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 PIP5K1B
Basic gene info.Gene symbolPIP5K1B
Gene namephosphatidylinositol-4-phosphate 5-kinase, type I, beta
SynonymsMSS4|STM7
CytomapUCSC genome browser: 9q13
Genomic locationchr9 :71320615-71624091
Type of geneprotein-coding
RefGenesNM_001031687.1,
NM_001278253.1,NM_003558.3,
Ensembl idENSG00000107242
DescriptionPIP5K1-betaPIP5KIbetaphosphatidylinositol 4-phosphate 5-kinase type I betaphosphatidylinositol 4-phosphate 5-kinase type-1 betaphosphatidylinositol-4-phosphate 5-kinase type-1 betaprotein STM-7ptdIns(4)P-5-kinase 1 betatype I phosphatidylinositol 4
Modification date20141207
dbXrefs MIM : 602745
HGNC : HGNC
Ensembl : ENSG00000107242
HPRD : 04121
Vega : OTTHUMG00000019976
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PIP5K1B
BioGPS: 8395
Gene Expression Atlas: ENSG00000107242
The Human Protein Atlas: ENSG00000107242
PathwayNCI Pathway Interaction Database: PIP5K1B
KEGG: PIP5K1B
REACTOME: PIP5K1B
ConsensusPathDB
Pathway Commons: PIP5K1B
MetabolismMetaCyc: PIP5K1B
HUMANCyc: PIP5K1B
RegulationEnsembl's Regulation: ENSG00000107242
miRBase: chr9 :71,320,615-71,624,091
TargetScan: NM_001031687
cisRED: ENSG00000107242
ContextiHOP: PIP5K1B
cancer metabolism search in PubMed: PIP5K1B
UCL Cancer Institute: PIP5K1B
Assigned class in ccmGDBC

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Phenotypic Information for PIP5K1B(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PIP5K1B
Familial Cancer Database: PIP5K1B
* 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
REACTOME_PHOSPHOLIPID_METABOLISM
REACTOME_PI_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: PIP5K1B
MedGen: PIP5K1B (Human Medical Genetics with Condition)
ClinVar: PIP5K1B
PhenotypeMGI: PIP5K1B (International Mouse Phenotyping Consortium)
PhenomicDB: PIP5K1B

Mutations for PIP5K1B
* 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
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- 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
breastPIP5K1Bchr97139326671393266PIP5K1Bchr97140633971406339
ovaryPIP5K1Bchr97138654771386567COL11A1chr1103567281103567301
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 PIP5K1B related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF358668PIP5K1B10212997158221271582242ABHD15114377172788921727889480
X92493CNKSR27116X2167255621672665PIP5K1B115276497132061671624091

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 12 16 3    1   
GAIN (# sample)    1 1 1        
LOSS (# sample) 1 11 15 2    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=1

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=2)
Stat. for Synonymous SNVs
(# total SNVs=1)
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
chr9:71437571-71437571p.K14R1
chr9:71509318-71509318p.G179*1
chr9:71509353-71509353p.N190N1
chr9:71509426-71509426p.R215C1

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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 2153 7    64   141 7
# mutation 2143 7    94   201 8
nonsynonymous SNV 1 32 4    82   161 5
synonymous SNV 1111 3    12   4  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
chr9:71509353p.N190N,PIP5K1B2
chr9:71509489p.R410L,PIP5K1B2
chr9:71549833p.L53I,PIP5K1B2
chr9:71478840p.E236K,PIP5K1B2
chr9:71555671p.S427L,PIP5K1B1
chr9:71532555p.S111S,PIP5K1B1
chr9:71549846p.L280I,PIP5K1B1
chr9:71491667p.E285E,PIP5K1B1
chr9:71555691p.E431K,PIP5K1B1
chr9:71509364p.I115M,PIP5K1B1

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 PIP5K1B 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 PIP5K1B

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

LINC00470___CHMP1B,CBWD3,FAM122A,FOXD4L5,FREM2,FXN,INPP5A,
KIAA1875,LOC442421,OR4D9,PIP5K1B,PPFIA4,PRKACG,PTAR1,
PWWP2B,SCARNA20,SHOC2,SIRPB1,SMC5,TJP2,ZMIZ1
ARMCX5,ATL1,DST,CCSER1,FGFR2,GRAMD3,KIAA1671,
KLF5,LRAT,MFSD6,MUC15,MYLK,NAP1L2,NTN4,
NUP35,OSBPL9,PIP5K1B,REPS1,SOX9,TES,TMEM30B

C1orf210,C4orf19,TMEM246,CASP7,CMPK1,CORO2A,ENPP4,
FAM120A,MOB3B,MUC13,PIP5K1B,PLS1,RAB14,RASEF,
RBM47,SCP2,SH3BGRL2,SLC17A5,SLC35A3,TJP2,TMEM171
ABHD3,APPL2,ATP1B3,CCDC68,CLCN2,EPS8,ABHD17C,
HHLA2,LGR4,LNX2,NR3C2,PIP4K2C,PIP5K1B,RIOK3,
SLC26A3,STX3,TAOK3,TJP3,TMEM45B,TRIM36,WASL
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 PIP5K1B


There's no related Drug.
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Cross referenced IDs for PIP5K1B
* 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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