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 PIK3CA
Basic gene info.Gene symbolPIK3CA
Gene namephosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha
SynonymsCLOVE|CWS5|MCAP|MCM|MCMTC|PI3K|p110-alpha
CytomapUCSC genome browser: 3q26.3
Genomic locationchr3 :178866310-178952497
Type of geneprotein-coding
RefGenesNM_006218.2,
Ensembl idENSG00000121879
DescriptionPI3-kinase p110 subunit alphaPI3K-alphaphosphatidylinositol 3-kinase, catalytic, 110-KD, alphaphosphatidylinositol 3-kinase, catalytic, alpha polypeptidephosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoformphosphatidylinosito
Modification date20141222
dbXrefs MIM : 171834
HGNC : HGNC
HPRD : 01382
ProteinUniProt: P42336
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PIK3CA
BioGPS: 5290
Gene Expression Atlas: ENSG00000121879
The Human Protein Atlas: ENSG00000121879
PathwayNCI Pathway Interaction Database: PIK3CA
KEGG: PIK3CA
REACTOME: PIK3CA
ConsensusPathDB
Pathway Commons: PIK3CA
MetabolismMetaCyc: PIK3CA
HUMANCyc: PIK3CA
RegulationEnsembl's Regulation: ENSG00000121879
miRBase: chr3 :178,866,310-178,952,497
TargetScan: NM_006218
cisRED: ENSG00000121879
ContextiHOP: PIK3CA
cancer metabolism search in PubMed: PIK3CA
UCL Cancer Institute: PIK3CA
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of PIK3CA in cancer cell metabolism1. Deming DA, Leystra AA, Farhoud M, Nettekoven L, Clipson L, et al. (2013) mTOR inhibition elicits a dramatic response in PI3K-dependent colon cancers. PLoS one 8: e60709. go to article
2. Fu X, Osborne CK, Schiff R (2013) Biology and therapeutic potential of PI3K signaling in ER+/HER2-negative breast cancer. The Breast 22: S12-S18. go to article

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Phenotypic Information for PIK3CA(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PIK3CA
Familial Cancer Database: PIK3CA
* 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 BLCA 6, BRCA 7, COAD 8, CRC 9, ESO 10, GBM 11, HNSC 12, KIRC 13, LUAD 14, LUSC 15, UCEC 16, STAD 17, GBM 18, HNSC 19,

Therapeutic Vulnerabilities in Cancer20

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/vaop/ncurrent/full/nature12965.html,
7 http://www.nature.com/nature/journal/v490/n7418/full/nature11412.html,
8 http://www.nature.com/nature/journal/v487/n7407/full/nature11252.html,
9 http://www.nature.com/nature/journal/v505/n7484/full/nature12912.html,
10 http://www.nature.com/nature/journal/v505/n7484/full/nature12912.html,
11 http://www.sciencedirect.com/science/article/pii/S0092867413012087,
12 https://www.sciencemag.org/content/333/6046/1157,
13 http://www.nature.com/nature/journal/v499/n7456/full/nature12222.html,
14 http://www.sciencedirect.com/science/article/pii/S0092867412010227,
15 http://www.nature.com/nature/journal/v489/n7417/full/nature11404.html,
16 http://www.nature.com/nature/journal/v497/n7447/full/nature12113.html,
17 http://www.nature.com/nature/journal/v513/n7517/full/nature13480.html,
18 http://www.nejm.org/doi/full/10.1056/NEJMoa1402121,
19 http://www.nature.com/nature/journal/v517/n7536/full/nature14129.html,
20Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

check002.gifMetabolic Pathway Description
KEGG_INOSITOL_PHOSPHATE_METABOLISM
KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS
REACTOME_PHOSPHOLIPID_METABOLISM
REACTOME_PI_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM 114480; phenotype.
114500; phenotype.
114550; phenotype.
167000; phenotype.
171834; gene.
182000; phenotype.
602501; phenotype.
612918; phenotype.
615108; phenotype.
Orphanet 140944; CLOVE syndrome.
144; Hereditary nonpolyposis colon cancer.
201; Cowden syndrome.
276280; Hemihyperplasia-multiple lipomatosis syndrome.
295239; Macrodactyly of fingers, unilateral.
295243; Macrodactyly of toes, unilateral.
314662; Segmental progressive overgrowth syndrome with fibroadipose hyperplasia.
60040; Megalencephaly-capillary malformation-polymicrogyria syndrome.
99802; Hemimegalencephaly.
DiseaseKEGG Disease: PIK3CA
MedGen: PIK3CA (Human Medical Genetics with Condition)
ClinVar: PIK3CA
PhenotypeMGI: PIK3CA (International Mouse Phenotyping Consortium)
PhenomicDB: PIK3CA

Mutations for PIK3CA
* 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
pancreasPIK3CAchr3178952260178952280chr3177916014177916034
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 PIK3CA related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CV347577DDX515360176249831362499340PIK3CA3516273178947888178951983
BI870214PPP2CA1083285133532781133533001PIK3CA3193413178893499178893521

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 # sample2  21 4 3 5     1
GAIN (# sample)2  1  3 3 5     1
LOSS (# sample)   11 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=2893

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=6717)
Stat. for Synonymous SNVs
(# total SNVs=182)
Stat. for Deletions
(# total SNVs=32)
Stat. for Insertions
(# total SNVs=30)

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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
chr3:178952085-178952085p.H1047R1918
chr3:178936091-178936091p.E545Q1181
chr3:178936082-178936082p.E542K766
chr3:178936092-178936092p.E545A224
chr3:178936094-178936094p.Q546E134
chr3:178916876-178916876p.R88Q89
chr3:178952074-178952074p.M1043I73
chr3:178936095-178936095p.Q546R70
chr3:178921553-178921553p.N345K67
chr3:178952084-178952084p.H1047Y54

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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=174

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample11249921628 63 162 19295 29492125
# mutation1143420923 23 112 17185 2834273
nonsynonymous SNV1039414423 23 112 14172 2730270
synonymous SNV14 69       313  14 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
chr3:178952085p.H1047R169
chr3:178936091p.E545K129
chr3:178936082p.E542K74
chr3:178921553p.R88Q23
chr3:178916876p.N345K23
chr3:178936095p.Q546R20
chr3:178938934p.E726K18
chr3:178917478p.G118D16
chr3:178928079p.E453Q14
chr3:178927980p.C420R12

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 PIK3CA 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 PIK3CA

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

AGPAT4,AMTN,ARG2,NPAP1,ABRACL,CENPW,CSN3,
DPPA5,FAM3D,FMO3,HEBP2,HIST1H4F,HYMAI,KCNMB2,
KCNMB3,LOC285205,OR5AU1,PIK3CA,PWRN1,TRPC2,ZMAT3
ARHGAP42,CDC42BPA,EXOC6B,KATNAL1,KCTD20,KLHL20,LNPEP,
MYCBP2,NR3C1,PBRM1,PIK3CA,PIKFYVE,PLEKHM3,PVRL3,
RAPGEF2,RBMS3,REV3L,SAMD8,SBF2,SLC30A4,SOS1

AKAP2,BBX,CREBRF,FAM168A,FAM63B,HEG1,HIPK3,
IL6ST,KIRREL,LRCH3,MYO5A,MYO9A,PIK3CA,PLEKHM3,
RASA2,REST,SNX29,TAOK1,TCF4,TTBK2,UBXN7
AKAP11,ATF7,CLASP1,CRTC3,DSTYK,DYNC1LI2,ERC1,
LAMC1,MACF1,MAP4,NAV2,NEK1,PDS5B,PIK3CA,
PTPN11,ROCK1,ROR1,SACS,TEAD1,TTBK2,UBE2H
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 PIK3CA
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P42336; -.
ChemistryChEMBL CHEMBL2111367; -.
ChemistryGuidetoPHARMACOLOGY 2153; -.
Organism-specific databasesPharmGKB PA33308; -.
Organism-specific databasesCTD 5290; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB08059phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alphaexperimental(1S,6BR,9AS,11R,11BR)-9A,11B-DIMETHYL-1-[(METHYLOXY)METHYL]-3,6,9-TRIOXO-1,6,6B,7,8,9,9A,10,11,11B-DECAHYDRO-3H-FURO[4,3,2-DE]INDENO[4,5-H][2]BENZOPYRAN-11-YL ACETATE
DB01248phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alphaapproved; investigationalDocetaxel
DB00171phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alphaapproved; nutraceuticalAdenosine triphosphate
DB00877phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alphaapproved; investigationalSirolimus
DB00122phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alphaapproved; nutraceuticalCholine
DB00394phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alphaapprovedBeclomethasone
DB00443phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alphaapprovedBetamethasone
DB01222phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alphaapproved; investigationalBudesonide
DB01410phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alphaapproved; investigationalCiclesonide
DB01260phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alphaapproved; investigationalDesonide
DB01234phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alphaapproved; investigationalDexamethasone
DB00180phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alphaapproved; investigationalFlunisolide
DB00588phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alphaapproved; investigationalFluticasone Propionate
DB00741phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alphaapprovedHydrocortisone
DB00959phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alphaapprovedMethylprednisolone
DB00764phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alphaapprovedMometasone
DB01384phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alphaapprovedParamethasone
DB00860phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alphaapprovedPrednisolone
DB00635phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alphaapprovedPrednisone
DB00896phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alphaapprovedRimexolone
DB00620phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alphaapprovedTriamcinolone
DB00131phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alphaapproved; nutraceuticalAdenosine monophosphate
DB00125phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alphaapproved; nutraceuticalL-Arginine
DB00155phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alphaapproved; nutraceuticalL-Citrulline
DB00435phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alphaapprovedNitric Oxide
DB00864phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alphaapproved; investigationalTacrolimus
DB00619phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alphaapprovedImatinib


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Cross referenced IDs for PIK3CA
* 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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