Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 symbolINPP5B
Gene nameinositol polyphosphate-5-phosphatase, 75kDa
Synonyms5PTase
CytomapUCSC genome browser: 1p34
Genomic locationchr1 :38326368-38412729
Type of geneprotein-coding
RefGenesNM_001297434.1,
NM_005540.2,
Ensembl idENSG00000204084
Descriptionphosphoinositide 5-phosphatasetype II inositol 1,4,5-trisphosphate 5-phosphatase
Modification date20141207
dbXrefs MIM : 147264
HGNC : HGNC
Ensembl : ENSG00000204084
HPRD : 00924
Vega : OTTHUMG00000004436
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_INPP5B
BioGPS: 3633
Gene Expression Atlas: ENSG00000204084
The Human Protein Atlas: ENSG00000204084
PathwayNCI Pathway Interaction Database: INPP5B
KEGG: INPP5B
REACTOME: INPP5B
ConsensusPathDB
Pathway Commons: INPP5B
MetabolismMetaCyc: INPP5B
HUMANCyc: INPP5B
RegulationEnsembl's Regulation: ENSG00000204084
miRBase: chr1 :38,326,368-38,412,729
TargetScan: NM_001297434
cisRED: ENSG00000204084
ContextiHOP: INPP5B
cancer metabolism search in PubMed: INPP5B
UCL Cancer Institute: INPP5B
Assigned class in ccmGDBC

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Phenotypic Information for INPP5B(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
KEGG_INOSITOL_PHOSPHATE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: INPP5B
MedGen: INPP5B (Human Medical Genetics with Condition)
ClinVar: INPP5B
PhenotypeMGI: INPP5B (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryINPP5Bchr13841106938411089CR1Lchr1207837809207837829
pancreasINPP5Bchr13839832938398349INPP5Bchr13840144738401467
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows INPP5B related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AA256218INPP5B120913832794338330032PDCL2064309125581560125581784
CR738758RANBP262302109401034109401258INPP5B22354313832745538327775
AW364441INPP5B1025113838387938384120INPP5B24661913839382738394518
BF988467SNX2212220156444892364452326INPP5B21460813833821138338604

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample1         1      
GAIN (# sample)1         1      
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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check002.gifSNV 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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check002.gifSomatic 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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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr1:38409491-38409491p.S113L3
chr1:38409559-38409559p.F90F2
chr1:38411445-38411445p.H82H2
chr1:38411462-38411462p.R77C2
chr1:38397636-38397636p.G198C2
chr1:38411934-38411934p.Y53C2
chr1:38397369-38397369p.G287S2
chr1:38397539-38397539p.R230L1
chr1:38406451-38406451p.Q137H1
chr1:38397551-38397551p.L226S1

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check002.gifSNV 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 ID1234567891011121314151617181920
# sample25 41 4131 481  11617
# mutation25 41 4132 481  12618
nonsynonymous SNV14 31 3131 371  56 5
synonymous SNV11 1  1  1 11   7 13
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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr1:38411462p.R40C2
chr1:38353034p.G395G,INPP5B1
chr1:38330081p.V162L,INPP5B1
chr1:38357097p.R77Q1
chr1:38338764p.L642L,INPP5B1
chr1:38343913p.D393G,INPP5B1
chr1:38409540p.Q128H,INPP5B1
chr1:38353060p.S76L1
chr1:38331520p.A639A,INPP5B1
chr1:38397639p.F392F,INPP5B1

check002.gifOther 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

check002.gifCopy 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

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV 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
check002.gifCo-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
check002.gifCo-Expressed gene's Protein-protein interaction 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

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check002.gifInteracting 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



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