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 INPP5E
Basic gene info.Gene symbolINPP5E
Gene nameinositol polyphosphate-5-phosphatase, 72 kDa
SynonymsCORS1|CPD4|JBTS1|MORMS|PPI5PIV
CytomapUCSC genome browser: 9q34.3
Genomic locationchr9 :139323066-139334256
Type of geneprotein-coding
RefGenesNM_019892.4,
Ensembl idENSG00000148384
Description72 kDa inositol polyphosphate 5-phosphatasephosphatidylinositol (4,5) bisphosphate 5-phosphatasephosphatidylinositol 4,5-bisphosphate 5-phosphatasephosphatidylinositol polyphosphate 5-phosphatase type IVphosphatidylinositol-4,5-bisphosphate 5-phosphat
Modification date20141219
dbXrefs MIM : 613037
HGNC : HGNC
Ensembl : ENSG00000148384
HPRD : 17151
Vega : OTTHUMG00000020927
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_INPP5E
BioGPS: 56623
Gene Expression Atlas: ENSG00000148384
The Human Protein Atlas: ENSG00000148384
PathwayNCI Pathway Interaction Database: INPP5E
KEGG: INPP5E
REACTOME: INPP5E
ConsensusPathDB
Pathway Commons: INPP5E
MetabolismMetaCyc: INPP5E
HUMANCyc: INPP5E
RegulationEnsembl's Regulation: ENSG00000148384
miRBase: chr9 :139,323,066-139,334,256
TargetScan: NM_019892
cisRED: ENSG00000148384
ContextiHOP: INPP5E
cancer metabolism search in PubMed: INPP5E
UCL Cancer Institute: INPP5E
Assigned class in ccmGDBC

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Phenotypic Information for INPP5E(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: INPP5E
Familial Cancer Database: INPP5E
* 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
REACTOME_PHOSPHOLIPID_METABOLISM
REACTOME_PI_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: INPP5E
MedGen: INPP5E (Human Medical Genetics with Condition)
ClinVar: INPP5E
PhenotypeMGI: INPP5E (International Mouse Phenotyping Consortium)
PhenomicDB: INPP5E

Mutations for INPP5E
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows INPP5E related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CN331953INPP5E1639139327456139327518INPP5E594939139324798139327019

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                
GAIN (# sample)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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=17)
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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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
chr9:139333264-139333264p.S203F2
chr9:139333269-139333269p.I201M2
chr9:139326304-139326304p.H507H2
chr9:139327500-139327500p.R396H2
chr9:139327520-139327520p.E389D1
chr9:139324254-139324254p.P603L1
chr9:139333230-139333230p.S214S1
chr9:139326437-139326437p.A463V1
chr9:139327599-139327599p.?1
chr9:139324835-139324835p.G566C1

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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
# sample1  31   2   3   36 1
# mutation1  31   2   3   36 1
nonsynonymous SNV   21   2   2    6 1
synonymous SNV1  1        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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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
chr9:139327500p.R396H2
chr9:139324835p.G566C1
chr9:139328514p.T551K1
chr9:139325467p.A503A1
chr9:139329253p.A503E1
chr9:139326316p.F478F1
chr9:139329257p.R468H1
chr9:139326317p.T467T1
chr9:139333230p.Q400H1
chr9:139326391p.E389D1

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 INPP5E 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 INPP5E

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

ANAPC2,ARHGAP33,ASB6,ENTHD2,RABL6,CAPN10,NELFB,
CROCCP2,EXD3,FBXW5,GPSM1,GTF3C5,INPP5E,RALGDS,
SDCCAG3,CLASRP,SNAPC4,TRAF2,UBAC1,DPH7,ZMYND19
ABTB1,ANKRD13D,ENTHD2,TMEM74B,CDK9,CENPT,EGFL8,
FAM160B2,FRS3,HDAC7,INPP5E,LCAT,LMBR1L,MAP3K11,
MTMR9LP,SLC39A13,TAZ,TJAP1,TNFRSF14,TNFRSF25,USF1

AGAP4,CCNL2,CDK10,CENPT,EGFL8,FAM193B,FAM73B,
GIGYF1,INPP5E,LENG8,LOC100130015,PILRB,RALGDS,CLASRP,
SNAPC4,TAF1C,TCTE3,TSC1,WDR27,DPH7,ZNF767P
AGAP4,ANO8,ARHGAP33,ATG16L2,BRICD5,CSAD,FAM156A,
FAM193B,GIGYF1,INPP5E,KLHL17,LENG8,LOC100133331,ASMTL-AS1,
PABPC1L,PILRB,PRICKLE4,TAF1C,TTLL3,WDR27,ZNF692
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 INPP5E


There's no related Drug.
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Cross referenced IDs for INPP5E
* 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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