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 PIK3CB
Basic gene info.Gene symbolPIK3CB
Gene namephosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit beta
SynonymsP110BETA|PI3K|PI3KBETA|PIK3C1
CytomapUCSC genome browser: 3q22.3
Genomic locationchr3 :138371539-138478201
Type of geneprotein-coding
RefGenesNM_001256045.1,
NM_006219.2,
Ensembl idENSG00000051382
DescriptionPI3-kinase p110 subunit betaPI3-kinase subunit betaPI3K-betaPtdIns-3-kinase p110phosphatidylinositol 4,5-bisphosphate 3-kinase 110 kDa catalytic subunit betaphosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit beta isoformphosphatidylino
Modification date20141207
dbXrefs MIM : 602925
HGNC : HGNC
Ensembl : ENSG00000051382
HPRD : 04234
ProteinUniProt: P42338
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PIK3CB
BioGPS: 5291
Gene Expression Atlas: ENSG00000051382
The Human Protein Atlas: ENSG00000051382
PathwayNCI Pathway Interaction Database: PIK3CB
KEGG: PIK3CB
REACTOME: PIK3CB
ConsensusPathDB
Pathway Commons: PIK3CB
MetabolismMetaCyc: PIK3CB
HUMANCyc: PIK3CB
RegulationEnsembl's Regulation: ENSG00000051382
miRBase: chr3 :138,371,539-138,478,201
TargetScan: NM_001256045
cisRED: ENSG00000051382
ContextiHOP: PIK3CB
cancer metabolism search in PubMed: PIK3CB
UCL Cancer Institute: PIK3CB
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of PIK3CB in cancer cell metabolism1. Ciraolo E, Iezzi M, Marone R, Marengo S, Curcio C, et al. (2008) Phosphoinositide 3-kinase p110β activity: key role in metabolism and mammary gland cancer but not development. Science signaling 1: ra3. go to article

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Phenotypic Information for PIK3CB(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PIK3CB
Familial Cancer Database: PIK3CB
* 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_INOSITOL_PHOSPHATE_METABOLISM
KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS
REACTOME_PHOSPHOLIPID_METABOLISM
REACTOME_PI_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM 602925; gene.
Orphanet
DiseaseKEGG Disease: PIK3CB
MedGen: PIK3CB (Human Medical Genetics with Condition)
ClinVar: PIK3CB
PhenotypeMGI: PIK3CB (International Mouse Phenotyping Consortium)
PhenomicDB: PIK3CB

Mutations for PIK3CB
* 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
pancreasPIK3CBchr3138450037138450057SELTchr3150328141150328161
pancreasPIK3CBchr3138450573138450593CDKN2B-AS1chr92200347322003493
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 PIK3CB 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 # sample        1        
GAIN (# sample)        1        
LOSS (# sample)                 
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=6

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=93)
Stat. for Synonymous SNVs
(# total SNVs=16)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=2)

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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
chr3:138400818-138400818p.L832W5
chr3:138374293-138374293p.E1051K4
chr3:138453486-138453486p.R321Q4
chr3:138374244-138374244p.D1067A4
chr3:138384011-138384011p.R847C3
chr3:138382764-138382764p.V927A3
chr3:138409866-138409866p.G671E2
chr3:138413754-138413754p.?2
chr3:138453578-138453578p.K290N2
chr3:138461575-138461575p.R149Q2

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample25 83 6 321934  96111
# mutation55 84 6 321934  109113
nonsynonymous SNV45 54 5 311824  77113
synonymous SNV1  3  1  1 11   32  
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
chr3:138374244p.D579A,PIK3CB3
chr3:138374293p.R359C,PIK3CB2
chr3:138453486p.K290N2
chr3:138384011p.E563K,PIK3CB2
chr3:138453578p.G252W2
chr3:138426123p.E470K2
chr3:138478104p.G28S2
chr3:138456596p.R321Q2
chr3:138376532p.T567A,PIK3CB1
chr3:138433362p.E66K,PIK3CB1

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 PIK3CB 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 PIK3CB

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

ARMC8,ATP6V1A,ATR,DBR1,DCUN1D1,DNAJC13,GSK3B,
KIAA2018,KPNA1,LRRC58,MAP3K2,OSBPL11,PIK3CB,PIK3R4,
PTPLB,STAG1,STRN,UBXN7,XRN1,ZBTB11,ZNF148
AP3M1,APPBP2,C6orf120,CD164,CDC73,DLG1,EXOC5,
FAM160B1,KIAA1715,PIK3CB,PKN2,PRKAR1A,REEP3,SERINC1,
SERINC3,SHOC2,TBC1D23,UBE4A,USP33,YIPF4,ZHX1

ACAP2,ATP11B,ATP2C1,CD2AP,CTNND1,DCUN1D1,DNAJC13,
GOLGA4,GSK3B,KALRN,KIAA2018,LIPH,MAP3K13,OSBPL11,
PAK2,PIK3CB,PIK3R4,PLS1,PTPLB,SENP2,ZNF148
CD2AP,CDCP1,CDH1,CORO2A,CTNND1,TMEM236,GCC2,
ITFG1,KIF3B,LASP1,LIMA1,MGAT4A,MOB3B,MYO6,
NCSTN,NR3C2,NUMB,PDCD6IP,PIK3CB,PLS1,TAOK3
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 PIK3CB


There's no related Drug.
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Cross referenced IDs for PIK3CB
* 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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