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 PIP4K2B

Basic gene info.	Gene symbol	PIP4K2B
	Gene name	phosphatidylinositol-5-phosphate 4-kinase, type II, beta
	Synonyms	PI5P4KB\|PIP5K2B\|PIP5KIIB\|PIP5KIIbeta
	Cytomap	UCSC genome browser: 17q12
	Genomic location	chr17 :36921943-36956158
	Type of gene	protein-coding
	RefGenes	NM_003559.4, NM_138687.1,
	Ensembl id	ENSG00000141720
	Description	1-phosphatidylinositol 5-phosphate 4-kinase 2-beta1-phosphatidylinositol-4-phosphate kinase1-phosphatidylinositol-5-phosphate 4-kinase 2-betaPI(5)P 4-kinase type II betaPIP4KII-betaPTDINS(4)P-5-kinasediphosphoinositide kinase 2-betaphosphatidylinos
	Modification date	20141207
dbXrefs	MIM : 603261
	HGNC : HGNC
	Ensembl : ENSG00000276293
	HPRD : 04463
	Vega : OTTHUMG00000188504
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PIP4K2B
	BioGPS: 8396
	Gene Expression Atlas: ENSG00000141720
	The Human Protein Atlas: ENSG00000141720
Pathway	NCI Pathway Interaction Database: PIP4K2B
	KEGG: PIP4K2B
	REACTOME: PIP4K2B
	ConsensusPathDB
	Pathway Commons: PIP4K2B
Metabolism	MetaCyc: PIP4K2B
	HUMANCyc: PIP4K2B
Regulation	Ensembl's Regulation: ENSG00000141720
	miRBase: chr17 :36,921,943-36,956,158
	TargetScan: NM_003559
	cisRED: ENSG00000141720
Context	iHOP: PIP4K2B
	cancer metabolism search in PubMed: PIP4K2B
	UCL Cancer Institute: PIP4K2B
Assigned class in ccmGDB	C

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Phenotypic Information for PIP4K2B(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PIP4K2B
	Familial Cancer Database: PIP4K2B

* 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
Orphanet
Disease	KEGG Disease: PIP4K2B
	MedGen: PIP4K2B (Human Medical Genetics with Condition)
	ClinVar: PIP4K2B
Phenotype	MGI: PIP4K2B (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PIP4K2B

Mutations for PIP4K2B

* 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 PIP4K2B 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
AA972703	PIP4K2B	2	91	17	36955896	36955987	APBA3	92	402	19	3751238	3752608
AF130850	PIP4K2B	5	86	17	36927442	36927527	DGCR5	74	1272	22	19014309	19015512
AA247774	PIP4K2B	1	132	17	36922170	36922301	PIP4K2B	126	391	17	36935745	36940572
BF849647	PIP4K2B	29	129	17	36943075	36943175	PIP4K2B	128	263	17	36933940	36934608
BF991438	PIP4K2B	1	155	17	36924516	36924670	PIP4K2B	148	255	17	36924325	36924432
BP428483	CDC20	6	228	1	43827923	43828782	PIP4K2B	217	319	17	36922424	36922526

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=2

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=23)	Stat. for Synonymous SNVs (# total SNVs=14)

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
chr17:36936775-36936775	p.R146H	2
chr17:36935738-36935738	p.L184L	2
chr17:36934599-36934599	p.S227S	1
chr17:36936743-36936743	p.V157L	1
chr17:36940575-36940575	p.R92H	1
chr17:36927329-36927329	p.R335Q	1
chr17:36934602-36934602	p.A226A	1
chr17:36936744-36936744	p.D156D	1
chr17:36943126-36943126	p.D69D	1
chr17:36927333-36927333	p.P334S	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=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	2	1		9			2		4			4	3	1			3	4	1	9
# mutation	2	1		8			2		4			4	3	1			3	4	1	11
nonsynonymous SNV	1			4			2					3	3	1			3	2	1	8
synonymous SNV	1	1		4					4			1						2		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
chr17:36926734	p.D375E	3
chr17:36935738	p.R146H	2
chr17:36927505	p.I276I	2
chr17:36936775	p.L184L	2
chr17:36934617	p.D287N	1
chr17:36936825	p.H286H	1
chr17:36955630	p.S131R	1
chr17:36927374	p.H286P	1
chr17:36935652	p.S129S	1
chr17:36940500	p.Y117F	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 PIP4K2B 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 PIP4K2B

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


C17orf96,C17orf98,CACNB1,CDK12,CISD3,CWC25,ERBB2, FBXL20,LASP1,LOC90110,MED1,MLLT6,MRPL45,PCGF2, PIP4K2B,PSMB3,RPL19,RPL23,RPL23P8,SOCS7,SRCIN1	ALDH5A1,AMOT,ARIH2,ASB8,FAM217B,FXR1,FYCO1, HERC1,HIF1AN,KIF1B,P2RY1,PAIP2B,PAX7,PIP4K2B, PPARGC1A,PRKAB2,PTCD3,SGCD,SIX4,TRAK1,ZNF106

AATF,ACACA,CACNB1,CDK12,CWC25,FBXL20,FXYD2, GRB7,KCTD2,LOC90110,MED1,MLLT6,PIP4K2B,RGSL1, SNAR-A2,SOCS7,SRCIN1,STARD3,STAT5B,SUPT6H,SYNRG	ARHGEF17,VSTM4,CCDC102A,CRTC3,DSTYK,FRMD4A,TP73-AS1, MAP3K3,NFATC4,NPR2,NR2F2,PHC1,PHF21A,PIP4K2B, RGAG4,SATB1,SIX5,STAT5B,TBKBP1,ZBTB4,ZNF512B

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 PIP4K2B

There's no related Drug.

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Cross referenced IDs for PIP4K2B

* 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