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 PIP5K1B

Basic gene info.	Gene symbol	PIP5K1B
	Gene name	phosphatidylinositol-4-phosphate 5-kinase, type I, beta
	Synonyms	MSS4\|STM7
	Cytomap	UCSC genome browser: 9q13
	Genomic location	chr9 :71320615-71624091
	Type of gene	protein-coding
	RefGenes	NM_001031687.1, NM_001278253.1,NM_003558.3,
	Ensembl id	ENSG00000107242
	Description	PIP5K1-betaPIP5KIbetaphosphatidylinositol 4-phosphate 5-kinase type I betaphosphatidylinositol 4-phosphate 5-kinase type-1 betaphosphatidylinositol-4-phosphate 5-kinase type-1 betaprotein STM-7ptdIns(4)P-5-kinase 1 betatype I phosphatidylinositol 4
	Modification date	20141207
dbXrefs	MIM : 602745
	HGNC : HGNC
	Ensembl : ENSG00000107242
	HPRD : 04121
	Vega : OTTHUMG00000019976
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PIP5K1B
	BioGPS: 8395
	Gene Expression Atlas: ENSG00000107242
	The Human Protein Atlas: ENSG00000107242
Pathway	NCI Pathway Interaction Database: PIP5K1B
	KEGG: PIP5K1B
	REACTOME: PIP5K1B
	ConsensusPathDB
	Pathway Commons: PIP5K1B
Metabolism	MetaCyc: PIP5K1B
	HUMANCyc: PIP5K1B
Regulation	Ensembl's Regulation: ENSG00000107242
	miRBase: chr9 :71,320,615-71,624,091
	TargetScan: NM_001031687
	cisRED: ENSG00000107242
Context	iHOP: PIP5K1B
	cancer metabolism search in PubMed: PIP5K1B
	UCL Cancer Institute: PIP5K1B
Assigned class in ccmGDB	C

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Phenotypic Information for PIP5K1B(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PIP5K1B
	Familial Cancer Database: PIP5K1B

* 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: PIP5K1B
	MedGen: PIP5K1B (Human Medical Genetics with Condition)
	ClinVar: PIP5K1B
Phenotype	MGI: PIP5K1B (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PIP5K1B

Mutations for PIP5K1B

* 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
breast	PIP5K1B	chr9	71393266	71393266	PIP5K1B	chr9	71406339	71406339
ovary	PIP5K1B	chr9	71386547	71386567	COL11A1	chr1	103567281	103567301

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 PIP5K1B 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
BF358668	PIP5K1B	102	129	9	71582212	71582242	ABHD15	114	377	17	27889217	27889480
X92493	CNKSR2	7	116	X	21672556	21672665	PIP5K1B	115	2764	9	71320616	71624091

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		1		1	2		16		3					1
GAIN (# sample)					1		1		1
LOSS (# sample)		1		1	1		15		2					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=1

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=2)	Stat. for Synonymous SNVs (# total SNVs=1)

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
chr9:71437571-71437571	p.K14R	1
chr9:71509318-71509318	p.G179*	1
chr9:71509353-71509353	p.N190N	1
chr9:71509426-71509426	p.R215C	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	1	5	3		7					6	4				14	1		7
# mutation		2	1	4	3		7					9	4				20	1		8
nonsynonymous SNV		1		3	2		4					8	2				16	1		5
synonymous SNV		1	1	1	1		3					1	2				4			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
chr9:71509489	p.N190N,PIP5K1B	2
chr9:71549833	p.R410L,PIP5K1B	2
chr9:71478840	p.L53I,PIP5K1B	2
chr9:71509353	p.E236K,PIP5K1B	2
chr9:71509406	p.L152L,PIP5K1B	1
chr9:71555697	p.D293Y,PIP5K1B	1
chr9:71532595	p.L454L,PIP5K1B	1
chr9:71503911	p.L166P,PIP5K1B	1
chr9:71549884	p.K301K,PIP5K1B	1
chr9:71509424	p.G455R,PIP5K1B	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 PIP5K1B 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 PIP5K1B

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


LINC00470___CHMP1B,CBWD3,FAM122A,FOXD4L5,FREM2,FXN,INPP5A, KIAA1875,LOC442421,OR4D9,PIP5K1B,PPFIA4,PRKACG,PTAR1, PWWP2B,SCARNA20,SHOC2,SIRPB1,SMC5,TJP2,ZMIZ1	ARMCX5,ATL1,DST,CCSER1,FGFR2,GRAMD3,KIAA1671, KLF5,LRAT,MFSD6,MUC15,MYLK,NAP1L2,NTN4, NUP35,OSBPL9,PIP5K1B,REPS1,SOX9,TES,TMEM30B

C1orf210,C4orf19,TMEM246,CASP7,CMPK1,CORO2A,ENPP4, FAM120A,MOB3B,MUC13,PIP5K1B,PLS1,RAB14,RASEF, RBM47,SCP2,SH3BGRL2,SLC17A5,SLC35A3,TJP2,TMEM171	ABHD3,APPL2,ATP1B3,CCDC68,CLCN2,EPS8,ABHD17C, HHLA2,LGR4,LNX2,NR3C2,PIP4K2C,PIP5K1B,RIOK3, SLC26A3,STX3,TAOK3,TJP3,TMEM45B,TRIM36,WASL

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 PIP5K1B

There's no related Drug.

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Cross referenced IDs for PIP5K1B

* 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