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 PIP4K2A
Basic gene info.Gene symbolPIP4K2A
Gene namephosphatidylinositol-5-phosphate 4-kinase, type II, alpha
SynonymsPI5P4KA|PIP5K2A|PIP5KII-alpha|PIP5KIIA|PIPK
CytomapUCSC genome browser: 10p12.2
Genomic locationchr10 :22823765-23003503
Type of geneprotein-coding
RefGenesNM_005028.4,
Ensembl idENSG00000150867
Description1-phosphatidylinositol 5-phosphate 4-kinase 2-alpha1-phosphatidylinositol-4-phosphate kinase1-phosphatidylinositol-4-phosphate-5-kinase1-phosphatidylinositol-5-phosphate 4-kinase 2-alphaPI(5)P 4-kinase type II alphaPIP4KII-alphaPIP5KIIIPIP5KIIalpha
Modification date20141207
dbXrefs MIM : 603140
HGNC : HGNC
Ensembl : ENSG00000150867
HPRD : 11931
Vega : OTTHUMG00000017810
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PIP4K2A
BioGPS: 5305
Gene Expression Atlas: ENSG00000150867
The Human Protein Atlas: ENSG00000150867
PathwayNCI Pathway Interaction Database: PIP4K2A
KEGG: PIP4K2A
REACTOME: PIP4K2A
ConsensusPathDB
Pathway Commons: PIP4K2A
MetabolismMetaCyc: PIP4K2A
HUMANCyc: PIP4K2A
RegulationEnsembl's Regulation: ENSG00000150867
miRBase: chr10 :22,823,765-23,003,503
TargetScan: NM_005028
cisRED: ENSG00000150867
ContextiHOP: PIP4K2A
cancer metabolism search in PubMed: PIP4K2A
UCL Cancer Institute: PIP4K2A
Assigned class in ccmGDBC

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Phenotypic Information for PIP4K2A(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PIP4K2A
Familial Cancer Database: PIP4K2A
* 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: PIP4K2A
MedGen: PIP4K2A (Human Medical Genetics with Condition)
ClinVar: PIP4K2A
PhenotypeMGI: PIP4K2A (International Mouse Phenotyping Consortium)
PhenomicDB: PIP4K2A

Mutations for PIP4K2A
* 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
breastPIP4K2Achr102294496322944963PIP4K2Achr102297498222974982
pancreasPIP4K2Achr102293151922931539PIP4K2Achr102293157022931590
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 PIP4K2A related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BC036779PIP4K2A1342102300311123003452RPS6KC134115521213415911213446808
BM925273PIP4K2A18359102300311123003452RPS6KC13588931213415911213446127
BG007476PSMG26367181272056812725566PIP4K2A366420102283491722834971

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 # sample22 1  1 3 1  1   
GAIN (# sample)21 1  1 2 1      
LOSS (# sample) 1      1    1   
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=13

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=50)
Stat. for Synonymous SNVs
(# total SNVs=15)
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
chr10:22880652-22880652p.R133H12
chr10:22830773-22830773p.F332F3
chr10:22880563-22880563p.H163Y2
chr10:22898640-22898640p.E51K2
chr10:22839628-22839628p.N251S2
chr10:22880621-22880621p.I143I2
chr10:22896899-22896899p.R99H2
chr10:22862345-22862345p.F178L2
chr10:22830970-22830970p.A267T1
chr10:22898568-22898568p.D75N1

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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
# sample31 11  1 21 731  55 9
# mutation31 9  1 21 731  55 9
nonsynonymous SNV21 5    2  531  44 6
synonymous SNV1  4  1  1 2    11 3
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
chr10:22862345p.G380G2
chr10:22830773p.R99H2
chr10:22828900p.F178L2
chr10:22896899p.F332F2
chr10:22828956p.F400L1
chr10:22896910p.A267T1
chr10:22830872p.R102L1
chr10:23003251p.E257G1
chr10:22880610p.T362A1
chr10:22828982p.V254V1

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 PIP4K2A 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 PIP4K2A

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

ARHGAP25,CD28,CD3G,CD5,CD96,DOCK2,EVI2B,
GVINP1,GZMK,IKZF1,IL16,ITK,PIP4K2A,PRKCB,
PTPRC,PYHIN1,SAMD3,SH2D1A,SLAMF6,WIPF1,ZNF831
B2M,CSF2RB,DOCK2,ELMO1,EVI2B,FLI1,GIMAP2,
IFNAR2,IL18R1,LCP2,PIK3AP1,PIP4K2A,PLEK,RAB8B,
RASSF2,SAMHD1,SAMSN1,SLFN11,SYT11,TFEC,WIPF1

APBB1IP,ARHGEF6,CCDC88A,DOCK10,DOCK2,NXPE3,FAM78A,
FLI1,FMNL1,GIMAP1,GIMAP4,GIMAP6,GIMAP8,HCLS1,
HVCN1,PPP1R18,LRRC8C,MYO5A,PIP4K2A,SLA,WIPF1
ANKRD44,APBB1IP,ARHGAP25,ARHGAP30,BEND4,CHST11,FLI1,
FMNL3,HVCN1,INPP5D,KIAA0922,NCKAP1L,ORAI2,PIK3CD,
PIP4K2A,RAB39B,RFTN1,SH2D3C,SPOCK2,TRAF1,WIPF1
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 PIP4K2A


There's no related Drug.
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Cross referenced IDs for PIP4K2A
* 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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