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 PI4K2A
Basic gene info.Gene symbolPI4K2A
Gene namephosphatidylinositol 4-kinase type 2 alpha
SynonymsPI4KII|PIK42A
CytomapUCSC genome browser: 10q24
Genomic locationchr10 :99400442-99436187
Type of geneprotein-coding
RefGenesNM_018425.3,
Ensembl idENSG00000155252
Descriptionphosphatidylinositol 4-kinase type 2-alphaphosphatidylinositol 4-kinase type II (PI4KII)phosphatidylinositol 4-kinase type II-alpha
Modification date20141218
dbXrefs MIM : 609763
HGNC : HGNC
Ensembl : ENSG00000155252
HPRD : 11431
Vega : OTTHUMG00000018863
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PI4K2A
BioGPS: 55361
Gene Expression Atlas: ENSG00000155252
The Human Protein Atlas: ENSG00000155252
PathwayNCI Pathway Interaction Database: PI4K2A
KEGG: PI4K2A
REACTOME: PI4K2A
ConsensusPathDB
Pathway Commons: PI4K2A
MetabolismMetaCyc: PI4K2A
HUMANCyc: PI4K2A
RegulationEnsembl's Regulation: ENSG00000155252
miRBase: chr10 :99,400,442-99,436,187
TargetScan: NM_018425
cisRED: ENSG00000155252
ContextiHOP: PI4K2A
cancer metabolism search in PubMed: PI4K2A
UCL Cancer Institute: PI4K2A
Assigned class in ccmGDBC

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Phenotypic Information for PI4K2A(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PI4K2A
Familial Cancer Database: PI4K2A
* 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: PI4K2A
MedGen: PI4K2A (Human Medical Genetics with Condition)
ClinVar: PI4K2A
PhenotypeMGI: PI4K2A (International Mouse Phenotyping Consortium)
PhenomicDB: PI4K2A

Mutations for PI4K2A
* 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
ovaryPI4K2Achr109940166299401682PI4K2Achr109940208399402103
ovaryPI4K2Achr109942317699423196PI4K2Achr109940569999405719
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 PI4K2A related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CA307215PI4K2A18537109943528999435808PFDN5534725125369185253693162
AK129943PI4K2A1172109937424399374414ALDH3B11681786116778722967796143

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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=26)
Stat. for Synonymous SNVs
(# total SNVs=5)
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
chr10:99416701-99416701p.V298M2
chr10:99410891-99410891p.R210H2
chr10:99416703-99416703p.V298V2
chr10:99416092-99416092p.V229V1
chr10:99416721-99416721p.I304I1
chr10:99433441-99433441p.S461F1
chr10:99410715-99410715p.F151F1
chr10:99416585-99416585p.S259L1
chr10:99416722-99416722p.R305C1
chr10:99410762-99410762p.T167I1

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample22 91   11 3 1 123 3
# mutation22 81   11 3 1 123 3
nonsynonymous SNV11 61   11 3 1  13 3
synonymous SNV11 2           11   
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
chr10:99416703p.V298V2
chr10:99416633p.R328W1
chr10:99433422p.P176P1
chr10:99410715p.D382Y1
chr10:99416641p.L203P1
chr10:99433434p.S389S1
chr10:99410789p.N206K1
chr10:99416695p.R455S1
chr10:99433441p.P209P1
chr10:99410790p.V229V1

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 PI4K2A 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 PI4K2A

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

ADAP2,AXL,C10orf76,C3AR1,CALHM2,CD33,CD68,
CSF1R,CTSB,HAVCR2,LIPA,LRRC25,MARVELD1,PI4K2A,
PLEKHO2,PSAP,RASGRP4,SFXN3,SIGLEC7,SIGLEC9,SLCO2B1
ADAP2,ARRB2,C1QA,C1QB,C1QC,C2,CD4,
CD86,CLEC10A,FCER1G,HAVCR2,HCK,LGMN,LILRB2,
LILRB4,NCF4,NFAM1,PI4K2A,PSAP,SPI1,TBXAS1

WBP1L,C1orf162,C1R,CSF1,DFNA5,FAM20A,FBLN2,
HAVCR2,PPP1R18,LAIR1,MAFB,MRAS,NRP2,PI4K2A,
PLEKHO2,SERPINF1,SERPING1,SLAMF8,SPI1,TMEM86A,VIM
CGREF1,CHRM4,CREB3L2,DGKZ,GNS,GOLGA8CP,GREB1L,
IRAK2,KIFC3,MPP1,NBAS,NEDD4,PI4K2A,PLOD1,
REG4,SEMA3G,SERPINF2,SFXN3,SIRPA,TK2,UNC5CL
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 PI4K2A


There's no related Drug.
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Cross referenced IDs for PI4K2A
* 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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