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 INPP4B
Basic gene info.Gene symbolINPP4B
Gene nameinositol polyphosphate-4-phosphatase, type II, 105kDa
Synonyms-
CytomapUCSC genome browser: 4q31.21
Genomic locationchr4 :142949181-143767604
Type of geneprotein-coding
RefGenesNM_001101669.1,
NM_003866.2,
Ensembl idENSG00000109452
Descriptioninositol polyphosphate 4-phosphatase II; 4-phosphatase IIinositol polyphosphate 4-phosphatase type IIinositol polyphosphate-4-phosphatase, type II, 105kDtype II inositol 3,4-bisphosphate 4-phosphatasetype II inositol-3,4-bisphosphate 4-phosphatase
Modification date20141207
dbXrefs MIM : 607494
HGNC : HGNC
Ensembl : ENSG00000109452
HPRD : 06322
Vega : OTTHUMG00000161341
ProteinUniProt: O15327
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_INPP4B
BioGPS: 8821
Gene Expression Atlas: ENSG00000109452
The Human Protein Atlas: ENSG00000109452
PathwayNCI Pathway Interaction Database: INPP4B
KEGG: INPP4B
REACTOME: INPP4B
ConsensusPathDB
Pathway Commons: INPP4B
MetabolismMetaCyc: INPP4B
HUMANCyc: INPP4B
RegulationEnsembl's Regulation: ENSG00000109452
miRBase: chr4 :142,949,181-143,767,604
TargetScan: NM_001101669
cisRED: ENSG00000109452
ContextiHOP: INPP4B
cancer metabolism search in PubMed: INPP4B
UCL Cancer Institute: INPP4B
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of INPP4B in cancer cell metabolism1. Min JW, Kim KI, Kim HA, Kim EK, Noh WC, et al. (2013) INPP4B-mediated tumor resistance is associated with modulation of glucose metabolism via hexokinase 2 regulation in laryngeal cancer cells. Biochem Biophys Res Commun 440: 137-142. doi: 10.1016/j.bbrc.2013.09.041. go to article
2. Lopez SM, Hodgson MC, Packianathan C, Bingol-Ozakpinar O, Uras F, et al. (2013) Determinants of the tumor suppressor INPP4B protein and lipid phosphatase activities. Biochem Biophys Res Commun 440: 277-282. doi: 10.1016/j.bbrc.2013.09.077. go to article
3. Zhang X, Chen H, Wang X, Zhao W, Chen JJ (2014) Expression and transcriptional profiling of the LKB1 tumor suppressor in cervical cancer cells. Gynecol Oncol 134: 372-378. doi: 10.1016/j.ygyno.2014.04.050. go to article

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Phenotypic Information for INPP4B(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: INPP4B
Familial Cancer Database: INPP4B
* 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 607494; gene.
Orphanet
DiseaseKEGG Disease: INPP4B
MedGen: INPP4B (Human Medical Genetics with Condition)
ClinVar: INPP4B
PhenotypeMGI: INPP4B (International Mouse Phenotyping Consortium)
PhenomicDB: INPP4B

Mutations for INPP4B
* 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
* 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
ovaryINPP4Bchr4142966858142966878chr4142708424142708444
ovaryINPP4Bchr4143112579143112599chr84212090242120922
ovaryINPP4Bchr4143112771143112791SLC20A2chr84228967242289692
ovaryINPP4Bchr4143162513143162533INPP4Bchr4143158755143158775
ovaryINPP4Bchr4143353923143353943chr4144708014144708034
ovaryINPP4Bchr4143376718143376738INPP4Bchr4143373158143373178
ovaryINPP4Bchr4143502810143502830DEPTORchr8121037892121037912
pancreasINPP4Bchr4142971601142971621INPP4Bchr4142971722142971742
pancreasINPP4Bchr4142975114142975134INPP4Bchr4142975210142975230
pancreasINPP4Bchr4143018635143018655chr4155616362155616382
pancreasINPP4Bchr4143044679143044699INPP4Bchr4143046841143046861
pancreasINPP4Bchr4143130541143130561INPP4Bchr4143617879143617899
pancreasINPP4Bchr4143598663143598683INPP4Bchr4143578418143578438
pancreasINPP4Bchr4143756618143756638GAB1chr4144393092144393112
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 INPP4B related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DB020243INPP4B12394143687891143689122IST1237544167192447271928762
BP360877MAPK10151148727568287281206INPP4B5105824143067074143067145
AK057258INPP4B12384143687891143689122IST12361735167192447271961793
CB044109INPP4B1892434142963302142963356GPX32426725150406475150407696
BG990026INPP4B17364142957046142957065ELL330318154408454644086052
S60878INPP4B8344143719085143719135WBSCR17153577089778670897806
BF895764SKAP23144172681306226813470INPP4B4364884143233000143233052
BG952183EGFLAM11915653832066738320731INPP4B1433114143072468143072636

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 # sample31 1  5 2 3  22 4
GAIN (# sample)2  1  3 2 2  11 2
LOSS (# sample)11    2   1  11 2
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=111)
Stat. for Synonymous SNVs
(# total SNVs=29)
Stat. for Deletions
(# total SNVs=2)
Stat. for Insertions
(# total SNVs=3)

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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
chr4:143324153-143324153p.I104V4
chr4:143081713-143081713p.T454R4
chr4:143159105-143159105p.R250*4
chr4:143067097-143067097p.V539A3
chr4:143029297-143029297p.E775K3
chr4:143094806-143094806p.S446S3
chr4:143094812-143094812p.K444N2
chr4:143067070-143067070p.G548D2
chr4:143114284-143114284p.G379G2
chr4:143181690-143181690p.P215T2

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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
# sample56 13  6 21 2042  38 15
# mutation56 15  7 21 2152  39 17
nonsynonymous SNV35 11  6 11 1452  26 11
synonymous SNV21 4  1 1  7    13 6
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
chr4:143029297p.E775K,INPP4B3
chr4:143181690p.P215T,INPP4B2
chr4:143007359p.A207S,INPP4B2
chr4:143181714p.R250Q,INPP4B2
chr4:143159104p.L809I,INPP4B2
chr4:143045814p.L777V,INPP4B1
chr4:143181683p.L607P,INPP4B1
chr4:142949964p.I424L,INPP4B1
chr4:143007357p.S217I,INPP4B1
chr4:143094803p.T124T,INPP4B1

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 INPP4B 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 INPP4B

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.
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check002.gifProtein Expression Plot (RPPA)
*RPPA protein expression data were extracted from TCPA (The Cancer Proteome Atlas). Normalized data based on replicated based normalization (RBN) was used to draw following figures.

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

AFF1,AHNAK,ARFIP1,ATG2B,BOD1L1,SMIM14,CREBRF,
CCNG2,FNIP1,INPP4B,KIAA0232,KIAA1109,LCOR,LRBA,
MAP3K1,MKL2,PTPN13,RAB27B,STAM2,WDFY3,ZNF844
AFF3,ANKRD30A,ANKS1B,ARHGAP32,ERBB4,FAM161B,IGF1R,
INPP4B,IQCH,LYPD6,MAGI3,MYB,MYO6,JADE3,
RAB27B,RABEP1,RASEF,ST8SIA6,SYTL2,SYTL5,TSPAN5

ACTBL2,ANXA8,BPI,C8orf86,CGB1,CPA4,CST6,
FAM3C,IL20RB,INPP4B,LIPK,LRAT,MUC16,MYH16,
PEX5L,PSG6,PSG9,SIGLEC15,THEG,WNT7A,ZNF365
CAST,CEBPG,CORO2A,DHCR24,GPD2,INPP4B,KIF16B,
LHFPL2,LUZP1,PICALM,PLS1,PSMD11,RAB14,RNF103,
SLC41A2,SMAP1,TMEM135,TOP1P1,UGCG,VDAC1,ZDHHC21
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 INPP4B


There's no related Drug.
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Cross referenced IDs for INPP4B
* 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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