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 PIK3R3

Basic gene info.	Gene symbol	PIK3R3
	Gene name	phosphoinositide-3-kinase, regulatory subunit 3 (gamma)
	Synonyms	p55\|p55-GAMMA
	Cytomap	UCSC genome browser: 1p34.1
	Genomic location	chr1 :46505811-46598708
	Type of gene	protein-coding
	RefGenes	NM_001114172.1, NM_003629.3,
	Ensembl id	ENSG00000117461
	Description	100% 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 date	20141207
dbXrefs	MIM : 606076
	HGNC : HGNC
	Ensembl : ENSG00000117461
	HPRD : 05831
	Vega : OTTHUMG00000008096
Protein	UniProt: Q92569 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PIK3R3
	BioGPS: 8503
	Gene Expression Atlas: ENSG00000117461
	The Human Protein Atlas: ENSG00000117461
Pathway	NCI Pathway Interaction Database: PIK3R3
	KEGG: PIK3R3
	REACTOME: PIK3R3
	ConsensusPathDB
	Pathway Commons: PIK3R3
Metabolism	MetaCyc: PIK3R3
	HUMANCyc: PIK3R3
Regulation	Ensembl's Regulation: ENSG00000117461
	miRBase: chr1 :46,505,811-46,598,708
	TargetScan: NM_001114172
	cisRED: ENSG00000117461
Context	iHOP: PIK3R3
	cancer metabolism search in PubMed: PIK3R3
	UCL Cancer Institute: PIK3R3
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for PIK3R3(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_PI_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM	606076; gene.
Orphanet
Disease	KEGG Disease: PIK3R3
	MedGen: PIK3R3 (Human Medical Genetics with Condition)
	ClinVar: PIK3R3
Phenotype	MGI: PIK3R3 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	PIK3R3	chr1	46506999	46507019		chr1	921843	921863
ovary	PIK3R3	chr1	46577155	46577175		chr1	94301551	94301571
pancreas	PIK3R3	chr1	46569328	46569348	PIK3R3	chr1	46576457	46576477

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 PIK3R3 related fusion information.

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

BE515277

UQCRH

502

46769360

46775989

PIK3R3

502

708

46519492

46519698

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

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)

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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=3

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Somatic 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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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
chr1:46521530-46521530	p.K293T	3
chr1:46512277-46512277	p.V321A	3
chr1:46527688-46527688	p.F226Y	2
chr1:46512262-46512262	p.L326R	2
chr1:46511630-46511630	p.R383C	2
chr1:46521517-46521517	p.S297S	2
chr1:46527650-46527650	p.E239*	2
chr1:46509434-46509434	p.Q433K	1
chr1:46527683-46527683	p.E228K	1
chr1:46511683-46511683	p.R365L	1

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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=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		3		7	1		3					4	1				2	4		5
# mutation		2		9	1		3					4	1				2	5		5
nonsynonymous SNV		2		6	1		3					4	1				2	4		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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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
chr1:46512262	p.R383C,PIK3R3	2
chr1:46521530	p.L326R,PIK3R3	2
chr1:46511630	p.K293T,PIK3R3	2
chr1:46509456	p.G414D,PIK3R3	1
chr1:46543232	p.S265L,PIK3R3	1
chr1:46509490	p.G412G,PIK3R3	1
chr1:46521491	p.E201K,PIK3R3	1
chr1:46546384	p.V396A,PIK3R3	1
chr1:46509495	p.S192R,PIK3R3	1
chr1:46521524	p.P127L,PIK3R3	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 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

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


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

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 PIK3R3

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Organism-specific databases	PharmGKB	PA33314; -.
Organism-specific databases	CTD	8503; -.

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 3 (gamma)	approved	Isoproterenol

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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