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 ITPKB
Basic gene info.Gene symbolITPKB
Gene nameinositol-trisphosphate 3-kinase B
SynonymsIP3-3KB|IP3K|IP3K-B|IP3KB|PIG37
CytomapUCSC genome browser: 1q42.13
Genomic locationchr1 :226819390-226926876
Type of geneprotein-coding
RefGenesNM_002221.3,
Ensembl idENSG00000143772
DescriptionIP3 3-kinase BIP3K Binositol 1,4,5-trisphosphate 3-kinase BinsP 3-kinase Bproliferation-inducing protein 37
Modification date20141207
dbXrefs MIM : 147522
HGNC : HGNC
Ensembl : ENSG00000143772
HPRD : 00942
Vega : OTTHUMG00000037582
ProteinUniProt: P27987
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ITPKB
BioGPS: 3707
Gene Expression Atlas: ENSG00000143772
The Human Protein Atlas: ENSG00000143772
PathwayNCI Pathway Interaction Database: ITPKB
KEGG: ITPKB
REACTOME: ITPKB
ConsensusPathDB
Pathway Commons: ITPKB
MetabolismMetaCyc: ITPKB
HUMANCyc: ITPKB
RegulationEnsembl's Regulation: ENSG00000143772
miRBase: chr1 :226,819,390-226,926,876
TargetScan: NM_002221
cisRED: ENSG00000143772
ContextiHOP: ITPKB
cancer metabolism search in PubMed: ITPKB
UCL Cancer Institute: ITPKB
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of ITPKB in cancer cell metabolism1. Sumantran VN, Mishra P, Sudhakar N (2015) Microarray analysis of differentially expressed genes regulating lipid metabolism during melanoma progression. Indian J Biochem Biophys 52: 125-131. go to article
2. Hoofd C, Devreker F, Deneubourg L, Deleu S, Nguyen TM, et al. (2012) A specific increase in inositol 1,4,5-trisphosphate 3-kinase B expression upon differentiation of human embryonic stem cells. Cell Signal 24: 1461-1470. doi: 10.1016/j.cellsig.2012.03.006. go to article

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Phenotypic Information for ITPKB(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ITPKB
Familial Cancer Database: ITPKB
* 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 DLBCL 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/v505/n7484/full/nature12912.html,
7Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

check002.gifMetabolic Pathway Description
KEGG_INOSITOL_PHOSPHATE_METABOLISM

check002.gifOthers
OMIM 147522; gene.
Orphanet
DiseaseKEGG Disease: ITPKB
MedGen: ITPKB (Human Medical Genetics with Condition)
ClinVar: ITPKB
PhenotypeMGI: ITPKB (International Mouse Phenotyping Consortium)
PhenomicDB: ITPKB

Mutations for ITPKB
* 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
large_intestineITPKBchr1226820468226820468chr337463223746322
large_intestineITPKBchr1226878767226878767LYSTchr1235842628235842628
large_intestineITPKBchr1226878902226878902GNG4chr1235803414235803414
ovaryITPKBchr1226897363226897383chr84251636342516383
ovaryITPKBchr1226908328226908348ITPKBchr1226909237226909257
ovaryITPKBchr1226923887226923907ZNF669chr1247266415247266435
pancreasITPKBchr1226872505226872705chr1224179464224179664
pancreasITPKBchr1226877643226877663PCNXL2chr1233195229233195249
pancreasITPKBchr1226891054226891074chr1223589077223589097
pancreasITPKBchr1226924906226924926ITPKBchr1226924971226924991
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 ITPKB related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BU155062ITPKB491291226819575226819655ITPKB1283291226819391226819593
AW965410NFKB112904103500096103504106ITPKB2896291226819401226819743
DB347287PNO1142326840265968403089ITPKB4205061226851529226851615
BQ338653UNC80151062210682535210682626ITPKB962961226820241226820442
BF734773KANSL31512729725916497259279ITPKB1241791226819390226819445

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   
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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=48)
Stat. for Synonymous SNVs
(# total SNVs=11)
Stat. for Deletions
(# total SNVs=1)
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
chr1:226822488-226822488p.T435A3
chr1:226923323-226923323p.E139K2
chr1:226836376-226836376p.A203T2
chr1:226825421-226825421p.R388*2
chr1:226836430-226836430p.P185S2
chr1:226827351-226827351p.D346D2
chr1:226923335-226923335p.S135P2
chr1:226822561-226822561p.I410I2
chr1:226827342-226827342p.V349V1
chr1:226829751-226829751p.I300M1

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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
# sample15 14  4 5  1094  711 13
# mutation15 15  5 5  11104  811 14
nonsynonymous SNV15 12  5 3  853  57 9
synonymous SNV   3    2  351  34 5
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
chr1:226822488p.T909A3
chr1:226923450p.A160S2
chr1:226836376p.A677T2
chr1:226924682p.P238P2
chr1:226924446p.I570I2
chr1:226924822p.G361G1
chr1:226829707p.R165H1
chr1:226923713p.V823V1
chr1:226835066p.R698L1
chr1:226924191p.P545P1

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 ITPKB 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 ITPKB

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

ACTG2,ALK,ARHGEF9,ATP4B,CDX4,FBLN2,FBXO32,
FUT5,GPR64,HIF3A,ITPKB,MAML2,NALCN,PAPSS1,
RGMA,ROPN1,TBX19,TP53BP2,TRPM6,UGT8,VGLL4
ARHGEF15,CD300LG,DOCK6,FGD5,GPIHBP1,GPR146,HSPA12B,
ITPKB,NOTCH4,NPR1,PALM,PCDH12,PDE2A,PPP1R16B,
ROBO4,SCARF1,SHANK3,TENC1,TIE1,USHBP1,VWF

AMOTL1,ANK2,ATP8B2,BAALC,CLIP3,DSTYK,ITPKB,
ITPR1,JAM2,JAM3,KIF17,MFNG,NAP1L3,PKNOX2,
PNMAL2,SETBP1,SLC9A9,SYNE1,SYT11,TENC1,ZNF512B
BNC2,CAND2,CDON,DOCK3,FAM129A,GRB10,HSPA2,
ITPKB,CTIF,MTCL1,LAMB2,LYNX1,MID2,MYOCD,
NBEA,PIP5K1C,PRICKLE2,ROR2,WFS1,ZBTB4,ZNF853
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 ITPKB


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