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 PIP5K1A
Basic gene info.Gene symbolPIP5K1A
Gene namephosphatidylinositol-4-phosphate 5-kinase, type I, alpha
Synonyms-
CytomapUCSC genome browser: 1q21.3
Genomic locationchr1 :151171020-151222007
Type of geneprotein-coding
RefGenesNM_001135636.1,
NM_001135637.1,NM_001135638.1,NM_003557.2,
Ensembl idENSG00000143398
Description68 kDa type I phosphatidylinositol 4-phosphate 5-kinase alpha68 kDa type I phosphatidylinositol-4-phosphate 5-kinase alphaPIP5K1-alphaPIP5KIalphaphosphatidylinositol 4-phosphate 5-kinase type I alphaphosphatidylinositol 4-phosphate 5-kinase type-1 al
Modification date20141207
dbXrefs MIM : 603275
HGNC : HGNC
Ensembl : ENSG00000143398
Vega : OTTHUMG00000012351
ProteinUniProt: Q99755
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PIP5K1A
BioGPS: 8394
Gene Expression Atlas: ENSG00000143398
The Human Protein Atlas: ENSG00000143398
PathwayNCI Pathway Interaction Database: PIP5K1A
KEGG: PIP5K1A
REACTOME: PIP5K1A
ConsensusPathDB
Pathway Commons: PIP5K1A
MetabolismMetaCyc: PIP5K1A
HUMANCyc: PIP5K1A
RegulationEnsembl's Regulation: ENSG00000143398
miRBase: chr1 :151,171,020-151,222,007
TargetScan: NM_001135636
cisRED: ENSG00000143398
ContextiHOP: PIP5K1A
cancer metabolism search in PubMed: PIP5K1A
UCL Cancer Institute: PIP5K1A
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for PIP5K1A(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PIP5K1A
Familial Cancer Database: PIP5K1A
* 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
KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS

check002.gifOthers
OMIM 603275; gene.
Orphanet
DiseaseKEGG Disease: PIP5K1A
MedGen: PIP5K1A (Human Medical Genetics with Condition)
ClinVar: PIP5K1A
PhenotypeMGI: PIP5K1A (International Mouse Phenotyping Consortium)
PhenomicDB: PIP5K1A

Mutations for PIP5K1A
* 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
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryPIP5K1Achr1151211579151211599PIP5K1Achr1151214312151214332
pancreasPIP5K1Achr1151212636151212656chr1153400235153400255
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 PIP5K1A related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CD388184NSF103613174479899544799500PIP5K1A6096321151210665151210701
BQ321472CAMKK212035012121698291121698521PIP5K1A3445081151171640151171802
BE172039NEDD4L1325185606470556065256PIP5K1A3124001151172777151172868

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=1

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=3)
Stat. for Synonymous SNVs
(# total SNVs=0)
There's no s-snv.
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
chr1:151199812-151199812p.G45D1
chr1:151204828-151204828p.P145L1
chr1:151205165-151205165p.P196A1
chr1:151214632-151214632p.G453D1
chr1:151215011-151215011p.L523L1

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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
# sample3317  3    661  65 9
# mutation6337  3    661  75 10
nonsynonymous SNV4115  3    561  54 8
synonymous SNV2222       1    21 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
chr1:151214646p.R431W,PIP5K1A2
chr1:151205165p.L153L,PIP5K1A2
chr1:151171540p.S23C,PIP5K1A2
chr1:151205035p.P197A,PIP5K1A2
chr1:151206804p.V103L,PIP5K1A1
chr1:151204201p.R208P,PIP5K1A1
chr1:151212450p.G426S,PIP5K1A1
chr1:151205059p.E105A,PIP5K1A1
chr1:151219399p.M242I,PIP5K1A1
chr1:151206841p.R126C,PIP5K1A1

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 PIP5K1A 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 PIP5K1A

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

ARNT,CDC42SE1,COPA,GABPB2,GATAD2B,GON4L,LYSMD1,
PI4KB,PIP5K1A,PIPSL,POGK,POGZ,PRUNE,RNF115,
RPRD2,SETDB1,SLC25A44,SNX27,TADA1,UBAP2L,ZNF687
PCNXL4,SPRTN,SDE2,SUCO,CCP110,FZD6,HSPA14,
MEX3C,MTBP,NUPL1,PIP5K1A,PRKCI,PURB,RBM12,
RBMXL1,SMARCA5,SPTY2D1,TDG,TGS1,TOPORS,VEZF1

ATF6,SPRTN,SDE2,CDC42SE1,CDC73,DEDD,DUSP12,
IPO9,PEX19,PI4KB,PIP5K1A,DESI2,PRCC,RBBP5,
RNF115,SNAP47,TAF1A,TSEN15,TSNAX,XPR1,ZNF669
AP1S3,ARL5B,VCPKMT,MIR22HG,C1orf27,SDE2,TYW5,
CCNH,CCNL1,DDX5,IFRD1,LARP1B,PIP5K1A,PRPF39,
RGS1,SLC19A2,TDG,TIPARP,TUBE1,UFM1,YRDC
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 PIP5K1A
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB Q99755; -.
ChemistryChEMBL CHEMBL5969; -.
ChemistryGuidetoPHARMACOLOGY 2164; -.
Organism-specific databasesPharmGKB PA33327; -.
Organism-specific databasesCTD 8394; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00122phosphatidylinositol-4-phosphate 5-kinase, type I, alphaapproved; nutraceuticalCholine


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Cross referenced IDs for PIP5K1A
* 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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