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 symbolINPP4A
Gene nameinositol polyphosphate-4-phosphatase, type I, 107kDa
SynonymsINPP4|TVAS1
CytomapUCSC genome browser: 2q11.2
Genomic locationchr2 :99061320-99198284
Type of geneprotein-coding
RefGenesNM_001134224.1,
NM_001134225.1,NM_001566.2,NM_004027.2,
Ensembl idENSG00000040933
Descriptioninositol polyphosphate-4-phosphatase, type I, 107kDtype I inositol 3,4-bisphosphate 4-phosphatasetype I inositol-3,4-bisphosphate 4-phosphatase
Modification date20141207
dbXrefs MIM : 600916
HGNC : HGNC
Ensembl : ENSG00000040933
HPRD : 02949
Vega : OTTHUMG00000153106
ProteinUniProt: Q96PE3
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_INPP4A
BioGPS: 3631
Gene Expression Atlas: ENSG00000040933
The Human Protein Atlas: ENSG00000040933
PathwayNCI Pathway Interaction Database: INPP4A
KEGG: INPP4A
REACTOME: INPP4A
ConsensusPathDB
Pathway Commons: INPP4A
MetabolismMetaCyc: INPP4A
HUMANCyc: INPP4A
RegulationEnsembl's Regulation: ENSG00000040933
miRBase: chr2 :99,061,320-99,198,284
TargetScan: NM_001134224
cisRED: ENSG00000040933
ContextiHOP: INPP4A
cancer metabolism search in PubMed: INPP4A
UCL Cancer Institute: INPP4A
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for INPP4A(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
KEGG_INOSITOL_PHOSPHATE_METABOLISM

check002.gifOthers
OMIM 600916; gene.
Orphanet
DiseaseKEGG Disease: INPP4A
MedGen: INPP4A (Human Medical Genetics with Condition)
ClinVar: INPP4A
PhenotypeMGI: INPP4A (International Mouse Phenotyping Consortium)
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.

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

- Statistics for Tissue and Mutation typeTop
- 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.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryINPP4Achr29914086399140883ZNF492chr192284383322843853
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 INPP4A related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
FJ423742HJURP31592234746145234746300INPP4A15824529919351999193606

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 # sample        2        
GAIN (# sample)        2        
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=61)
Stat. for Synonymous SNVs
(# total SNVs=14)
Stat. for Deletions
(# total SNVs=3)
Stat. for Insertions
(# total SNVs=1)

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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
chr2:99155399-99155399p.R209*2
chr2:99169414-99169414p.L448L2
chr2:99137182-99137182p.E47*2
chr2:99204042-99204042p.E969K2
chr2:99155410-99155410p.Y212fs*12
chr2:99182536-99182536p.D780G2
chr2:99203982-99203982p.R949C2
chr2:99181196-99181196p.A713S2
chr2:99182574-99182574p.R793*2
chr2:99154342-99154342p.R162C2

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample14 14  6 3  772  96 13
# mutation14 15  6 3  772  108 16
nonsynonymous SNV12 12  4 1  351  56 13
synonymous SNV 2 3  2 2  421  52 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
chr2:99204042p.E964K,INPP4A3
chr2:99175935p.P611H,INPP4A2
chr2:99203982p.R944C,INPP4A2
chr2:99154342p.R162S,INPP4A2
chr2:99155368p.V198V,INPP4A1
chr2:99172245p.L379L,INPP4A1
chr2:99156091p.T599I,INPP4A1
chr2:99181225p.V789V,INPP4A1
chr2:99136536p.L202W,INPP4A1
chr2:99170737p.I409I,INPP4A1

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 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

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

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
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 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



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