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 PI4KA

Basic gene info.	Gene symbol	PI4KA
	Gene name	phosphatidylinositol 4-kinase, catalytic, alpha
	Synonyms	PI4K-ALPHA\|PIK4CA\|pi4K230
	Cytomap	UCSC genome browser: 22q11.21
	Genomic location	chr22 :21061978-21088955
	Type of gene	protein-coding
	RefGenes	NM_058004.3, NM_002650.2,
	Ensembl id	ENSG00000241973
	Description	PI4-kinase alphaphosphatidylinositol 4-kinase 230phosphatidylinositol 4-kinase alphaphosphatidylinositol 4-kinase, type III, alphaptdIns-4-kinase alpha
	Modification date	20141222
dbXrefs	MIM : 600286
	HGNC : HGNC
	Ensembl : ENSG00000241973
	HPRD : 08972
	Vega : OTTHUMG00000167440
Protein	UniProt: P42356 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PI4KA
	BioGPS: 5297
	Gene Expression Atlas: ENSG00000241973
	The Human Protein Atlas: ENSG00000241973
Pathway	NCI Pathway Interaction Database: PI4KA
	KEGG: PI4KA
	REACTOME: PI4KA
	ConsensusPathDB
	Pathway Commons: PI4KA
Metabolism	MetaCyc: PI4KA
	HUMANCyc: PI4KA
Regulation	Ensembl's Regulation: ENSG00000241973
	miRBase: chr22 :21,061,978-21,088,955
	TargetScan: NM_058004
	cisRED: ENSG00000241973
Context	iHOP: PI4KA
	cancer metabolism search in PubMed: PI4KA
	UCL Cancer Institute: PI4KA
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for PI4KA(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PI4KA
	Familial Cancer Database: PI4KA

* 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
Orphanet
Disease	KEGG Disease: PI4KA
	MedGen: PI4KA (Human Medical Genetics with Condition)
	ClinVar: PI4KA
Phenotype	MGI: PI4KA (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PI4KA

Mutations for PI4KA

* 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 PI4KA 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
AK297634	GNL3	1	729	3	52720048	52724720	PI4KA	728	1029	22	21081519	21081820
BE006728	PI4KA	8	101	22	21161654	21161747	GBP3	96	294	1	89477432	89477630
BE006730	PI4KA	8	101	22	21161654	21161747	GBP3	96	294	1	89477432	89477630
BE006741	PI4KA	8	101	22	21161654	21161747	GBP3	96	294	1	89477432	89477630
BE006742	PI4KA	8	101	22	21161654	21161747	GBP3	96	299	1	89477427	89477630
BE006743	PI4KA	8	101	22	21161654	21161747	GBP3	96	294	1	89477432	89477630
BE006738	PI4KA	8	101	22	21161654	21161747	GBP3	96	294	1	89477432	89477630
BE006729	PI4KA	8	101	22	21161654	21161747	GBP3	96	299	1	89477427	89477630
BI059304	PI4KA	28	261	22	21172797	21174121	WIPI2	253	454	7	5266433	5266634
BE006734	PI4KA	8	101	22	21161654	21161747	GBP3	96	299	1	89477427	89477630

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=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=137)	Stat. for Synonymous SNVs (# total SNVs=29)

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

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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
chr22:21071997-21071997	p.P1714P	4
chr22:21105625-21105625	p.A979T	3
chr22:21096961-21096961	p.R1125H	2
chr22:21064203-21064203	p.L1998F	2
chr22:21119230-21119230	p.L803L	2
chr22:21101886-21101886	p.Q1058Q	2
chr22:21075595-21075595	p.Q1645*	2
chr22:21104270-21104270	p.D998Y	2
chr22:21083628-21083628	p.P1494L	2
chr22:21174038-21174038	p.R169Q	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=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		6	2	25	1		5		7		1	18	10	1			23	13		20
# mutation		6	2	28	1		5		7		1	18	11	1			29	14		23
nonsynonymous SNV		5	1	21	1		4		7		1	11	8	1			16	11		21
synonymous SNV		1	1	7			1					7	3				13	3		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
chr22:21088834	p.R227Q	2
chr22:21150562	p.A717T	2
chr22:21174038	p.V194V,PI4KA	2
chr22:21188862	p.R2L,PI4KA	2
chr22:21084262	p.R119W	2
chr22:21147483	p.S256T	1
chr22:21062353	p.L1231L	1
chr22:21167743	p.K109K	1
chr22:21082084	p.A1101T	1
chr22:21098990	p.D909Y	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 PI4KA 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 PI4KA

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


BAZ2A,BCL2L13,PRR14L,CABIN1,CDYL2,CRKL,SPECC1L, DEPDC5,EIF4ENIF1,EP300,HMGXB4,HPS4,LDOC1L,LRBA, MAPK1,MTMR3,PEX26,PI4KA,RASEF,SF3A1,SNAP29	ANKRD52,ARID1A,PRRC2A,PRRC2B,SLX4,EP400,GCN1L1, HERC2,INCENP,ITPR3,KDM5C,KIAA0556,PI4KA,POLE, RSPH3,SEC16A,SEC24C,SMC1A,SNRNP200,SRCAP,TRRAP

AKAP13,PRR14L,CABIN1,SPECC1L,EP300,GBF1,GTPBP1, HERC1,IL17RA,KIAA1671,LDOC1L,MAPK1,MICAL3,MTMR3, MYH9,PACSIN2,PI4KA,RAD54L2,SF3A1,VPS13D,ZC3H7B	BRD4,CREBBP,DHX38,EP300,FAM193A,FLII,GBF1, GTF3C1,HNRNPUL2,KDM2A,MED12,KAT6A,NCOR2,PI4KA, PTPN23,RAPGEF1,SMG6,SNRNP200,SUPT5H,UBR4,ZNF592

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 PI4KA

There's no related Drug.

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Cross referenced IDs for PI4KA

* 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