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 INPP4A

Basic gene info.	Gene symbol	INPP4A
	Gene name	inositol polyphosphate-4-phosphatase, type I, 107kDa
	Synonyms	INPP4\|TVAS1
	Cytomap	UCSC genome browser: 2q11.2
	Genomic location	chr2 :99061320-99198284
	Type of gene	protein-coding
	RefGenes	NM_001134224.1, NM_001134225.1,NM_001566.2,NM_004027.2,
	Ensembl id	ENSG00000040933
	Description	inositol polyphosphate-4-phosphatase, type I, 107kDtype I inositol 3,4-bisphosphate 4-phosphatasetype I inositol-3,4-bisphosphate 4-phosphatase
	Modification date	20141207
dbXrefs	MIM : 600916
	HGNC : HGNC
	Ensembl : ENSG00000040933
	HPRD : 02949
	Vega : OTTHUMG00000153106
Protein	UniProt: Q96PE3 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_INPP4A
	BioGPS: 3631
	Gene Expression Atlas: ENSG00000040933
	The Human Protein Atlas: ENSG00000040933
Pathway	NCI Pathway Interaction Database: INPP4A
	KEGG: INPP4A
	REACTOME: INPP4A
	ConsensusPathDB
	Pathway Commons: INPP4A
Metabolism	MetaCyc: INPP4A
	HUMANCyc: INPP4A
Regulation	Ensembl's Regulation: ENSG00000040933
	miRBase: chr2 :99,061,320-99,198,284
	TargetScan: NM_001134224
	cisRED: ENSG00000040933
Context	iHOP: INPP4A
	cancer metabolism search in PubMed: INPP4A
	UCL Cancer Institute: INPP4A
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for INPP4A(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: INPP4A
	Familial Cancer Database: INPP4A

* 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 UCEC ⁶,	Therapeutic Vulnerabilities in Cancer⁷

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,
6 http://www.nature.com/nature/journal/v497/n7447/full/nature12113.html,
7Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

Metabolic Pathway Description
KEGG_INOSITOL_PHOSPHATE_METABOLISM

Others
OMIM	600916; gene.
Orphanet
Disease	KEGG Disease: INPP4A
	MedGen: INPP4A (Human Medical Genetics with Condition)
	ClinVar: INPP4A
Phenotype	MGI: INPP4A (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: INPP4A

Mutations for INPP4A

* 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

There's no intra-chromosomal structural variation.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	INPP4A	chr2	99140863	99140883	ZNF492	chr19	22843833	22843853

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 INPP4A 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

FJ423742

HJURP

159

234746145

234746300

INPP4A

158

245

99193519

99193606

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=61)	Stat. for Synonymous SNVs (# total SNVs=14)

Stat. for Deletions (# total SNVs=3)	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
chr2:99169414-99169414	p.L448L	2
chr2:99137182-99137182	p.E47*	2
chr2:99204042-99204042	p.E969K	2
chr2:99155410-99155410	p.Y212fs*1	2
chr2:99182536-99182536	p.D780G	2
chr2:99203982-99203982	p.R949C	2
chr2:99181196-99181196	p.A713S	2
chr2:99182574-99182574	p.R793*	2
chr2:99154342-99154342	p.R162C	2
chr2:99193486-99193486	p.S894I	2

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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	1	4		14			6		3			7	7	2			9	6		13
# mutation	1	4		15			6		3			7	7	2			10	8		16
nonsynonymous SNV	1	2		12			4		1			3	5	1			5	6		13
synonymous SNV		2		3			2		2			4	2	1			5	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
chr2:99204042	p.E964K,INPP4A	3
chr2:99203982	p.P611H,INPP4A	2
chr2:99154342	p.R944C,INPP4A	2
chr2:99175935	p.R162S,INPP4A	2
chr2:99149901	p.V789V,INPP4A	1
chr2:99170757	p.V198V,INPP4A	1
chr2:99203969	p.L379L,INPP4A	1
chr2:99155400	p.T599I,INPP4A	1
chr2:99179969	p.V816F,INPP4A	1
chr2:99162460	p.G965R,INPP4A	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 INPP4A 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 INPP4A

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


ANKRD44,CEP85L,CCR4,CD226,DOCK11,DOCK2,FYB, GPR174,GVINP1,INPP4A,ITSN2,KCNA3,PIK3CG,PIKFYVE, PTPN4,PTPRC,RAPGEF1,SLFN12L,SOS1,STK4,XRN1	ANKRD44,ASXL2,CCDC88A,CEP170,CSGALNACT2,ELK4,FRYL, GVINP1,HOOK3,INPP4A,ITSN2,RIC1,NIN,PIK3CG, PIKFYVE,SETX,SSH1,STK4,SYNJ1,TRANK1,VPS13C

ABI3BP,ANKRD44,ARHGAP25,ARHGEF6,CARD8,DOCK2,FAM78A, FLI1,GIMAP6,GIMAP7,IKZF1,INPP4A,TP73-AS1,MFNG, PPP1R16B,PRKCB,PTPRC,RCSD1,SLC9A9,SYNE1,WIPF1	ATP8B2,BICD2,CEP170,CHST15,DOCK11,FAM117A,FAM120C, NXPE3,FBXO10,FNBP1,FRMD4A,IFFO1,INPP4A,KCNN3, KRBA1,MAP3K3,PHF20,PIP4K2B,TRERF1,TRPS1,UVRAG

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 INPP4A

There's no related Drug.

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Cross referenced IDs for INPP4A

* 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