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 ITPKA

Basic gene info.	Gene symbol	ITPKA
	Gene name	inositol-trisphosphate 3-kinase A
	Synonyms	IP3-3KA\|IP3KA
	Cytomap	UCSC genome browser: 15q15.1
	Genomic location	chr15 :41786055-41795757
	Type of gene	protein-coding
	RefGenes	NM_002220.2,
	Ensembl id	ENSG00000137825
	Description	IP3 3-kinase AIP3K Ainositol 1,4,5-trisphosphate 3-kinase AinsP 3-kinase A
	Modification date	20141222
dbXrefs	MIM : 147521
	HGNC : HGNC
	Ensembl : ENSG00000137825
	HPRD : 00941
	Vega : OTTHUMG00000130343
Protein	UniProt: P23677 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ITPKA
	BioGPS: 3706
	Gene Expression Atlas: ENSG00000137825
	The Human Protein Atlas: ENSG00000137825
Pathway	NCI Pathway Interaction Database: ITPKA
	KEGG: ITPKA
	REACTOME: ITPKA
	ConsensusPathDB
	Pathway Commons: ITPKA
Metabolism	MetaCyc: ITPKA
	HUMANCyc: ITPKA
Regulation	Ensembl's Regulation: ENSG00000137825
	miRBase: chr15 :41,786,055-41,795,757
	TargetScan: NM_002220
	cisRED: ENSG00000137825
Context	iHOP: ITPKA
	cancer metabolism search in PubMed: ITPKA
	UCL Cancer Institute: ITPKA
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of ITPKA in cancer cell metabolism	1. Hoofd C, Devreker F, Deneubourg L, Deleu S, Nguyen TM, et al. (2012) A specific increase in inositol 1,4,5-trisphosphate 3-kinase B expression upon differentiation of human embryonic stem cells. Cell Signal 24: 1461-1470. doi: 10.1016/j.cellsig.2012.03.006. go to article

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

Cancer Description
Cancer	CGAP: ITPKA
	Familial Cancer Database: ITPKA

* 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

Others
OMIM	147521; gene.
Orphanet
Disease	KEGG Disease: ITPKA
	MedGen: ITPKA (Human Medical Genetics with Condition)
	ClinVar: ITPKA
Phenotype	MGI: ITPKA (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: ITPKA

Mutations for ITPKA

* 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 ITPKA related fusion information.

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

BE175234

ITPKA

41788813

41788899

ITPKA

175

41788907

41788998

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=16)	Stat. for Synonymous SNVs (# total SNVs=2)

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
chr15:41793924-41793924	p.A226A	2
chr15:41793928-41793928	p.R228C	1
chr15:41794645-41794645	p.R352*	1
chr15:41786312-41786312	p.G63R	1
chr15:41793985-41793985	p.Q247K	1
chr15:41794660-41794660	p.R357C	1
chr15:41786384-41786384	p.E87*	1
chr15:41794232-41794232	p.R281W	1
chr15:41794697-41794697	p.V369A	1
chr15:41786466-41786466	p.L114P	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		1			2		2			3	1				1	2
# mutation	2	1		1			2		2			3	1				1	2
nonsynonymous SNV	2	1		1			1		2			2	1				1	1
synonymous SNV							1					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
chr15:41793928	p.R228C	2
chr15:41794697	p.L114P	1
chr15:41786466	p.P177S	1
chr15:41794987	p.Y186F	1
chr15:41793700	p.L222R	1
chr15:41795237	p.T301T	1
chr15:41793728	p.V310I	1
chr15:41795316	p.S341S	1
chr15:41793911	p.T349M	1
chr15:41794294	p.R357C	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 ITPKA 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 ITPKA

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


BAG1,BLVRB,C15orf59,LINC00313,CRYM,EGFL7,ENTPD8, MZT2B,FAM195A,GPX4,HEXIM2,ITPKA,LOC113230,MAB21L2, P2RX4,PISD,SIGIRR,SIL1,SLC6A19,TMEM205,TSPAN1	ALPP,ARL14,B3GNT6,CTSE,HNF4A,ITPKA,MAGEA4, MSLN,MUC21,NAPSA,NKX2-1,PAEP,PLA2G10,SERPINB3, SFTA3,SFTPA1,SFTPB,SFTPC,TRIM15,UPK3B,XKRX

ACOT7,AKR7A3,BRI3BP,GUCD1,CIB1,E2F2,EFHD2, GAL3ST1,GCHFR,ITPK1,ITPKA,LTK,NAGS,PLCB3, PLLP,PTPRH,RTN4R,SLC9A3R1,TRIM15,WRAP53,XPNPEP1	ACVR1B,C1orf210,CDKN2B,CTSD,EPN1,GPN2,IL17RE, ITPKA,KIAA1522,MGAT4B,NAAA,OAF,PIGS,PRKCZ, SLC26A6,SPINT1,SPIRE2,TMC4,VILL,VIPR1,VSIG10

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 ITPKA

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	P23677; -.
Organism-specific databases	PharmGKB	PA29975; -.
Organism-specific databases	CTD	3706; -.

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB01863	inositol-trisphosphate 3-kinase A	experimental	Inositol 1,3,4,5-Tetrakisphosphate
DB03401	inositol-trisphosphate 3-kinase A	experimental	D-Myo-Inositol-1,4,5-Triphosphate
DB03431	inositol-trisphosphate 3-kinase A	experimental	Adenosine-5'-Diphosphate
DB04395	inositol-trisphosphate 3-kinase A	experimental	Phosphoaminophosphonic Acid-Adenylate Ester

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Cross referenced IDs for ITPKA

* 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