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 INPP1
Basic gene info.Gene symbolINPP1
Gene nameinositol polyphosphate-1-phosphatase
Synonyms-
CytomapUCSC genome browser: 2q32
Genomic locationchr2 :191208195-191236391
Type of geneprotein-coding
RefGenesNM_001128928.1,
NM_002194.3,
Ensembl idENSG00000151689
DescriptionIPPIPPaseinositol polyphosphate 1-phosphatase
Modification date20141207
dbXrefs MIM : 147263
HGNC : HGNC
Ensembl : ENSG00000151689
HPRD : 00923
Vega : OTTHUMG00000132672
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_INPP1
BioGPS: 3628
Gene Expression Atlas: ENSG00000151689
The Human Protein Atlas: ENSG00000151689
PathwayNCI Pathway Interaction Database: INPP1
KEGG: INPP1
REACTOME: INPP1
ConsensusPathDB
Pathway Commons: INPP1
MetabolismMetaCyc: INPP1
HUMANCyc: INPP1
RegulationEnsembl's Regulation: ENSG00000151689
miRBase: chr2 :191,208,195-191,236,391
TargetScan: NM_001128928
cisRED: ENSG00000151689
ContextiHOP: INPP1
cancer metabolism search in PubMed: INPP1
UCL Cancer Institute: INPP1
Assigned class in ccmGDBC

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Phenotypic Information for INPP1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
KEGG_INOSITOL_PHOSPHATE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: INPP1
MedGen: INPP1 (Human Medical Genetics with Condition)
ClinVar: INPP1
PhenotypeMGI: INPP1 (International Mouse Phenotyping Consortium)
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.

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 INPP1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CK001646TMBIM6459125013534050135395INPP1576732191231419191235819
BE720207PSMD262793184021161184021806INPP12604582191236012191236210
BE720196PSMD222853184021161184021818INPP12664642191236012191236210

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   3  1   1      
GAIN (# sample)          1      
LOSS (# sample)   3  1          
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=5

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check002.gifSomatic 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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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
chr2:191235766-191235766p.C280R3
chr2:191233921-191233921p.G187C2
chr2:191235775-191235775p.R283C2
chr2:191231449-191231449p.S98S2
chr2:191233967-191233967p.N202S2
chr2:191231580-191231580p.N142S2
chr2:191233880-191233880p.G173E1
chr2:191235676-191235676p.T250P1
chr2:191224855-191224855p.L9L1
chr2:191236066-191236066p.R380W1

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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
# sample1119  2    711  2  3
# mutation1117  2    711  2  3
nonsynonymous SNV1 16  2    511  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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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
chr2:191235766p.C280R,INPP13
chr2:191233921p.G187S,INPP12
chr2:191235678p.L9L,INPP11
chr2:191236038p.C296F,INPP11
chr2:191224855p.L56Q,INPP11
chr2:191235713p.F313L,INPP11
chr2:191236066p.G78E,INPP11
chr2:191224995p.D316Y,INPP11
chr2:191236092p.G173E,INPP11
chr2:191227381p.A320S,INPP11

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 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

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

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
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 INPP1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB01356inositol polyphosphate-1-phosphataseapprovedLithium


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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



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