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 PI4KA
Basic gene info.Gene symbolPI4KA
Gene namephosphatidylinositol 4-kinase, catalytic, alpha
SynonymsPI4K-ALPHA|PIK4CA|pi4K230
CytomapUCSC genome browser: 22q11.21
Genomic locationchr22 :21061978-21088955
Type of geneprotein-coding
RefGenesNM_058004.3,
NM_002650.2,
Ensembl idENSG00000241973
DescriptionPI4-kinase alphaphosphatidylinositol 4-kinase 230phosphatidylinositol 4-kinase alphaphosphatidylinositol 4-kinase, type III, alphaptdIns-4-kinase alpha
Modification date20141222
dbXrefs MIM : 600286
HGNC : HGNC
Ensembl : ENSG00000241973
HPRD : 08972
Vega : OTTHUMG00000167440
ProteinUniProt: P42356
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PI4KA
BioGPS: 5297
Gene Expression Atlas: ENSG00000241973
The Human Protein Atlas: ENSG00000241973
PathwayNCI Pathway Interaction Database: PI4KA
KEGG: PI4KA
REACTOME: PI4KA
ConsensusPathDB
Pathway Commons: PI4KA
MetabolismMetaCyc: PI4KA
HUMANCyc: PI4KA
RegulationEnsembl's Regulation: ENSG00000241973
miRBase: chr22 :21,061,978-21,088,955
TargetScan: NM_058004
cisRED: ENSG00000241973
ContextiHOP: PI4KA
cancer metabolism search in PubMed: PI4KA
UCL Cancer Institute: PI4KA
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for PI4KA(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PI4KA
Familial Cancer Database: PI4KA
* 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
Orphanet
DiseaseKEGG Disease: PI4KA
MedGen: PI4KA (Human Medical Genetics with Condition)
ClinVar: PI4KA
PhenotypeMGI: PI4KA (International Mouse Phenotyping Consortium)
PhenomicDB: PI4KA

Mutations for PI4KA
* 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 PI4KA related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a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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=137)
Stat. for Synonymous SNVs
(# total SNVs=29)
Stat. for Deletions
(# total SNVs=3)
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
chr22:21071997-21071997p.P1714P4
chr22:21105625-21105625p.A979T3
chr22:21096961-21096961p.R1125H2
chr22:21064203-21064203p.L1998F2
chr22:21119230-21119230p.L803L2
chr22:21101886-21101886p.Q1058Q2
chr22:21075595-21075595p.Q1645*2
chr22:21104270-21104270p.D998Y2
chr22:21083628-21083628p.P1494L2
chr22:21174038-21174038p.R169Q2

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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
# sample 62251 5 7 118101  2313 20
# mutation 62281 5 7 118111  2914 23
nonsynonymous SNV 51211 4 7 11181  1611 21
synonymous SNV 117  1    73   133 2
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
chr22:21088834p.A717T2
chr22:21150562p.R227Q2
chr22:21174038p.V194V,PI4KA2
chr22:21188862p.R2L,PI4KA2
chr22:21084262p.R119W2
chr22:21156277p.S895Y1
chr22:21066863p.R802H,PI4KA1
chr22:21174157p.E723K1
chr22:21088025p.I460I,PI4KA1
chr22:21107308p.F496L1

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 PI4KA 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 PI4KA

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

BAZ2A,BCL2L13,PRR14L,CABIN1,CDYL2,CRKL,SPECC1L,
DEPDC5,EIF4ENIF1,EP300,HMGXB4,HPS4,LDOC1L,LRBA,
MAPK1,MTMR3,PEX26,PI4KA,RASEF,SF3A1,SNAP29
ANKRD52,ARID1A,PRRC2A,PRRC2B,SLX4,EP400,GCN1L1,
HERC2,INCENP,ITPR3,KDM5C,KIAA0556,PI4KA,POLE,
RSPH3,SEC16A,SEC24C,SMC1A,SNRNP200,SRCAP,TRRAP

AKAP13,PRR14L,CABIN1,SPECC1L,EP300,GBF1,GTPBP1,
HERC1,IL17RA,KIAA1671,LDOC1L,MAPK1,MICAL3,MTMR3,
MYH9,PACSIN2,PI4KA,RAD54L2,SF3A1,VPS13D,ZC3H7B
BRD4,CREBBP,DHX38,EP300,FAM193A,FLII,GBF1,
GTF3C1,HNRNPUL2,KDM2A,MED12,KAT6A,NCOR2,PI4KA,
PTPN23,RAPGEF1,SMG6,SNRNP200,SUPT5H,UBR4,ZNF592
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 PI4KA


There's no related Drug.
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Cross referenced IDs for PI4KA
* 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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