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 PIK3C3

Basic gene info.	Gene symbol	PIK3C3
	Gene name	phosphatidylinositol 3-kinase, catalytic subunit type 3
	Synonyms	VPS34\|hVps34
	Cytomap	UCSC genome browser: 18q12.3
	Genomic location	chr18 :39535198-39661446
	Type of gene	protein-coding
	RefGenes	NM_002647.2,
	Ensembl id	ENSG00000078142
	Description	PI3-kinase type 3PI3K type 3PtdIns-3-kinase type 3phosphatidylinositol 3-kinase catalytic subunit type 3phosphatidylinositol 3-kinase p100 subunitphosphoinositide-3-kinase, class 3
	Modification date	20141207
dbXrefs	MIM : 602609
	HGNC : HGNC
	HPRD : 04009
Protein	UniProt: Q8NEB9 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PIK3C3
	BioGPS: 5289
	Gene Expression Atlas: ENSG00000078142
	The Human Protein Atlas: ENSG00000078142
Pathway	NCI Pathway Interaction Database: PIK3C3
	KEGG: PIK3C3
	REACTOME: PIK3C3
	ConsensusPathDB
	Pathway Commons: PIK3C3
Metabolism	MetaCyc: PIK3C3
	HUMANCyc: PIK3C3
Regulation	Ensembl's Regulation: ENSG00000078142
	miRBase: chr18 :39,535,198-39,661,446
	TargetScan: NM_002647
	cisRED: ENSG00000078142
Context	iHOP: PIK3C3
	cancer metabolism search in PubMed: PIK3C3
	UCL Cancer Institute: PIK3C3
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of PIK3C3 in cancer cell metabolism	1. Zhao X-J, Zhuo H (2014) ECR-MAPK Regulation in Liver Early Development. BioMed research international. go to article

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Phenotypic Information for PIK3C3(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PIK3C3
	Familial Cancer Database: PIK3C3

* 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 REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_PI_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM	602609; gene.
Orphanet
Disease	KEGG Disease: PIK3C3
	MedGen: PIK3C3 (Human Medical Genetics with Condition)
	ClinVar: PIK3C3
Phenotype	MGI: PIK3C3 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PIK3C3

Mutations for PIK3C3

* 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
NS	PIK3C3	chr18	39633392	39633392	TLR2	chr4	154611152	154611152
pancreas	PIK3C3	chr18	39604230	39604250	LOC643542	chr18	65438483	65438503
pancreas	PIK3C3	chr18	39649532	39649552		chr13	62641163	62641183

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 PIK3C3 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
DW414072	PIK3C3	18	210	18	39535227	39542478	DAB2	206	317	5	39375145	39376168
CB124531	PIK3C3	30	630	18	39637909	39661363	LOC100132273	624	692	22	42504846	42504914

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=7

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=97)	Stat. for Synonymous SNVs (# total SNVs=14)

Stat. for Deletions (# total SNVs=3)	Stat. for Insertions (# total SNVs=1)

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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
chr18:39570422-39570422	p.?	21
chr18:39620697-39620697	p.S699G	4
chr18:39623726-39623726	p.E711D	3
chr18:39567803-39567803	p.M187L	3
chr18:39593453-39593453	p.E406D	2
chr18:39637995-39637995	p.T804T	2
chr18:39617690-39617690	p.T625M	2
chr18:39576650-39576650	p.D314N	2
chr18:39637886-39637886	p.R768L	2
chr18:39576652-39576652	p.D314D	2

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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=4

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	5	2	2	27	4		2		3			12	3	3			5	8		11
# mutation	5	2	2	23	4		2		3			13	3	3			5	10		16
nonsynonymous SNV	5	2	2	20	3		2		3			10	3	2			3	9		14
synonymous SNV				3	1							3		1			2	1		2

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
chr18:39620697	p.S699G	4
chr18:39575890	p.R275R	3
chr18:39576652	p.T804T	2
chr18:39593453	p.E406D	2
chr18:39637995	p.D314D	2
chr18:39567805	p.M187I	2
chr18:39613805	p.R378H	1
chr18:39647380	p.L542R	1
chr18:39584468	p.S687L	1
chr18:39620662	p.T804M	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 PIK3C3 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 PIK3C3

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


ADNP2,C18orf25,DYM,HDHD2,TRAPPC8,KIAA1328,KIAA1468, EPG5,LMAN1,MIB1,NARS,PIAS2,PIGN,PIK3C3, RPRD1A,SMAD2,SMAD4,VPS4B,ZNF24,ZNF271P,ZNF397	AFF4,BIRC6,TRAPPC11,ERCC6L2,CASP8AP2,KDM5A,GLTSCR1L, KIAA0586,KIAA2026,LATS1,NIPBL,NUP153,PIAS1,PIK3C3, RANBP2,RIF1,LTN1,SF3B1,SCAF11,THOC2,WAPAL

C18orf25,DYM,ELP2,ESCO1,TRAPPC8,KIAA1328,EPG5, MBD1,MEX3C,PIK3C3,ROCK1,RPRD1A,SLC39A6,SMAD2, SMAD4,SMCHD1,VPS4B,WDR7,ZNF24,ZNF271P,ZNF397	ATAD1,ATE1,TBC1D32,GPATCH11,CTDSPL2,DNAJB14,FBXO38, HDAC9,HDHD2,MAPK14,PDCL,PHAX,PIK3C3,RAB30, RBBP5,SIKE1,SP3,USP8,VPS41,ZNF19,ZNF41

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 PIK3C3

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	Q8NEB9; -.
Chemistry	ChEMBL	CHEMBL1075165; -.
Organism-specific databases	PharmGKB	PA33307; -.
Organism-specific databases	CTD	5289; -.

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
DB06836	phosphatidylinositol 3-kinase, catalytic subunit type 3	experimental	N-(5-(4-CHLORO-3-(2-HYDROXY-ETHYLSULFAMOYL)- PHENYLTHIAZOLE-2-YL)-ACETAMIDE

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Cross referenced IDs for PIK3C3

* 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