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 PI4K2A

Basic gene info.	Gene symbol	PI4K2A
	Gene name	phosphatidylinositol 4-kinase type 2 alpha
	Synonyms	PI4KII\|PIK42A
	Cytomap	UCSC genome browser: 10q24
	Genomic location	chr10 :99400442-99436187
	Type of gene	protein-coding
	RefGenes	NM_018425.3,
	Ensembl id	ENSG00000155252
	Description	phosphatidylinositol 4-kinase type 2-alphaphosphatidylinositol 4-kinase type II (PI4KII)phosphatidylinositol 4-kinase type II-alpha
	Modification date	20141218
dbXrefs	MIM : 609763
	HGNC : HGNC
	Ensembl : ENSG00000155252
	HPRD : 11431
	Vega : OTTHUMG00000018863
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PI4K2A
	BioGPS: 55361
	Gene Expression Atlas: ENSG00000155252
	The Human Protein Atlas: ENSG00000155252
Pathway	NCI Pathway Interaction Database: PI4K2A
	KEGG: PI4K2A
	REACTOME: PI4K2A
	ConsensusPathDB
	Pathway Commons: PI4K2A
Metabolism	MetaCyc: PI4K2A
	HUMANCyc: PI4K2A
Regulation	Ensembl's Regulation: ENSG00000155252
	miRBase: chr10 :99,400,442-99,436,187
	TargetScan: NM_018425
	cisRED: ENSG00000155252
Context	iHOP: PI4K2A
	cancer metabolism search in PubMed: PI4K2A
	UCL Cancer Institute: PI4K2A
Assigned class in ccmGDB	C

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Phenotypic Information for PI4K2A(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PI4K2A
	Familial Cancer Database: PI4K2A

* 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
REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_PI_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: PI4K2A
	MedGen: PI4K2A (Human Medical Genetics with Condition)
	ClinVar: PI4K2A
Phenotype	MGI: PI4K2A (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PI4K2A

Mutations for PI4K2A

* 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	PI4K2A	chr10	99401662	99401682	PI4K2A	chr10	99402083	99402103
ovary	PI4K2A	chr10	99423176	99423196	PI4K2A	chr10	99405699	99405719

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 PI4K2A 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
CA307215	PI4K2A	18	537	10	99435289	99435808	PFDN5	534	725	12	53691852	53693162
AK129943	PI4K2A	1	172	10	99374243	99374414	ALDH3B1	168	1786	11	67787229	67796143

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=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=26)	Stat. for Synonymous SNVs (# total SNVs=5)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=0)
There's no deleted snv.	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
chr10:99416701-99416701	p.V298M	2
chr10:99410891-99410891	p.R210H	2
chr10:99416703-99416703	p.V298V	2
chr10:99422676-99422676	p.D312G	1
chr10:99410796-99410796	p.C178*	1
chr10:99416633-99416633	p.R275Q	1
chr10:99422723-99422723	p.R328W	1
chr10:99410868-99410868	p.K202N	1
chr10:99416641-99416641	p.E278K	1
chr10:99422724-99422724	p.R328Q	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	2	2		9	1				1	1		3		1		1	2	3		3
# mutation	2	2		8	1				1	1		3		1		1	2	3		3
nonsynonymous SNV	1	1		6	1				1	1		3		1			1	3		3
synonymous SNV	1	1		2												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
chr10:99416703	p.V298V	2
chr10:99410870	p.P209P	1
chr10:99410880	p.R455S	1
chr10:99416705	p.V229V	1
chr10:99410889	p.R459W	1
chr10:99416722	p.S259L	1
chr10:99416092	p.S461F	1
chr10:99416723	p.E265K	1
chr10:99400513	p.W273R	1
chr10:99416585	p.R275Q	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 PI4K2A 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 PI4K2A

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


ADAP2,AXL,C10orf76,C3AR1,CALHM2,CD33,CD68, CSF1R,CTSB,HAVCR2,LIPA,LRRC25,MARVELD1,PI4K2A, PLEKHO2,PSAP,RASGRP4,SFXN3,SIGLEC7,SIGLEC9,SLCO2B1	ADAP2,ARRB2,C1QA,C1QB,C1QC,C2,CD4, CD86,CLEC10A,FCER1G,HAVCR2,HCK,LGMN,LILRB2, LILRB4,NCF4,NFAM1,PI4K2A,PSAP,SPI1,TBXAS1

WBP1L,C1orf162,C1R,CSF1,DFNA5,FAM20A,FBLN2, HAVCR2,PPP1R18,LAIR1,MAFB,MRAS,NRP2,PI4K2A, PLEKHO2,SERPINF1,SERPING1,SLAMF8,SPI1,TMEM86A,VIM	CGREF1,CHRM4,CREB3L2,DGKZ,GNS,GOLGA8CP,GREB1L, IRAK2,KIFC3,MPP1,NBAS,NEDD4,PI4K2A,PLOD1, REG4,SEMA3G,SERPINF2,SFXN3,SIRPA,TK2,UNC5CL

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 PI4K2A

There's no related Drug.

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Cross referenced IDs for PI4K2A

* 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