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 PIK3CG

Basic gene info.	Gene symbol	PIK3CG
	Gene name	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma
	Synonyms	PI3CG\|PI3K\|PI3Kgamma\|PIK3\|p110gamma\|p120-PI3K
	Cytomap	UCSC genome browser: 7q22.3
	Genomic location	chr7 :106505923-106547592
	Type of gene	protein-coding
	RefGenes	NM_001282426.1, NM_001282427.1,NM_002649.3,
	Ensembl id	ENSG00000105851
	Description	1-phosphatidylinositol 3-kinasePI3-kinase subunit gammaphosphatidylinositol 3 kinase gamma, p110 gammaphosphatidylinositol 3-kinase catalytic 110-kD gammaphosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoformphosphatidylinosit
	Modification date	20141207
dbXrefs	MIM : 601232
	HGNC : HGNC
	Ensembl : ENSG00000105851
	HPRD : 03135
	Vega : OTTHUMG00000157641
Protein	UniProt: P48736 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PIK3CG
	BioGPS: 5294
	Gene Expression Atlas: ENSG00000105851
	The Human Protein Atlas: ENSG00000105851
Pathway	NCI Pathway Interaction Database: PIK3CG
	KEGG: PIK3CG
	REACTOME: PIK3CG
	ConsensusPathDB
	Pathway Commons: PIK3CG
Metabolism	MetaCyc: PIK3CG
	HUMANCyc: PIK3CG
Regulation	Ensembl's Regulation: ENSG00000105851
	miRBase: chr7 :106,505,923-106,547,592
	TargetScan: NM_001282426
	cisRED: ENSG00000105851
Context	iHOP: PIK3CG
	cancer metabolism search in PubMed: PIK3CG
	UCL Cancer Institute: PIK3CG
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for PIK3CG(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PIK3CG
	Familial Cancer Database: PIK3CG

* 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_INOSITOL_PHOSPHATE_METABOLISM KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_PI_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM	601232; gene.
Orphanet
Disease	KEGG Disease: PIK3CG
	MedGen: PIK3CG (Human Medical Genetics with Condition)
	ClinVar: PIK3CG
Phenotype	MGI: PIK3CG (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PIK3CG

Mutations for PIK3CG

* 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
prostate	PIK3CG	chr7	106529581	106529581	PIK3CG	chr7	106532729	106532729
prostate	PIK3CG	chr7	106542180	106542180		chr7	106644860	106644860

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 PIK3CG 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

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=5

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=216)	Stat. for Synonymous SNVs (# total SNVs=93)

Stat. for Deletions (# total SNVs=1)	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
chr7:106513371-106513371	p.V759I	5
chr7:106526602-106526602	p.F965F	5
chr7:106509677-106509677	p.A557A	4
chr7:106545575-106545575	p.L1018L	4
chr7:106508257-106508257	p.A84V	4
chr7:106508490-106508490	p.V162I	4
chr7:106508826-106508826	p.V274I	4
chr7:106508473-106508473	p.A156V	3
chr7:106524689-106524689	p.D950D	3
chr7:106508673-106508673	p.V223I	3

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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=3

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	4	1	46	19		11		4			31	19	5	1	5	26	20	2	21
# mutation	3	4	1	51	21		11		4			32	21	5	1	5	30	21	2	29
nonsynonymous SNV	2	3	1	35	12		7		4			17	17	3	1	2	24	15	1	20
synonymous SNV	1	1		16	9		4					15	4	2		3	6	6	1	9

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
chr7:106508826	p.G283G,PIK3CG	3
chr7:106508855	p.A885T,PIK3CG	3
chr7:106526718	p.P1004L,PIK3CG	3
chr7:106523501	p.V274I,PIK3CG	3
chr7:106508673	p.V223I,PIK3CG	3
chr7:106508490	p.R49C,PIK3CG	2
chr7:106508825	p.K455K,PIK3CG	2
chr7:106509339	p.F965F,PIK3CG	2
chr7:106508180	p.L379I,PIK3CG	2
chr7:106508121	p.D884D,PIK3CG	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 PIK3CG 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 PIK3CG

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


ANKRD44,SCIMP,CD200R1,CD226,CYBB,DOCK2,EVI2B, FYB,GPR174,GVINP1,INPP5D,KCNA3,KLHL6,MARCH1, MPEG1,NCKAP1L,PIK3CG,PTPRC,SPN,TFEC,WDFY4	ANKRD44,CD28,CSF2RB,DOCK2,EVI2B,FYB,GPRIN3, GVINP1,INPP4A,MARCH1,PAG1,PIK3AP1,PIK3CG,PLEKHA2, PRKCB,PTPRC,SH2D1A,STK4,TLR6,TNFSF8,WIPF1

APBB1IP,ARHGAP25,ARHGAP30,BTK,CD180,CD226,CYSLTR1, DOCK10,DOCK2,EVI2B,FYB,GNG2,HCLS1,IKZF1, ITGA4,MPEG1,NCKAP1L,PIK3CG,PTPRC,RCSD1,WAS	NUGGC,CAMP,CD180,DOCK2,DOCK8,DOK3,GGA2, INPP5D,KLHL6,LRMP,MAP3K1,NUP210,P2RY8,PHF6, PIK3CG,PLCG2,POU2AF1,POU4F1,RGS13,SYK,TLR9

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 PIK3CG

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	P48736; -.
Chemistry	ChEMBL	CHEMBL3267; -.
Chemistry	GuidetoPHARMACOLOGY	2156; -.
Organism-specific databases	PharmGKB	PA33311; -.
Organism-specific databases	CTD	5294; -.

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
DB02010	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma	experimental	Staurosporine
DB02375	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma	experimental	Myricetin
DB02656	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma	experimental	2-(4-Morpholinyl)-8-Phenyl-4h-1-Benzopyran-4-One
DB04216	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma	experimental	Quercetin
DB04769	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma	experimental	5-QUINOXALIN-6-YLMETHYLENE-THIAZOLIDINE-2,4-DIONE
DB06831	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma	experimental	2-((9H-PURIN-6-YLTHIO)METHYL)-5-CHLORO-3-(2-METHOXYPHENYL)QUINAZOLIN-4(3H)-ONE
DB06836	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma	experimental	N-(5-(4-CHLORO-3-(2-HYDROXY-ETHYLSULFAMOYL)- PHENYLTHIAZOLE-2-YL)-ACETAMIDE
DB07073	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma	experimental	5,5-dimethyl-2-morpholin-4-yl-5,6-dihydro-1,3-benzothiazol-7(4H)-one
DB07335	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma	experimental	3-[4-AMINO-1-(1-METHYLETHYL)-1H-PYRAZOLO[3,4-D]PYRIMIDIN-3-YL]PHENOL
DB07503	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma	experimental	(5E)-5-[(2,2-DIFLUORO-1,3-BENZODIOXOL-5-YL)METHYLENE]-1,3-THIAZOLIDINE-2,4-DIONE
DB08059	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma	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
DB08300	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma	experimental	1-methyl-3-naphthalen-2-yl-1H-pyrazolo[3,4-d]pyrimidin-4-amine

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Cross referenced IDs for PIK3CG

* 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