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 PFKP
Basic gene info.Gene symbolPFKP
Gene namephosphofructokinase, platelet
SynonymsATP-PFK|PFK-C|PFK-P|PFKF
CytomapUCSC genome browser: 10p15.3-p15.2
Genomic locationchr10 :3110818-3178997
Type of geneprotein-coding
RefGenesNM_001242339.1,
NM_002627.4,
Ensembl idENSG00000067057
Description6-phosphofructokinase type C6-phosphofructokinase, platelet typeATP-PFKATP-dependent 6-phosphofructokinase, platelet typePhosphofructokinase, platelet typephosphofructo-1-kinase isozyme Cphosphofructokinase 1phosphohexokinase
Modification date20141207
dbXrefs MIM : 171840
HGNC : HGNC
Ensembl : ENSG00000067057
HPRD : 01384
Vega : OTTHUMG00000017556
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PFKP
BioGPS: 5214
Gene Expression Atlas: ENSG00000067057
The Human Protein Atlas: ENSG00000067057
PathwayNCI Pathway Interaction Database: PFKP
KEGG: PFKP
REACTOME: PFKP
ConsensusPathDB
Pathway Commons: PFKP
MetabolismMetaCyc: PFKP
HUMANCyc: PFKP
RegulationEnsembl's Regulation: ENSG00000067057
miRBase: chr10 :3,110,818-3,178,997
TargetScan: NM_001242339
cisRED: ENSG00000067057
ContextiHOP: PFKP
cancer metabolism search in PubMed: PFKP
UCL Cancer Institute: PFKP
Assigned class in ccmGDBC

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Phenotypic Information for PFKP(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PFKP
Familial Cancer Database: PFKP
* 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_GLYCOLYSIS_GLUCONEOGENESIS
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM
KEGG_GALACTOSE_METABOLISM
REACTOME_METABOLISM_OF_CARBOHYDRATES
REACTOME_GLUCOSE_METABOLISM

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

Mutations for PFKP
* 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 PFKP related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AA350049MARK111101220837603220837712PFKP1052921031705113170698
DB459081LYPLA1127085501346855014552PFKP2703701031544773154577
BP431482PFKP42691031786903178956STRAP258333121605587016055944
U33818PFKP11191031702033170322PABPC4118239414002650240041659
BI005429TG12758134125702134144076PFKP2664201031494213150966

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 # sample12        2      
GAIN (# sample) 1        2      
LOSS (# sample)11               
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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=68)
Stat. for Synonymous SNVs
(# total SNVs=27)
Stat. for Deletions
(# total SNVs=4)
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
chr10:3149418-3149418p.R265fs*24
chr10:3176752-3176752p.K700N3
chr10:3151664-3151664p.V361M2
chr10:3178006-3178006p.E734G2
chr10:3147342-3147342p.R219Q2
chr10:3155602-3155602p.P421P2
chr10:3154433-3154433p.A370V2
chr10:3178031-3178032p.?2
chr10:3155620-3155620p.A427A2
chr10:3150932-3150932p.I304V2

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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 3 121 3 1  52211 1029
# mutation 3 111 3 1  63211 10210
nonsynonymous SNV 2 91 3    32211 827
synonymous SNV 1 2    1  31    2 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
chr10:3151612p.N667N,PFKP2
chr10:3175485p.R48C,PFKP2
chr10:3155602p.C343C,PFKP2
chr10:3124609p.P421P,PFKP2
chr10:3177999p.N426S,PFKP1
chr10:3149487p.D648N,PFKP1
chr10:3155654p.N151N,PFKP1
chr10:3174604p.V429I,PFKP1
chr10:3141502p.N667Y,PFKP1
chr10:3150944p.A158V,PFKP1

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 PFKP 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 PFKP

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

ATP5C1,BTG3,MSANTD3,CDC123,CDC20,ENO1,GPI,
GTPBP4,HSPA14,IFRD1,MCM10,NUDT5,OPTN,PDSS1,
PFKP,PITRM1,PLK1,RBM17,S100A10,SUV39H2,TUBA1C
ACOT7,ACTN4,CAPN1,CCDC102A,CHPF2,FAM129B,FBLIM1,
KCTD17,NCS1,PFKP,PLEKHA4,PPP6R1,SEPT9,SLC39A1,
SPHK1,TAGLN,THOC6,TRIM47,VASP,WDR1,ZYX

ASPHD2,MYRF,DNAAF3,CDC42EP1,CDCP1,DOCK5,DUSP4,
ENO1,GPR126,LMNA,PFKP,PGAM1,PKM,PLLP,
PRSS12,RAB27B,SDHA,SEMA4B,SGPP2,SLC16A3,WRAP53
ARHGDIA,CDKN1A,CEACAM5,CTTN,DNAJC5,GTPBP1,LHFPL2,
LRP10,MXD1,PCBP1,PFKP,PLEKHA7,PLIN3,SLC37A1,
SMPD1,STK24,TRIM14,XDH,YKT6,ZER1,ZNFX1
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 PFKP


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