTOME_GLUCOSE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: TPI1
MedGen: TPI1 (Human Medical Genetics with Condition)
ClinVar: TPI1
PhenotypeMGI: TPI1 (International Mouse Phenotyping Consortium)
PhenomicDB: TPI1

Mutations for TPI1
* 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 TPI1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BC054482TPI151021269766956976792TOP2B9555932565696525661417
DW413329CHD217143159346772093470537TPI11443201269797516979927
CA431273TPI1191891269798226979992ILF3187774191080147410802067
BQ000670SERPINH118298117528354675283826TPI12946831269795386979927
BG751641CAPNS14536193663690536641020TPI15296331269798646979968
AI652202TPI118721269799386979992MAPK146920563607669736076833
AF086180TPI11881269798776979964PFKL83322214574700845747247
BC004230RPL2844532195589731155899744TPI152917531269767026979993
BC009885RPL2844532195589731155899744TPI152917531269767026979993

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

Top
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.

Top
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

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=27)
Stat. for Synonymous SNVs
(# total SNVs=6)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.There's no inserted snv.

Top
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
chr12:6978532-6978532p.F145F2
chr12:6978338-6978338p.E105D2
chr12:6978433-6978433p.Q112H1
chr12:6979213-6979213p.A182S1
chr12:6976815-6976815p.L29V1
chr12:6978441-6978441p.A115V1
chr12:6979227-6979227p.H186H1
chr12:6978057-6978057p.I49V1
chr12:6978455-6978455p.E120Q1
chr12:6979278-6979278p.Q203Q1

Top
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
# sample 1 3  2 3  84    3 5
# mutation 1 3  2 3  95    3 5
nonsynonymous SNV 1 3  2 3  74    2 4
synonymous SNV           21    1 1
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])

Top
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
chr12:6976727p.S36R3
chr12:6978532p.F145L,TPI12
chr12:6978441p.P45L,TPI11
chr12:6979473p.T176N,TPI11
chr12:6976815p.I49V,TPI11
chr12:6978443p.A182S,TPI11
chr12:6979488p.D86G,TPI11
chr12:6978046p.R206C,TPI11
chr12:6978455p.G88R,TPI11
chr12:6979535p.I207V,TPI11

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 TPI1 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]

Top
Gene Expression for TPI1

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

: Open all plots for all cancer types


Top
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

CCDC77,CDC20,CDCA3,DERA,EMG1,FOXM1,GAPDH,
LDHB,LTBR,MAGOHB,MLF2,MRPL51,NCAPD2,NDUFA9,
NOP2,PHB2,RAD51AP1,TEAD4,TPI1,UQCRH,USP5
AIMP2,AK1,ALDOA,CARM1,CCDC28B,COQ9,DYRK1B,
ENDOG,FKBP3,GAMT,GAPDH,MDH2,MYL6B,LINC00116,
NDUFS2,SH2B2,SHISA4,SLC25A11,TPI1,UBAC1,UQCRC1

ATP5B,CDCA3,COX6A1,EIF5A,EIF5AL1,ENO1,GAPDH,
H2AFZ,MLF2,MRPL51,NDUFA9,PGAM1,PHB2,PSMD9,
RAN,SRSF9,SLC25A3,TPI1,TUBA1B,TUBA1C,USP5
ANXA4,AP2S1,ASL,AURKAIP1,C2orf47,COX6B1,EDF1,
ETFB,GDI2,LMAN2,MDH2,MGST2,MPDU1,NDUFC1,
POP4,TACO1,TALDO1,EMC3,TMEM208,TPI1,UQCRC1
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

Top
check002.gifInteracting Genes (from Pathway Commons)

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

Top
Pharmacological Information for TPI1
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
DB01709triosephosphate isomerase 1experimental2-Phosphoglyceric Acid
DB01779triosephosphate isomerase 1experimentalGlycerol-2-Phosphate
DB02515triosephosphate isomerase 1experimental3-Phosphoglycerol
DB02726triosephosphate isomerase 1experimental2-Phosphoglycolic Acid
DB02951triosephosphate isomerase 1experimental3-Hydroxypyruvic Acid
DB04510triosephosphate isomerase 1experimental3-Phosphoglyceric Acid
DB01695triosephosphate isomerase 1experimentalN-Hydroxy-4-Phosphono-Butanamide
DB03026triosephosphate isomerase 1experimentalPhosphoglycolohydroxamic Acid
DB03132triosephosphate isomerase 1experimental3-(2-Benzothiazolylthio)-1-Propanesulfonic Acid
DB03135triosephosphate isomerase 1experimental[2(Formyl-Hydroxy-Amino)-Ethyl]-Phosphonic Acid
DB03314triosephosphate isomerase 1experimentalFluorotryptophane
DB03379triosephosphate isomerase 1experimental2-Carboxyethylphosphonic Acid
DB03900triosephosphate isomerase 1experimental2-Methyl-2-Propanol
DB04326triosephosphate isomerase 1experimental1,3-Dihydroxyacetonephosphate
DB04447triosephosphate isomerase 1experimental1,4-Dithiothreitol
DB07387triosephosphate isomerase 1experimental3-(BUTYLSULPHONYL)-PROPANOIC ACID
DB00121triosephosphate isomerase 1approved; nutraceuticalBiotin


Top
Cross referenced IDs for TPI1
* 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



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas