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 PIK3R3
Basic gene info.Gene symbolPIK3R3
Gene namephosphoinositide-3-kinase, regulatory subunit 3 (gamma)
Synonymsp55|p55-GAMMA
CytomapUCSC genome browser: 1p34.1
Genomic locationchr1 :46505811-46598708
Type of geneprotein-coding
RefGenesNM_001114172.1,
NM_003629.3,
Ensembl idENSG00000117461
Description100% homology to SWISS-PROT Q92569PI3-kinase regulatory subunit gammaPI3-kinase subunit p55-gammaPI3K regulatory subunit gammap55PIKphosphatidylinositol 3-kinase 55 kDa regulatory subunit gammaphosphatidylinositol 3-kinase regulatory subunit gammap
Modification date20141207
dbXrefs MIM : 606076
HGNC : HGNC
Ensembl : ENSG00000117461
HPRD : 05831
Vega : OTTHUMG00000008096
ProteinUniProt: Q92569
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PIK3R3
BioGPS: 8503
Gene Expression Atlas: ENSG00000117461
The Human Protein Atlas: ENSG00000117461
PathwayNCI Pathway Interaction Database: PIK3R3
KEGG: PIK3R3
REACTOME: PIK3R3
ConsensusPathDB
Pathway Commons: PIK3R3
MetabolismMetaCyc: PIK3R3
HUMANCyc: PIK3R3
RegulationEnsembl's Regulation: ENSG00000117461
miRBase: chr1 :46,505,811-46,598,708
TargetScan: NM_001114172
cisRED: ENSG00000117461
ContextiHOP: PIK3R3
cancer metabolism search in PubMed: PIK3R3
UCL Cancer Institute: PIK3R3
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for PIK3R3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PIK3R3
Familial Cancer Database: PIK3R3
* 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_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS
REACTOME_PHOSPHOLIPID_METABOLISM
REACTOME_PI_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM 606076; gene.
Orphanet
DiseaseKEGG Disease: PIK3R3
MedGen: PIK3R3 (Human Medical Genetics with Condition)
ClinVar: PIK3R3
PhenotypeMGI: PIK3R3 (International Mouse Phenotyping Consortium)
PhenomicDB: PIK3R3

Mutations for PIK3R3
* 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
ovaryPIK3R3chr14650699946507019chr1921843921863
ovaryPIK3R3chr14657715546577175chr19430155194301571
pancreasPIK3R3chr14656932846569348PIK3R3chr14657645746576477
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 PIK3R3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE515277UQCRH3450214676936046775989PIK3R350270814651949246519698

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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=39)
Stat. for Synonymous SNVs
(# total SNVs=6)
Stat. for Deletions
(# total SNVs=3)
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
chr1:46521530-46521530p.K293T3
chr1:46512277-46512277p.V321A3
chr1:46511630-46511630p.R383C2
chr1:46521517-46521517p.S297S2
chr1:46527650-46527650p.E239*2
chr1:46527688-46527688p.F226Y2
chr1:46512262-46512262p.L326R2
chr1:46521491-46521491p.R306Q1
chr1:46509358-46509358p.S458L1
chr1:46521644-46521644p.?1

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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
# sample 3 71 3    41   24 5
# mutation 2 91 3    41   25 5
nonsynonymous SNV 2 61 3    41   24 4
synonymous SNV   3             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])

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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
chr1:46512262p.K293T,PIK3R32
chr1:46521530p.R383C,PIK3R32
chr1:46511630p.L326R,PIK3R32
chr1:46531746p.S458S,PIK3R31
chr1:46509395p.R306Q,PIK3R31
chr1:46511683p.V446I,PIK3R31
chr1:46531771p.M295T,PIK3R31
chr1:46509434p.Q433K,PIK3R31
chr1:46511694p.H431Y,PIK3R31
chr1:46532698p.Q284H,PIK3R31

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 PIK3R3 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 PIK3R3

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

AKIRIN1,AQR,CACUL1,CAP1,RHOV___CHP1,DTWD2,GPBP1L1,
IPP,KDM4A,KIAA1522,MTF1,NFIA,NRD1,NSUN4,
PIK3R3,RLF,RNF11,SRBD1,TC2N,YIPF1,ZMPSTE24
ADAM15,ASRGL1,CBX2,FAM124A,GJA5,GPR85,KCTD12,
LAP3,MALL,MYD88,NR2F2,PCDH1,PIK3R3,RAPGEF5,
SELP,SEPN1,SPNS2,SYT15,TRPM6,VEGFC,ZBTB46

AGL,ARSJ,DAPP1,DCLK2,ESAM,HIPK1,ICMT,
IL18R1,JAK1,LRRC8C,LUZP1,MTF1,PIK3R3,PNPLA3,
SASH1,PEAK1,SH2B3,SMAD1,SMAP2,TXLNA,WDR7
ACTB,APBB2,LINC00346,COL18A1,COL6A3,DDX24,DLC1,
EHBP1L1,LATS2,LRRC8A,NES,NFKB2,PCDHB13,PCDHGB2,
PIK3R3,PLEKHG2,RASIP1,SVEP1,TFE3,TMEM158,WISP1
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 PIK3R3
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA33314; -.
Organism-specific databasesCTD 8503; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB01064phosphoinositide-3-kinase, regulatory subunit 3 (gamma)approvedIsoproterenol


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Cross referenced IDs for PIK3R3
* 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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