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 PIP4K2A

Basic gene info.	Gene symbol	PIP4K2A
	Gene name	phosphatidylinositol-5-phosphate 4-kinase, type II, alpha
	Synonyms	PI5P4KA\|PIP5K2A\|PIP5KII-alpha\|PIP5KIIA\|PIPK
	Cytomap	UCSC genome browser: 10p12.2
	Genomic location	chr10 :22823765-23003503
	Type of gene	protein-coding
	RefGenes	NM_005028.4,
	Ensembl id	ENSG00000150867
	Description	1-phosphatidylinositol 5-phosphate 4-kinase 2-alpha1-phosphatidylinositol-4-phosphate kinase1-phosphatidylinositol-4-phosphate-5-kinase1-phosphatidylinositol-5-phosphate 4-kinase 2-alphaPI(5)P 4-kinase type II alphaPIP4KII-alphaPIP5KIIIPIP5KIIalpha
	Modification date	20141207
dbXrefs	MIM : 603140
	HGNC : HGNC
	Ensembl : ENSG00000150867
	HPRD : 11931
	Vega : OTTHUMG00000017810
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PIP4K2A
	BioGPS: 5305
	Gene Expression Atlas: ENSG00000150867
	The Human Protein Atlas: ENSG00000150867
Pathway	NCI Pathway Interaction Database: PIP4K2A
	KEGG: PIP4K2A
	REACTOME: PIP4K2A
	ConsensusPathDB
	Pathway Commons: PIP4K2A
Metabolism	MetaCyc: PIP4K2A
	HUMANCyc: PIP4K2A
Regulation	Ensembl's Regulation: ENSG00000150867
	miRBase: chr10 :22,823,765-23,003,503
	TargetScan: NM_005028
	cisRED: ENSG00000150867
Context	iHOP: PIP4K2A
	cancer metabolism search in PubMed: PIP4K2A
	UCL Cancer Institute: PIP4K2A
Assigned class in ccmGDB	C

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Phenotypic Information for PIP4K2A(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PIP4K2A
	Familial Cancer Database: PIP4K2A

* 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: PIP4K2A
	MedGen: PIP4K2A (Human Medical Genetics with Condition)
	ClinVar: PIP4K2A
Phenotype	MGI: PIP4K2A (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PIP4K2A

Mutations for PIP4K2A

* 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
breast	PIP4K2A	chr10	22944963	22944963	PIP4K2A	chr10	22974982	22974982
pancreas	PIP4K2A	chr10	22931519	22931539	PIP4K2A	chr10	22931570	22931590

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 PIP4K2A 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
BC036779	PIP4K2A	1	342	10	23003111	23003452	RPS6KC1	341	1552	1	213415911	213446808
BM925273	PIP4K2A	18	359	10	23003111	23003452	RPS6KC1	358	893	1	213415911	213446127
BG007476	PSMG2	6	367	18	12720568	12725566	PIP4K2A	366	420	10	22834917	22834971

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	ns	ovary	pancre	prost	skin	stoma	thyro	urina
Total # sample	2	2		1			1		3		1			1
GAIN (# sample)	2	1		1			1		2		1
LOSS (# sample)		1							1					1

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=13

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=50)	Stat. for Synonymous SNVs (# total SNVs=15)

Stat. for Deletions (# total SNVs=1)	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
chr10:22880652-22880652	p.R133H	12
chr10:22830773-22830773	p.F332F	3
chr10:22880563-22880563	p.H163Y	2
chr10:22898640-22898640	p.E51K	2
chr10:22839628-22839628	p.N251S	2
chr10:22880621-22880621	p.I143I	2
chr10:22896899-22896899	p.R99H	2
chr10:22862345-22862345	p.F178L	2
chr10:22880665-22880665	p.R129C	1
chr10:22830796-22830796	p.P325S	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	1		11			1		2	1		7	3	1			5	5		9
# mutation	3	1		9			1		2	1		7	3	1			5	5		9
nonsynonymous SNV	2	1		5					2			5	3	1			4	4		6
synonymous SNV	1			4			1			1		2					1	1		3

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
chr10:22830773	p.F178L	2
chr10:22896899	p.F332F	2
chr10:22828900	p.R99H	2
chr10:22862345	p.G380G	2
chr10:23003251	p.R208R	1
chr10:22830872	p.D75N	1
chr10:22880610	p.R349G	1
chr10:22896936	p.V189F	1
chr10:22828982	p.A68A	1
chr10:22830915	p.K342N	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 PIP4K2A 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 PIP4K2A

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


ARHGAP25,CD28,CD3G,CD5,CD96,DOCK2,EVI2B, GVINP1,GZMK,IKZF1,IL16,ITK,PIP4K2A,PRKCB, PTPRC,PYHIN1,SAMD3,SH2D1A,SLAMF6,WIPF1,ZNF831	B2M,CSF2RB,DOCK2,ELMO1,EVI2B,FLI1,GIMAP2, IFNAR2,IL18R1,LCP2,PIK3AP1,PIP4K2A,PLEK,RAB8B, RASSF2,SAMHD1,SAMSN1,SLFN11,SYT11,TFEC,WIPF1

APBB1IP,ARHGEF6,CCDC88A,DOCK10,DOCK2,NXPE3,FAM78A, FLI1,FMNL1,GIMAP1,GIMAP4,GIMAP6,GIMAP8,HCLS1, HVCN1,PPP1R18,LRRC8C,MYO5A,PIP4K2A,SLA,WIPF1	ANKRD44,APBB1IP,ARHGAP25,ARHGAP30,BEND4,CHST11,FLI1, FMNL3,HVCN1,INPP5D,KIAA0922,NCKAP1L,ORAI2,PIK3CD, PIP4K2A,RAB39B,RFTN1,SH2D3C,SPOCK2,TRAF1,WIPF1

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 PIP4K2A

There's no related Drug.

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Cross referenced IDs for PIP4K2A

* 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