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 PI4K2B
Basic gene info.Gene symbolPI4K2B
Gene namephosphatidylinositol 4-kinase type 2 beta
SynonymsPI4KIIB|PIK42B
CytomapUCSC genome browser: 4p15.2
Genomic locationchr4 :25235652-25280831
Type of geneprotein-coding
RefGenesNM_018323.3,
Ensembl idENSG00000038210
DescriptionPI4KII-BETAphosphatidylinositol 4-kinase type 2-betaphosphatidylinositol 4-kinase type II-betaphosphatidylinositol 4-kinase type-II beta
Modification date20141207
dbXrefs MIM : 612101
HGNC : HGNC
Ensembl : ENSG00000038210
HPRD : 15132
Vega : OTTHUMG00000128564
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PI4K2B
BioGPS: 55300
Gene Expression Atlas: ENSG00000038210
The Human Protein Atlas: ENSG00000038210
PathwayNCI Pathway Interaction Database: PI4K2B
KEGG: PI4K2B
REACTOME: PI4K2B
ConsensusPathDB
Pathway Commons: PI4K2B
MetabolismMetaCyc: PI4K2B
HUMANCyc: PI4K2B
RegulationEnsembl's Regulation: ENSG00000038210
miRBase: chr4 :25,235,652-25,280,831
TargetScan: NM_018323
cisRED: ENSG00000038210
ContextiHOP: PI4K2B
cancer metabolism search in PubMed: PI4K2B
UCL Cancer Institute: PI4K2B
Assigned class in ccmGDBC

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Phenotypic Information for PI4K2B(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PI4K2B
Familial Cancer Database: PI4K2B
* 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
REACTOME_PHOSPHOLIPID_METABOLISM
REACTOME_PI_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: PI4K2B
MedGen: PI4K2B (Human Medical Genetics with Condition)
ClinVar: PI4K2B
PhenotypeMGI: PI4K2B (International Mouse Phenotyping Consortium)
PhenomicDB: PI4K2B

Mutations for PI4K2B
* 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
There's no inter-chromosomal structural variation.
- 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
ovaryPI4K2Bchr42524368625243706chr42521977225219792
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 PI4K2B related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AW936523PI4K2B1230642525501125255306PI4K2B30255842523818225238438

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
There's no copy number variation information in COSMIC data for this gene.

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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=6

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=40)
Stat. for Synonymous SNVs
(# total SNVs=4)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
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
chr4:25262148-25262148p.R305G4
chr4:25256861-25256861p.H200Y2
chr4:25258231-25258231p.K231*2
chr4:25258233-25258233p.K231N2
chr4:25235801-25235801p.E6K2
chr4:25270155-25270155p.N390S1
chr4:25260689-25260689p.Y263D1
chr4:25262208-25262208p.H325Y1
chr4:25253995-25253995p.A107A1
chr4:25270159-25270159p.F391F1

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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=6

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 2 14  2 2  313  6417
# mutation 2 12  2 2  313  5418
nonsynonymous SNV 2 10    2  312  2317
synonymous SNV   2  2      1  31 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
chr4:25262148p.R305G4
chr4:25258233p.K231N3
chr4:25256832p.A190V2
chr4:25256861p.H200Y2
chr4:25258202p.A221V2
chr4:25258232p.R305T1
chr4:25262206p.T429I1
chr4:25270809p.R305S1
chr4:25256819p.G458G1
chr4:25265389p.Q317R1

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 PI4K2B 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 PI4K2B

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

ACTR2,CLINT1,DCUN1D1,DHX15,KIAA1033,KLF3,MOB1A,
NCAPG,PDS5A,PI4K2B,PPP1CB,PPP3R1,SCYL2,SEC24A,
SLC30A6,SMC2,SMC5,SMEK2,STRN,TMPO,XPO1
ABCE1,ABI1,C5orf28,CD47,DSC2,ETNK1,FBXO5,
NUS1,OAT,PHF6,PI4K2B,PPAT,PRKCI,PRPF40A,
RFC3,RNF138,PTBP3,TMEM123,TMPO,USP1,ZNF131

CCNA2,COQ2,COX18,DCK,DEPDC1,DHX15,GRSF1,
MAD2L1,NCAPG,NUP54,PACRGL,PDS5A,PGM2,PI4K2B,
PPA2,RMI1,SLBP,SLC30A9,TMEM33,UBE2K,ZCCHC4
ABCB10,AK2,C1GALT1,INIP,CXorf38,ERP44,GCH1,
GSR,H2AFY,MGST2,MPDU1,NECAP1,OXNAD1,PI4K2B,
PPP2R2A,RAB1A,RTCA,S100A14,TPD52,TSPAN8,ZBTB8OS
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 PI4K2B


There's no related Drug.
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Cross referenced IDs for PI4K2B
* 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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