Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

Home

	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 PIK3R2

Basic gene info.	Gene symbol	PIK3R2
	Gene name	phosphoinositide-3-kinase, regulatory subunit 2 (beta)
	Synonyms	MPPH\|MPPH1\|P85B\|p85\|p85-BETA
	Cytomap	UCSC genome browser: 19q13.2-q13.4
	Genomic location	chr19 :18264015-18281343
	Type of gene	protein-coding
	RefGenes	NM_005027.3, NR_073517.1,
	Ensembl id	ENSG00000105647
	Description	PI3-kinase subunit p85-betaPI3K regulatory subunit betaphosphatidylinositol 3-kinase 85 kDa regulatory subunit betaphosphatidylinositol 3-kinase regulatory subunit betaphosphatidylinositol 3-kinase, regulatory subunit, polypeptide 2 (p85 beta)ptdIns-
	Modification date	20141207
dbXrefs	MIM : 603157
	HGNC : HGNC
	Ensembl : ENSG00000105647
	HPRD : 04404
	Vega : OTTHUMG00000183383
Protein	UniProt: O00459 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PIK3R2
	BioGPS: 5296
	Gene Expression Atlas: ENSG00000105647
	The Human Protein Atlas: ENSG00000105647
Pathway	NCI Pathway Interaction Database: PIK3R2
	KEGG: PIK3R2
	REACTOME: PIK3R2
	ConsensusPathDB
	Pathway Commons: PIK3R2
Metabolism	MetaCyc: PIK3R2
	HUMANCyc: PIK3R2
Regulation	Ensembl's Regulation: ENSG00000105647
	miRBase: chr19 :18,264,015-18,281,343
	TargetScan: NM_005027
	cisRED: ENSG00000105647
Context	iHOP: PIK3R2
	cancer metabolism search in PubMed: PIK3R2
	UCL Cancer Institute: PIK3R2
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

Top

Phenotypic Information for PIK3R2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PIK3R2
	Familial Cancer Database: PIK3R2

* 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/

Metabolic Pathway Description
KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_PI_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM	603157; gene. 603387; phenotype.
Orphanet	83473; Megalencephaly - polymicrogyria - postaxial polydactyly - hydrocephalus.
Disease	KEGG Disease: PIK3R2
	MedGen: PIK3R2 (Human Medical Genetics with Condition)
	ClinVar: PIK3R2
Phenotype	MGI: PIK3R2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PIK3R2

Mutations for PIK3R2

* 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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PIK3R2 related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
AA496625	PIK3R2	10	90	19	18288845	18288925	SETX	84	320	9	135150689	135153481
BG314628	PIK3R2	1	208	19	18286174	18288526	PIK3R2	206	435	19	18284631	18285931
BG545738	PIK3R2	3	156	19	18279228	18279560	ARIH1	144	745	15	72877991	72878594
BP385893	PIK3R2	1	220	19	18284637	18285922	CRYBA2	220	496	2	219854912	219855640
BF897883	PIK3R2	9	301	19	18284680	18287982	PIK3R2	299	452	19	18288001	18288572

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

Top

Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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)

Top

SNV 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=4

Top

Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=43)	Stat. for Synonymous SNVs (# total SNVs=19)

Stat. for Deletions (# total SNVs=3)	Stat. for Insertions (# total SNVs=2)

Top

Top 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 position	Mutation(aa)	Unique sampleID count
chr19:18273784-18273784	p.G373R	4
chr19:18274130-18274130	p.H450Y	3
chr19:18276981-18276981	p.M476I	3
chr19:18271301-18271301	p.P115S	2
chr19:18272854-18272854	p.A298A	2
chr19:18274111-18274111	p.G443G	2
chr19:18273857-18273857	p.S397F	2
chr19:18277996-18277996	p.R539H	2
chr19:18278043-18278043	p.E555K	1
chr19:18266968-18266968	p.P93P	1

Top

SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	2			3	2		3		2	2		5	6	2		1	6	9		11
# mutation	2			2	2		3		2	2		5	6	2		1	7	10		11
nonsynonymous SNV	1			1	2		3		2	1		2	4	1		1	4	8		6
synonymous SNV	1			1						1		3	2	1			3	2		5

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])

Top

Top 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 Position	Mutation(aa)	Unique sampleID count
chr19:18273784	p.P303P	2
chr19:18273019	p.R345W	2
chr19:18273240	p.G373R	2
chr19:18271916	p.E543V	1
chr19:18277087	p.G722C	1
chr19:18279596	p.A298V	1
chr19:18273314	p.R420L	1
chr19:18274130	p.D566Y	1
chr19:18272782	p.A298A	1
chr19:18277949	p.R420R	1

Other 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

Copy Number for PIK3R2 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]

Top

Gene Expression for PIK3R2

Gene 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.

Differential 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))

Top

CNV vs Gene Expression Plot

* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types

Top

Gene-Gene Network Information

Co-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


ARMC6,ASNA1,ATP13A1,KXD1,CRTC1,DDX49,EEF2, FAM32A,ISYNA1,KLHL26,LSM4,MPV17L2,NACC1,PIK3R2, PRKACA,RAB3D,RAB8A,RAVER1,SH3GL1,UPF1,WIZ	AGRN,AP1M2,DAK,FBXW9,H2AFY2,IPO4,KLRG2, LAD1,MARCKSL1,NCDN,NIPSNAP1,PAK4,PIK3R2,PKP3, PYCR1,RTKN,SEZ6L2,SLC35B2,SMARCA4,SMPDL3B,TMEM132A

ATAD3A,CEP131,BEND3,BTBD2,CARM1,CHERP,DGKZ, IVD,LONP1,MBD3,NCLN,PIK3R2,PRKCZ,PTCD1, RAB3D,RNF208,RRP1B,SAMD1,SLC19A1,SSBP4,TMEM161A	ABHD14B,BTBD2,FAM213B,CNNM3,COX19,FN3K,GAS6, GIT1,HOXA3,IGSF8,MEN1,NECAB3,PABPC1,PGAP2, PIK3R2,REPIN1,RNF43,RTKN,TIGD5,TP53I13,TYSND1

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

Top

Interacting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top

Pharmacological Information for PIK3R2

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Organism-specific databases	PharmGKB	PA33313; -.
Organism-specific databases	CTD	5296; -.

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB01064	phosphoinositide-3-kinase, regulatory subunit 2 (beta)	approved	Isoproterenol

Top

Cross referenced IDs for PIK3R2

* 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