Cancer Cell Metabolism Gene Database

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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 PTEN
Basic gene info.Gene symbolPTEN
Gene namephosphatase and tensin homolog
Synonyms10q23del|BZS|CWS1|DEC|GLM2|MHAM|MMAC1|PTEN1|TEP1
CytomapUCSC genome browser: 10q23.3
Genomic locationchr10 :89623194-89728532
Type of geneprotein-coding
RefGenesNM_000314.4,
Ensembl idENSG00000171862
DescriptionMMAC1 phosphatase and tensin homolog deleted on chromosome 10mitochondrial PTENalphamitochondrial phosphatase and tensin protein alphamutated in multiple advanced cancers 1phosphatase and tensin-like proteinphosphatidylinositol 3,4,5-trisphosphate 3-
Modification date20141222
dbXrefs MIM : 601728
HGNC : HGNC
HPRD : 03431
ProteinUniProt: P60484
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PTEN
BioGPS: 5728
Gene Expression Atlas: ENSG00000171862
The Human Protein Atlas: ENSG00000171862
PathwayNCI Pathway Interaction Database: PTEN
KEGG: PTEN
REACTOME: PTEN
ConsensusPathDB
Pathway Commons: PTEN
MetabolismMetaCyc: PTEN
HUMANCyc: PTEN
RegulationEnsembl's Regulation: ENSG00000171862
miRBase: chr10 :89,623,194-89,728,532
TargetScan: NM_000314
cisRED: ENSG00000171862
ContextiHOP: PTEN
cancer metabolism search in PubMed: PTEN
UCL Cancer Institute: PTEN
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of PTEN in cancer cell metabolism1. Liang H, He S, Yang J, Jia X, Wang P, et al. (2014) PTEN╬▒, a PTEN isoform translated through alternative initiation, regulates mitochondrial function and energy metabolism. Cell metabolism 19: 836-848. go to article
2. Vignarajan S, Xie C, Yao M, Sun Y, Simanainen U, et al. (2014) Loss of PTEN stabilizes the lipid modifying enzyme cytosolic phospholipase A2╬▒ via AKT in prostate cancer cells. Oncotarget 5: 6289. go to article
3. Ciuffreda L, Falcone I, Incani UC, Del Curatolo A, Conciatori F, et al. (2014) PTEN expression and function in adult cancer stem cells and prospects for therapeutic targeting. Advances in biological regulation 56: 66-80. go to article
4. Morani F, Phadngam S, Follo C, Titone R, Thongrakard V, et al. (2014) PTEN deficiency and mutant p53 confer glucose-addiction to thyroid cancer cells: impact of glucose depletion on cell proliferation, cell survival, autophagy and cell migration. Genes & cancer 5: 226. go to article

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Phenotypic Information for PTEN(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PTEN
Familial Cancer Database: PTEN
* 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 BRCA 6, GBM 7, HNSC 8, KIRC 9, LUSC 10, MEL 11, UCEC 12, STAD 13, SKCM 14, THCA 15, GBM 16,

Therapeutic Vulnerabilities in Cancer17

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.nature.com/nature/journal/v490/n7418/full/nature11412.html,
7 http://www.sciencedirect.com/science/article/pii/S0092867413012087,
8 https://www.sciencemag.org/content/333/6046/1157,
9 http://www.nature.com/nature/journal/v499/n7456/full/nature12222.html,
10 http://www.nature.com/nature/journal/v489/n7417/full/nature11404.html,
11 http://www.nature.com/nature/journal/v505/n7484/full/nature12912.html,
12 http://www.nature.com/nature/journal/v497/n7447/full/nature12113.html,
13 http://www.nature.com/nature/journal/v513/n7517/full/nature13480.html,
14 http://www.sciencedirect.com/science/article/pii/S0092867415006340,
15 http://www.sciencedirect.com/science/article/pii/S0092867414012380,
16 http://www.nejm.org/doi/full/10.1056/NEJMoa1402121,
17Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

check002.gifMetabolic Pathway Description
KEGG_INOSITOL_PHOSPHATE_METABOLISM
REACTOME_PHOSPHOLIPID_METABOLISM
REACTOME_PI_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM 137800; phenotype.
153480; phenotype.
158350; phenotype.
176807; phenotype.
275355; phenotype.
276950; phenotype.
601728; gene.
605309; phenotype.
608089; phenotype.
612242; phenotype.
613028; phenotype.
Orphanet 109; Bannayan-Riley-Ruvalcaba syndrome.
137608; Segmental outgrowth - lipomatosis - arteriovenous malformation - epidermal nevus.
145; Hereditary breast and ovarian cancer syndrome.
201; Cowden syndrome.
210548; Macrocephaly-autism syndrome.
2969; Proteus-like syndrome.
65285; Lhermitte-Duclos disease.
67037; Squamous cell carcinoma of head and neck.
744; Proteus syndrome.
79076; Juvenile polyposis of infancy.
DiseaseKEGG Disease: PTEN
MedGen: PTEN (Human Medical Genetics with Condition)
ClinVar: PTEN
PhenotypeMGI: PTEN (International Mouse Phenotyping Consortium)
PhenomicDB: PTEN

Mutations for PTEN
* 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
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- 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
breastPTENchr108967413289674132PTENchr108969215089692150
central_nervous_systemPTENchr108963286489632864PTENchr108969805589698055
large_intestinePTENchr108965205389652053chr108974250389742503
ovaryPTENchr108962889689628916RNLSchr109008638090086400
ovaryPTENchr108965637089656390chr8137548339137548359
ovaryPTENchr108968088489680904PTENchr108965354089653560
ovaryPTENchr108970222389702243PTENchr108968832789688347
pancreasPTENchr108962831589628335PTENchr108963080789630827
pancreasPTENchr108967565789675677PTENchr108967993089679950
pancreasPTENchr108971274989712769chr109036886890368888
prostatePTENchr108962566189627661PCGF5chr109300014493002144
prostatePTENchr108962627289626272chr109144282591442825
prostatePTENchr108962766489629664chr1160692788160694788
prostatePTENchr108966629089666290PANK1chr109133964291339642
skinPTENchr108970029989700299PTENchr108971234189712341
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 PTEN related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BI823499SEC31A145948379988183812291PTEN456804108972504289725387
BG610830PTEN1640108972595989726595PEBP163268812118582915118582972

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 # sample1313 5 54 6 3 561  
GAIN (# sample)   1 11          
LOSS (# sample)1313 4 43 6 3 561  
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=246

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=1833)
Stat. for Synonymous SNVs
(# total SNVs=170)
Stat. for Deletions
(# total SNVs=641)
Stat. for Insertions
(# total SNVs=289)

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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
chr10:89692904-89692904p.R130G177
chr10:89692905-89692905p.R130P125
chr10:89717672-89717672p.R233fs*2598
chr10:89717775-89717775p.K267fs*947
chr10:89711899-89711899p.R173C42
chr10:89720799-89720802p.T319fs*137
chr10:89720817-89720817p.N323fs*2131
chr10:89624227-89725229p.0?28
chr10:89720817-89720818p.N323fs*227
chr10:89720852-89720852p.R335*27

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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=60

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample28 20751 3281 76212812188
# mutation27 24946 3281 68212816158
nonsynonymous SNV27 17446 3281 68212812155
synonymous SNV   77             4 3
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
chr10:89692905p.R130Q34
chr10:89692904p.R130G26
chr10:89725072p.E352G11
chr10:89692923p.C136F8
chr10:89720700p.E284G7
chr10:89692791p.K128R6
chr10:89692899p.D92G6
chr10:89692863p.E150A6
chr10:89692965p.D116G6
chr10:89653819p.R161R5

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 PTEN 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 PTEN

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.
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check002.gifProtein Expression Plot (RPPA)
*RPPA protein expression data were extracted from TCPA (The Cancer Proteome Atlas). Normalized data based on replicated based normalization (RBN) was used to draw following figures.

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

ATAD1,ATF7,BMPR2,CREB1,DTWD2,FAM160B1,GNG12,
KLLN,MFAP3,PJA2,PTEN,PTENP1,RFX7,SH3D19,
SLK,SP1,TCF12,TM9SF3,WAPAL,ZEB1,ZNF484
ABHD5,ACER3,ACVR1C,ADH5,ADRBK2,AZI2,BNIP3L,
CD302,CEPT1,COL4A3BP,EIF4EBP2,EPB41L4B,FAM13A,FOXN2,
GNAI1,GPR180,KLLN,PTEN,PTENP1,SLC7A6,STON1

ATAD1,BTRC,WBP1L,CHUK,CPEB3,FAM160B1,FAM178A,
GBF1,KLLN,PCGF5,PTEN,PTENP1,SEL1L,SH3PXD2A,
SHOC2,SLK,SUFU,TCTN3,TNKS2,TRIM8,WAPAL
CNOT6L,COL4A3BP,CSNK2A1,CSNK2A3,HOXB5,LOC90110,METTL7A,
NBR1,PHF3,PPP1R3D,PTEN,PTENP1,PTPRA,PUM2,
RSBN1,RTN3,SATL1,SP3,STX6,TAB2,ZNF490
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 PTEN
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P60484; -.
ChemistryChEMBL CHEMBL2052032; -.
Organism-specific databasesPharmGKB PA33942; -.
Organism-specific databasesCTD 5728; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00877phosphatase and tensin homologapproved; investigationalSirolimus
DB00619phosphatase and tensin homologapprovedImatinib
DB00201phosphatase and tensin homologapprovedCaffeine
DB00515phosphatase and tensin homologapprovedCisplatin
DB01248phosphatase and tensin homologapproved; investigationalDocetaxel
DB00544phosphatase and tensin homologapprovedFluorouracil
DB00650phosphatase and tensin homologapprovedLeucovorin
DB00848phosphatase and tensin homologapprovedLevamisole
DB01132phosphatase and tensin homologapproved; investigationalPioglitazone
DB00412phosphatase and tensin homologapproved; investigationalRosiglitazone


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Cross referenced IDs for PTEN
* 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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