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

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 PIK3R1

Basic gene info.	Gene symbol	PIK3R1
	Gene name	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)
	Synonyms	AGM7\|GRB1\|IMD36\|p85\|p85-ALPHA
	Cytomap	UCSC genome browser: 5q13.1
	Genomic location	chr5 :67586466-67597649
	Type of gene	protein-coding
	RefGenes	NM_001242466.1, NM_181504.3,NM_181523.2,NM_181524.1,
	Ensembl id	ENSG00000145675
	Description	PI3-kinase subunit p85-alphaPI3K regulatory subunit alphaphosphatidylinositol 3-kinase 85 kDa regulatory subunit alphaphosphatidylinositol 3-kinase regulatory subunit alphaphosphatidylinositol 3-kinase, regulatory subunit, polypeptide 1 (p85 alpha)ph
	Modification date	20141221
dbXrefs	MIM : 171833
	HGNC : HGNC
	Ensembl : ENSG00000145675
	HPRD : 01381
	Vega : OTTHUMG00000131251
Protein	UniProt: P27986 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PIK3R1
	BioGPS: 5295
	Gene Expression Atlas: ENSG00000145675
	The Human Protein Atlas: ENSG00000145675
Pathway	NCI Pathway Interaction Database: PIK3R1
	KEGG: PIK3R1
	REACTOME: PIK3R1
	ConsensusPathDB
	Pathway Commons: PIK3R1
Metabolism	MetaCyc: PIK3R1
	HUMANCyc: PIK3R1
Regulation	Ensembl's Regulation: ENSG00000145675
	miRBase: chr5 :67,586,466-67,597,649
	TargetScan: NM_001242466
	cisRED: ENSG00000145675
Context	iHOP: PIK3R1
	cancer metabolism search in PubMed: PIK3R1
	UCL Cancer Institute: PIK3R1
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of PIK3R1 in cancer cell metabolism	1. Hellwinkel OJ, Rogmann JP, Asong LE, Luebke AM, Eichelberg C, et al. (2008) A comprehensive analysis of transcript signatures of the phosphatidylinositol‐3 kinase/protein kinase B signal‐transduction pathway in prostate cancer. BJU international 101: 1454-1460. go to article

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Phenotypic Information for PIK3R1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PIK3R1
	Familial Cancer Database: PIK3R1

* 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, UCEC ⁸, GBM ⁹,	Therapeutic Vulnerabilities in Cancer¹⁰

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 http://www.nature.com/nature/journal/v497/n7447/full/nature12113.html,
9 http://www.nejm.org/doi/full/10.1056/NEJMoa1402121,
10Therapeutic 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	171833; gene. 171833; gene. 269880; phenotype. 269880; phenotype. 615214; phenotype. 615214; phenotype.
Orphanet	3163; SHORT syndrome. 3163; SHORT syndrome. 33110; Autosomal agammaglobulinemia. 33110; Autosomal agammaglobulinemia.
Disease	KEGG Disease: PIK3R1
	MedGen: PIK3R1 (Human Medical Genetics with Condition)
	ClinVar: PIK3R1
Phenotype	MGI: PIK3R1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PIK3R1

Mutations for PIK3R1

* 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

- Statistics for Tissue and Mutation type

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- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
breast	PIK3R1	chr5	67587611	67587611		chr16	74740421	74740421
central_nervous_system	PIK3R1	chr5	67590608	67590608		chr5	67465996	67465996

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PIK3R1 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
BF849250	LRCH1	6	162	13	47155365	47155523	PIK3R1	144	440	5	67593268	67593562
BX648791	NFIA	1	4560	1	61817423	61821979	PIK3R1	4560	5386	5	67593366	67594192
BU742563	PIK3R1	8	278	5	67594299	67594570	PIK3R1	272	651	5	67595900	67596280

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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

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

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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=13

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=251)	Stat. for Synonymous SNVs (# total SNVs=27)

Stat. for Deletions (# total SNVs=97)	Stat. for Insertions (# total SNVs=31)

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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
chr5:67588951-67588951	p.R348*	22
chr5:67589138-67589138	p.G376R	12
chr5:67591106-67591106	p.K567E	8
chr5:67591246-67591246	p.?	7
chr5:67591097-67591097	p.N564D	7
chr5:67591086-67591086	p.D560G	7
chr5:67592108-67592108	p.R642*	6
chr5:67591128-67591128	p.R574I	6
chr5:67591125-67591125	p.L573P	6
chr5:67589628-67589628	p.D464G	6

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SNV Counts per Each Loci in TCGA data

: non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=8

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	9	1	48	16		4		2	2		6	3	2			6	6	1	27
# mutation	2	9	1	35	11		4		2	3		6	3	2			6	6	1	28
nonsynonymous SNV	2	8	1	24	10		4		2	1		2	2	1			2	6	1	25
synonymous SNV		1		11	1					2		4	1	1			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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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
chr5:67589138	p.G13R,PIK3R1	8
chr5:67589628	p.D101G,PIK3R1	7
chr5:67591097	p.N201D,PIK3R1	7
chr5:67591086	p.D197G,PIK3R1	5
chr5:67591106	p.L210P,PIK3R1	3
chr5:67590446	p.R211G,PIK3R1	3
chr5:67591125	p.R140L,PIK3R1	3
chr5:67591127	p.K204E,PIK3R1	3
chr5:67589627	p.K96E,PIK3R1	2
chr5:67591034	p.K96K,PIK3R1	2

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 PIK3R1 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 PIK3R1

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))

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CNV 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

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


ARID5B,ARRDC3,ATF7,MIR99AHG,DST,FRMD4B,IQGAP2, MTUS1,NUMB,PDZD2,PIK3R1,PJA2,PRDM2,RBMS3, RFX7,SH3RF2,SP1,TLR3,TSHZ2,UTRN,YAP1	EPC2,FAM13B,FNBP1L,HPS5,GLTSCR1L,KANSL1,MAML2, OGFRL1,PIK3R1,PLCB1,PUM1,RNF169,THUMPD1,TUG1, ZNF136,ZNF197,ZNF268,ZNF430,ZNF677,ZNF84,ZZZ3

ARL15,ATAD2B,DNMT3A,FOXO3B,GDF10,GOLIM4,KCTD16, KRT32,KRT38,MYL3,MYO10,NAV2,NCKAP5,NRXN3, OLFML3,PHYHIPL,PIK3R1,PRSS23,STK38L,TP53BP1,UGT2A3	AP3B2,ATP2B3,ATXN1,CDH2,CNR1,CRMP1,DNAJC6, DPYSL5,EZH1,GFRA1,LGI3,LIFR,NCAM2,PCDHA3, JADE1,PIK3R1,PJA2,RBPJ,RNF38,SEZ6L,WDR47

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

: Open all plots for all cancer types

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Interacting 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 PIK3R1

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	P27986; -.
Chemistry	ChEMBL	CHEMBL2111367; -.
Chemistry	BindingDB	P27986; -.
Chemistry	ChEMBL	CHEMBL2111367; -.
Organism-specific databases	PharmGKB	PA33312; -.
Organism-specific databases	PharmGKB	PA33312; -.
Organism-specific databases	CTD	5295; -.
Organism-specific databases	CTD	5295; -.

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 1 (alpha)	approved	Isoproterenol
DB08059	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	experimental	(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
DB00171	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	approved; nutraceutical	Adenosine triphosphate
DB00877	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	approved; investigational	Sirolimus
DB00122	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	approved; nutraceutical	Choline
DB00394	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	approved	Beclomethasone
DB00443	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	approved	Betamethasone
DB01222	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	approved; investigational	Budesonide
DB01410	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	approved; investigational	Ciclesonide
DB01260	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	approved; investigational	Desonide
DB01234	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	approved; investigational	Dexamethasone
DB00180	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	approved; investigational	Flunisolide
DB00588	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	approved; investigational	Fluticasone Propionate
DB00741	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	approved	Hydrocortisone
DB00959	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	approved	Methylprednisolone
DB00764	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	approved	Mometasone
DB01384	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	approved	Paramethasone
DB00860	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	approved	Prednisolone
DB00635	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	approved	Prednisone
DB00896	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	approved	Rimexolone
DB00620	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	approved	Triamcinolone
DB00131	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	approved; nutraceutical	Adenosine monophosphate
DB00125	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	approved; nutraceutical	L-Arginine
DB00155	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	approved; nutraceutical	L-Citrulline
DB00435	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	approved	Nitric Oxide
DB00864	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	approved; investigational	Tacrolimus
DB00619	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	approved	Imatinib

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Cross referenced IDs for PIK3R1

* 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