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 INPPL1
Basic gene info.Gene symbolINPPL1
Gene nameinositol polyphosphate phosphatase-like 1
SynonymsOPSMD|SHIP2
CytomapUCSC genome browser: 11q13
Genomic locationchr11 :71935881-71950188
Type of geneprotein-coding
RefGenesNM_001567.3,
Ensembl idENSG00000165458
Description51C proteinINPPL-1SH2 domain-containing inositol 5'-phosphatase 2SH2 domain-containing inositol-5'-phosphatase 2SHIP-2phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase 2protein 51C
Modification date20141207
dbXrefs MIM : 600829
HGNC : HGNC
Ensembl : ENSG00000165458
HPRD : 02900
Vega : OTTHUMG00000167879
ProteinUniProt: O15357
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_INPPL1
BioGPS: 3636
Gene Expression Atlas: ENSG00000165458
The Human Protein Atlas: ENSG00000165458
PathwayNCI Pathway Interaction Database: INPPL1
KEGG: INPPL1
REACTOME: INPPL1
ConsensusPathDB
Pathway Commons: INPPL1
MetabolismMetaCyc: INPPL1
HUMANCyc: INPPL1
RegulationEnsembl's Regulation: ENSG00000165458
miRBase: chr11 :71,935,881-71,950,188
TargetScan: NM_001567
cisRED: ENSG00000165458
ContextiHOP: INPPL1
cancer metabolism search in PubMed: INPPL1
UCL Cancer Institute: INPPL1
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for INPPL1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: INPPL1
Familial Cancer Database: INPPL1
* 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
REACTOME_PHOSPHOLIPID_METABOLISM
REACTOME_PI_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM 125853; phenotype.
258480; phenotype.
600829; gene.
Orphanet 2746; Opsismodysplasia.
DiseaseKEGG Disease: INPPL1
MedGen: INPPL1 (Human Medical Genetics with Condition)
ClinVar: INPPL1
PhenotypeMGI: INPPL1 (International Mouse Phenotyping Consortium)
PhenomicDB: INPPL1

Mutations for INPPL1
* 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 INPPL1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE280713INPPL11444117194448871946231INPPL1436460117194622471946248
BE765401INPPL117139117194414271944542INPPL1133262117194475371945418
BC071891INPPL122307117194874171949358NPM130815865170814870170837881
BG991798INPPL119391117194930471949677INPPL1385491117194619371946391
BF990573INPPL1193117194070471940796COIL83165175501643555016517

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        1    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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=84)
Stat. for Synonymous SNVs
(# total SNVs=32)
Stat. for Deletions
(# total SNVs=5)
Stat. for Insertions
(# total SNVs=2)

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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
chr11:71946427-71946427p.G864D4
chr11:71942192-71942192p.R486C3
chr11:71949087-71949087p.A1185D3
chr11:71948748-71948748p.R1156fs*463
chr11:71940223-71940223p.H203P2
chr11:71943960-71943960p.L631L2
chr11:71946494-71946494p.Y886Y2
chr11:71943961-71943961p.L632I2
chr11:71941449-71941449p.G378G2
chr11:71946908-71946908p.P919P2

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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=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample46 191 2 11 1223  1312116
# mutation56 151 1 11 1323  1712122
nonsynonymous SNV34 91 1 11 921  910 14
synonymous SNV22 6       4 2  8218
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
chr11:71939260p.R70H3
chr11:71942192p.R486C3
chr11:71946427p.G864D3
chr11:71941250p.R342Q2
chr11:71941449p.T493M2
chr11:71939802p.R498S2
chr11:71942214p.G378G2
chr11:71949087p.Y886Y2
chr11:71942228p.A1185D2
chr11:71946494p.P143P2

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 INPPL1 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 INPPL1

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

ARAP1,ARHGEF17,ARRB1,ATG16L2,ANAPC15,LAMTOR1,CLPB,
ELMO3,INPPL1,KIAA0895L,LRTOMT,NUMA1,PCNXL3,PHRF1,
RELT,RNF121,RTEL1,TNRC18,ULK1,ZFYVE27,ZNF512B
ATG4D,ATXN7L2,BAG6,D2HGDH,DPP9,DVL1,GTF3C1,
INPPL1,INTS1,MARK4,MIB2,MYO18A,PANK4,PTCD1,
PPP6R2,SPG7,TARS2,TMEM201,UCKL1,USP19,ZNF76

ANKRD13D,ARAP1,CEP164,CEP250,CRAMP1L,DENND4B,DOCK6,
LINC01000,GIGYF1,IGHMBP2,INPPL1,KDM2A,NFRKB,NUMA1,
PCNXL3,SETD1A,SIN3B,SLC26A1,SRRM2,ZNF142,ZNF335
ANKRD11,PRRC2A,SLX4,HECTD4,CAMTA2,CIC,CRAMP1L,
FAM160B2,FAM193A,GIGYF1,GYS1,INPPL1,GSE1,PSMG3-AS1,
NEURL4,PLCG1,PLXNB1,PRR12,SETD1B,SH3PXD2A,SIN3B
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 INPPL1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB O15357; -.
ChemistryChEMBL CHEMBL2331064; -.
Organism-specific databasesPharmGKB PA29888; -.
Organism-specific databasesCTD 3636; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00877inositol polyphosphate phosphatase-like 1approved; investigationalSirolimus


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Cross referenced IDs for INPPL1
* 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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