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 PFKFB4
Basic gene info.Gene symbolPFKFB4
Gene name6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4
Synonyms-
CytomapUCSC genome browser: 3p22-p21
Genomic locationchr3 :48555116-48594227
Type of geneprotein-coding
RefGenesNM_004567.2,
Ensembl idENSG00000114268
Description6-phosphofructo-2-kinase/fructose-2,6-biphosphatase-46-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 46PF-2-K/Fru-2,6-P2ase 46PF-2-K/Fru-2,6-P2ase testis-type isozymePFK/FBPase 4bifunctional enzyme with kinase and biphosphatase activities
Modification date20141207
dbXrefs MIM : 605320
HGNC : HGNC
Ensembl : ENSG00000114268
HPRD : 05613
Vega : OTTHUMG00000133528
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PFKFB4
BioGPS: 5210
Gene Expression Atlas: ENSG00000114268
The Human Protein Atlas: ENSG00000114268
PathwayNCI Pathway Interaction Database: PFKFB4
KEGG: PFKFB4
REACTOME: PFKFB4
ConsensusPathDB
Pathway Commons: PFKFB4
MetabolismMetaCyc: PFKFB4
HUMANCyc: PFKFB4
RegulationEnsembl's Regulation: ENSG00000114268
miRBase: chr3 :48,555,116-48,594,227
TargetScan: NM_004567
cisRED: ENSG00000114268
ContextiHOP: PFKFB4
cancer metabolism search in PubMed: PFKFB4
UCL Cancer Institute: PFKFB4
Assigned class in ccmGDBC

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Phenotypic Information for PFKFB4(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PFKFB4
Familial Cancer Database: PFKFB4
* 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_FRUCTOSE_AND_MANNOSE_METABOLISM
REACTOME_METABOLISM_OF_CARBOHYDRATES
REACTOME_GLUCOSE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: PFKFB4
MedGen: PFKFB4 (Human Medical Genetics with Condition)
ClinVar: PFKFB4
PhenotypeMGI: PFKFB4 (International Mouse Phenotyping Consortium)
PhenomicDB: PFKFB4

Mutations for PFKFB4
* 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
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryPFKFB4chr34856645948566479chr205212785652127876
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 PFKFB4 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CV325109SPATA1316243132480804224808266PFKFB423638634858332448583474

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
There's no copy number variation information in COSMIC data for this gene.

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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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=33)
Stat. for Synonymous SNVs
(# total SNVs=9)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
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
chr3:48573041-48573041p.L297L2
chr3:48563038-48563038p.R351Q2
chr3:48563046-48563046p.F348F2
chr3:48573763-48573763p.R256W2
chr3:48561136-48561136p.A407V2
chr3:48572957-48572957p.N325N2
chr3:48573023-48573023p.Q303H1
chr3:48594160-48594160p.M17I1
chr3:48559432-48559432p.R446Q1
chr3:48573845-48573845p.N228N1

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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
# sample11 51 2 1  7  1 93 6
# mutation11 51 2 1  7  1 93 7
nonsynonymous SNV 1 41 1    6  1 52 4
synonymous SNV1  1  1 1  1    41 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
chr3:48573763p.F348F2
chr3:48563046p.R256R2
chr3:48576698p.P375S1
chr3:48561153p.S201F1
chr3:48572951p.K362N1
chr3:48576723p.C197F1
chr3:48561204p.K362E1
chr3:48573722p.S176R1
chr3:48577140p.R351Q1
chr3:48561233p.A167A1

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 PFKFB4 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 PFKFB4

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

ADM,ALDOA,ANKRD37,BNIP3,CA9,ENO2,FSHB,
GPI,LDHA,NCKIPSD,NDRG1,P4HA1,PFKFB4,PGAM1,
PGK1,PKM,SHISA5,SLC16A3,SLC2A1,SPAG4,WDR54
ACSS1,ARHGAP39,DCAF11,EIF2B5,FAM102A,GPRC5C,KIF22,
LLGL2,LRRC56,MAPK13,PFKFB4,PLA2G4F,PPP2R4,RAB17,
ROGDI,SNAP47,SNRPD3,SYNGR1,TRAFD1,WRNIP1,ZBTB42

AGR2,ASRGL1,TEX40,HID1,CCNJL,CHST5,CREB3L1,
DLL1,EGLN3,FAM174B,FAM57A,GFI1,GMDS,IMPA2,
KLK1,LRRIQ4,P4HA1,PFKFB4,PGAM1,SGSM3,ST6GALNAC1
ABCC2,SMIM24,CYP2D6,CYP3A4,DAK,DNASE1,GRAMD1B,
KDM8,KCNH6,MME,MRO,NR0B2,PFKFB4,PLB1,
PRODH,RBP3,REEP6,SERPINA1,SLC5A9,SLC7A7,SULT2A1
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 PFKFB4
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB043956-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4experimentalPhosphoaminophosphonic Acid-Adenylate Ester
DB044936-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4experimentalFructose-6-Phosphate
DB005156-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4approvedCisplatin


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Cross referenced IDs for PFKFB4
* 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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