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 INPP1

Basic gene info.	Gene symbol	INPP1
	Gene name	inositol polyphosphate-1-phosphatase
	Synonyms	-
	Cytomap	UCSC genome browser: 2q32
	Genomic location	chr2 :191208195-191236391
	Type of gene	protein-coding
	RefGenes	NM_001128928.1, NM_002194.3,
	Ensembl id	ENSG00000151689
	Description	IPPIPPaseinositol polyphosphate 1-phosphatase
	Modification date	20141207
dbXrefs	MIM : 147263
	HGNC : HGNC
	Ensembl : ENSG00000151689
	HPRD : 00923
	Vega : OTTHUMG00000132672
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_INPP1
	BioGPS: 3628
	Gene Expression Atlas: ENSG00000151689
	The Human Protein Atlas: ENSG00000151689
Pathway	NCI Pathway Interaction Database: INPP1
	KEGG: INPP1
	REACTOME: INPP1
	ConsensusPathDB
	Pathway Commons: INPP1
Metabolism	MetaCyc: INPP1
	HUMANCyc: INPP1
Regulation	Ensembl's Regulation: ENSG00000151689
	miRBase: chr2 :191,208,195-191,236,391
	TargetScan: NM_001128928
	cisRED: ENSG00000151689
Context	iHOP: INPP1
	cancer metabolism search in PubMed: INPP1
	UCL Cancer Institute: INPP1
Assigned class in ccmGDB	C

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Phenotypic Information for INPP1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: INPP1
	Familial Cancer Database: INPP1

* 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
Orphanet
Disease	KEGG Disease: INPP1
	MedGen: INPP1 (Human Medical Genetics with Condition)
	ClinVar: INPP1
Phenotype	MGI: INPP1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: INPP1

Mutations for INPP1

* 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 INPP1 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
CK001646	TMBIM6	4	59	12	50135340	50135395	INPP1	57	673	2	191231419	191235819
BE720207	PSMD2	6	279	3	184021161	184021806	INPP1	260	458	2	191236012	191236210
BE720196	PSMD2	2	285	3	184021161	184021818	INPP1	266	464	2	191236012	191236210

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=5

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=29)	Stat. for Synonymous SNVs (# total SNVs=7)

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
chr2:191235766-191235766	p.C280R	3
chr2:191235775-191235775	p.R283C	2
chr2:191231449-191231449	p.S98S	2
chr2:191233967-191233967	p.N202S	2
chr2:191231580-191231580	p.N142S	2
chr2:191233921-191233921	p.G187C	2
chr2:191227381-191227381	p.G78E	1
chr2:191236128-191236128	p.*400Y	1
chr2:191233942-191233942	p.G194W	1
chr2:191235768-191235768	p.C280C	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	1	1	1	9			2					7	1	1			2			3
# mutation	1	1	1	7			2					7	1	1			2			3
nonsynonymous SNV	1		1	6			2					5	1	1			2			2
synonymous SNV		1		1								2								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
chr2:191235766	p.C280R,INPP1	3
chr2:191233921	p.G187S,INPP1	2
chr2:191235776	p.D316Y,INPP1	1
chr2:191233922	p.G78E,INPP1	1
chr2:191235815	p.A320S,INPP1	1
chr2:191233942	p.G173E,INPP1	1
chr2:191235867	p.P342L,INPP1	1
chr2:191233948	p.G370G,INPP1	1
chr2:191235874	p.G187D,INPP1	1
chr2:191235578	p.R380W,INPP1	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 INPP1 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 INPP1

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


ARAP3,C10orf54,MIR22HG,CAV1,CEP112,CFI,CLEC1A, ENG,ETS2,GGTA1P,INPP1,JAZF1,MOB3C,NAB1, OAF,PPAP2A,PPM1F,RCBTB2,RHOJ,SOX7,SPRY2	BATF3,CLCF1,CMTM3,CPZ,DNAJB11,IL4R,INPP1, MALL,PDLIM1,PLEKHO1,PXN,RAB34,RFX2,RNF19B, TAGLN2,TPM4,TRIM47,TUBA1A,VASP,WBP5,ZYX

ANXA2,ANXA2P2,ASPHD2,CYSTM1,CAPN8,CCDC68,CD55, CIB1,CREB3L1,INPP1,KCNK1,LIPH,LPCAT4,MAP3K5, S100A14,S100A16,SEMA4B,STYK1,TMEM92,TSPAN3,VPS37B	ANXA2,BZW1,MIR22HG,CHUK,ETF1,HRH1,INPP1, JMJD6,MAP2K3,MFSD2A,PLEK2,PPP2CA,PSMD12,S100A16, SERPINB1,SERPINB8,SERTAD1,SRXN1,TNFRSF12A,UBQLN1,XIRP1

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 INPP1

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

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
DB01356	inositol polyphosphate-1-phosphatase	approved	Lithium

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Cross referenced IDs for INPP1

* 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