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 TPTE2
Basic gene info.Gene symbolTPTE2
Gene nametransmembrane phosphoinositide 3-phosphatase and tensin homolog 2
SynonymsTPIP
CytomapUCSC genome browser: 13q12.11
Genomic locationchr13 :19997018-20110903
Type of geneprotein-coding
RefGenesNM_199255.1,
NM_001141968.1,NM_001271850.1,NM_130785.3,NM_199254.2,
NR_073485.1,NR_073486.1,NR_073487.1,
Ensembl idENSG00000132958
DescriptionPTEN-like inositol lipid phosphataseTPIP lipid phosphataseTPTE and PTEN homologous inositol lipid phosphataselipid phosphatase TPIPphosphatidylinositol 3,4,5-trisphosphate 3-phosphatase TPTE2phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase TPTE
Modification date20141207
dbXrefs MIM : 606791
HGNC : HGNC
Ensembl : ENSG00000132958
HPRD : 06003
Vega : OTTHUMG00000016493
ProteinUniProt: Q6XPS3
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_TPTE2
BioGPS: 93492
Gene Expression Atlas: ENSG00000132958
The Human Protein Atlas: ENSG00000132958
PathwayNCI Pathway Interaction Database: TPTE2
KEGG: TPTE2
REACTOME: TPTE2
ConsensusPathDB
Pathway Commons: TPTE2
MetabolismMetaCyc: TPTE2
HUMANCyc: TPTE2
RegulationEnsembl's Regulation: ENSG00000132958
miRBase: chr13 :19,997,018-20,110,903
TargetScan: NM_199255
cisRED: ENSG00000132958
ContextiHOP: TPTE2
cancer metabolism search in PubMed: TPTE2
UCL Cancer Institute: TPTE2
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for TPTE2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: TPTE2
Familial Cancer Database: TPTE2
* 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 GBM 6,

Therapeutic Vulnerabilities in Cancer7

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,
6 http://www.sciencedirect.com/science/article/pii/S0092867413012087,
7Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

check002.gifMetabolic Pathway Description
REACTOME_PHOSPHOLIPID_METABOLISM
REACTOME_PI_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM 606791; gene.
606791; gene.
Orphanet
DiseaseKEGG Disease: TPTE2
MedGen: TPTE2 (Human Medical Genetics with Condition)
ClinVar: TPTE2
PhenotypeMGI: TPTE2 (International Mouse Phenotyping Consortium)
PhenomicDB: TPTE2

Mutations for TPTE2
* 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
ovaryTPTE2chr132002874020028760TBC1D4chr137586595175865971
pancreasTPTE2chr132009819720098217chr132011302520113045
pancreasTPTE2chr132010087020100890chr132515137725151397
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 TPTE2 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     2 1 1      
GAIN (# sample)1     2          
LOSS (# sample)        1 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=9

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=86)
Stat. for Synonymous SNVs
(# total SNVs=20)
Stat. for Deletions
(# total SNVs=1)
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
chr13:20012252-20012252p.E262K9
chr13:20025334-20025334p.R181Q7
chr13:20067011-20067011p.L33R5
chr13:20039688-20039688p.R100*5
chr13:20067033-20067033p.S26G4
chr13:20048070-20048070p.R89*4
chr13:20006719-20006719p.?4
chr13:20006620-20006620p.S328S4
chr13:19997210-19997210p.E444K3
chr13:20006680-20006680p.L308L3

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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=5

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample32 145 6 6 110103 33214214
# mutation32 125 6 7 110103 33513119
nonsynonymous SNV22 115 3 6 1882 32811115
synonymous SNV1  1  3 1  221  72 4
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
chr13:20012252p.E10K,TPTE25
chr13:20025334p.R181Q,TPTE25
chr13:20056687p.S40R,TPTE24
chr13:20067596p.M41V,TPTE23
chr13:20067628p.G79A,TPTE23
chr13:20048099p.A19A,TPTE23
chr13:20056686p.E9K,TPTE23
chr13:19997208p.G122R,TPTE22
chr13:20025355p.E192D,TPTE22
chr13:20039417p.R193I,TPTE22

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 TPTE2 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 TPTE2

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

AGMAT,BAIAP2L2,LINC00473,TMEM252,CDH17,CTH,DEFA6,
HNF4A,HULC,LGALS4,LOC100101938,LY6G6D,MEP1A,MOGAT3,
MUC13,OR2L1P,PRODH,SPANXC,TPTE2,TPTE2P3,VIL1
BTN3A1,CTLA4,CXorf65,FLJ40330,GABBR2,GML,HESX1,
HLA-DOB,INPP5B,LAG3,LAMP3,LOC100188949,LOC284749,PATL2,
PNOC,RUFY4,SLAMF6,SP100,SP110,TPTE2,ZBP1

ADAM6,CD180,CPNE5,DERL3,FCRL5,FLJ40330,IRF4,
KCNA3,KCNN3,KIAA0125,LAX1,LOC100233209,LOC96610,LTF,
MZB1,PARP15,PIM2,PNOC,SLAMF1,TPTE2,TRIM55
ADA,BFSP2,BTN1A1,C16orf74,C3orf20,CCR4,DOK3,
DTHD1,EOMES,KCNA3,KLHL6,LOC100233209,NLRP11,ORAI2,
PMS2P3,RASGRP3,RGS14,SUSD3,TLR6,TPTE2,TRAF3IP3
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 TPTE2


There's no related Drug.
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Cross referenced IDs for TPTE2
* 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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