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 INPP5B

Basic gene info.	Gene symbol	INPP5B
	Gene name	inositol polyphosphate-5-phosphatase, 75kDa
	Synonyms	5PTase
	Cytomap	UCSC genome browser: 1p34
	Genomic location	chr1 :38326368-38412729
	Type of gene	protein-coding
	RefGenes	NM_001297434.1, NM_005540.2,
	Ensembl id	ENSG00000204084
	Description	phosphoinositide 5-phosphatasetype II inositol 1,4,5-trisphosphate 5-phosphatase
	Modification date	20141207
dbXrefs	MIM : 147264
	HGNC : HGNC
	Ensembl : ENSG00000204084
	HPRD : 00924
	Vega : OTTHUMG00000004436
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_INPP5B
	BioGPS: 3633
	Gene Expression Atlas: ENSG00000204084
	The Human Protein Atlas: ENSG00000204084
Pathway	NCI Pathway Interaction Database: INPP5B
	KEGG: INPP5B
	REACTOME: INPP5B
	ConsensusPathDB
	Pathway Commons: INPP5B
Metabolism	MetaCyc: INPP5B
	HUMANCyc: INPP5B
Regulation	Ensembl's Regulation: ENSG00000204084
	miRBase: chr1 :38,326,368-38,412,729
	TargetScan: NM_001297434
	cisRED: ENSG00000204084
Context	iHOP: INPP5B
	cancer metabolism search in PubMed: INPP5B
	UCL Cancer Institute: INPP5B
Assigned class in ccmGDB	C

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Phenotypic Information for INPP5B(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: INPP5B
	Familial Cancer Database: INPP5B

* 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: INPP5B
	MedGen: INPP5B (Human Medical Genetics with Condition)
	ClinVar: INPP5B
Phenotype	MGI: INPP5B (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: INPP5B

Mutations for INPP5B

* 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

There's no inter-chromosomal structural variation.

- 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
ovary	INPP5B	chr1	38411069	38411089	CR1L	chr1	207837809	207837829
pancreas	INPP5B	chr1	38398329	38398349	INPP5B	chr1	38401447	38401467

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 INPP5B 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
AA256218	INPP5B	1	209	1	38327943	38330032	PDCL	206	430	9	125581560	125581784
CR738758	RANBP2	6	230	2	109401034	109401258	INPP5B	223	543	1	38327455	38327775
AW364441	INPP5B	10	251	1	38383879	38384120	INPP5B	246	619	1	38393827	38394518
BF988467	SNX22	12	220	15	64448923	64452326	INPP5B	214	608	1	38338211	38338604

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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=22)	Stat. for Synonymous SNVs (# total SNVs=5)

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
chr1:38409491-38409491	p.S113L	3
chr1:38411934-38411934	p.Y53C	2
chr1:38397369-38397369	p.G287S	2
chr1:38409559-38409559	p.F90F	2
chr1:38411445-38411445	p.H82H	2
chr1:38411462-38411462	p.R77C	2
chr1:38397636-38397636	p.G198C	2
chr1:38409493-38409493	p.V112V	1
chr1:38397639-38397639	p.R197C	1
chr1:38409499-38409499	p.V110V	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	5		4	1		4	1	3	1		4	8	1			11	6	1	7
# mutation	2	5		4	1		4	1	3	2		4	8	1			12	6	1	8
nonsynonymous SNV	1	4		3	1		3	1	3	1		3	7	1			5	6		5
synonymous SNV	1	1		1			1			1		1	1				7		1	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
chr1:38411462	p.R40C	2
chr1:38341331	p.R77Q	1
chr1:38406451	p.L642L,INPP5B	1
chr1:38351367	p.G395G,INPP5B	1
chr1:38332195	p.V162L,INPP5B	1
chr1:38354008	p.S76L	1
chr1:38406470	p.A639A,INPP5B	1
chr1:38341357	p.D393G,INPP5B	1
chr1:38328018	p.Q128H,INPP5B	1
chr1:38351420	p.V75V	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 INPP5B 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 INPP5B

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


CNTRL,CLCN6,AGO4,GLT1D1,IL18R1,INPP5B,IPCEF1, LOC283314,LOC286367,LRMP,NLRP1,NPHP3,PHF21A,POU6F1, PTBP2,RRN3P1,SCN3A,SF3A3,SV2B,TIA1,TMEM39B	CELF6,CEP120,DMTF1,GATAD1,GOLGA6L10,GPRASP1,INPP5B, KCNMB3,CEP162,MLLT10,NPHP3,PHF21A,S100PBP,SEPT7P2, PNISR,TTF1,TUBGCP3,USPL1,ZMAT1,KRBOX4,ZNF75D

ADORA2A,CLSTN3,DLG4,FES,GAB3,GPSM3,IFFO1, IL16,INPP5B,JAK3,KCND1,MACF1,MAP3K12,MFNG, NISCH,PARVG,RASSF2,S100PBP,SIPA1,TRAF1,ZNF154	ANKRD23,ASXL1,ATM,BZRAP1,CEP97,INPP5B,L3MBTL1, NBPF15,NLRP1,OBSCN,PNISR,SLC25A27,SPIN3,SYNGAP1, TRAF5,TTLL3,ZCCHC11,ZNF37BP,ZNF589,ZNF594,ZNF767P

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 INPP5B

There's no related Drug.

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Cross referenced IDs for INPP5B

* 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