Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 symbol	PFKFB4
	Gene name	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4
	Synonyms	-
	Cytomap	UCSC genome browser: 3p22-p21
	Genomic location	chr3 :48555116-48594227
	Type of gene	protein-coding
	RefGenes	NM_004567.2,
	Ensembl id	ENSG00000114268
	Description	6-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 date	20141207
dbXrefs	MIM : 605320
	HGNC : HGNC
	Ensembl : ENSG00000114268
	HPRD : 05613
	Vega : OTTHUMG00000133528
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PFKFB4
	BioGPS: 5210
	Gene Expression Atlas: ENSG00000114268
	The Human Protein Atlas: ENSG00000114268
Pathway	NCI Pathway Interaction Database: PFKFB4
	KEGG: PFKFB4
	REACTOME: PFKFB4
	ConsensusPathDB
	Pathway Commons: PFKFB4
Metabolism	MetaCyc: PFKFB4
	HUMANCyc: PFKFB4
Regulation	Ensembl's Regulation: ENSG00000114268
	miRBase: chr3 :48,555,116-48,594,227
	TargetScan: NM_004567
	cisRED: ENSG00000114268
Context	iHOP: PFKFB4
	cancer metabolism search in PubMed: PFKFB4
	UCL Cancer Institute: PFKFB4
Assigned class in ccmGDB	C

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Phenotypic Information for PFKFB4(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM REACTOME_METABOLISM_OF_CARBOHYDRATES REACTOME_GLUCOSE_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: PFKFB4
	MedGen: PFKFB4 (Human Medical Genetics with Condition)
	ClinVar: PFKFB4
Phenotype	MGI: PFKFB4 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	PFKFB4	chr3	48566459	48566479		chr20	52127856	52127876

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PFKFB4 related fusion information.

Head Gene

Tail Gene

Accession

Gene_a

qStart_a

qEnd_a

Chromosome_a

tStart_a

tEnd_a

Gene_a

qStart_a

qEnd_a

Chromosome_a

tStart_a

tEnd_a

CV325109

SPATA13

243

24808042

24808266

PFKFB4

236

386

48583324

48583474

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy 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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SNV 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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Somatic 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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Top 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 position	Mutation(aa)	Unique sampleID count
chr3:48572957-48572957	p.N325N	2
chr3:48573041-48573041	p.L297L	2
chr3:48563038-48563038	p.R351Q	2
chr3:48563046-48563046	p.F348F	2
chr3:48573763-48573763	p.R256W	2
chr3:48561136-48561136	p.A407V	2
chr3:48561154-48561154	p.Y401C	1
chr3:48576037-48576037	p.S176R	1
chr3:48563100-48563100	p.G330G	1
chr3:48587594-48587594	p.K57N	1

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	1	1		5	1		2		1			7			1		9	3		6
# mutation	1	1		5	1		2		1			7			1		9	3		7
nonsynonymous SNV		1		4	1		1					6			1		5	2		4
synonymous SNV	1			1			1		1			1					4	1		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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Top 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 Position	Mutation(aa)	Unique sampleID count
chr3:48563046	p.R256R	2
chr3:48573763	p.F348F	2
chr3:48575961	p.R446L	1
chr3:48560975	p.G269G	1
chr3:48587623	p.K57N	1
chr3:48563078	p.A427V	1
chr3:48575973	p.R267R	1
chr3:48560992	p.P48S	1
chr3:48587628	p.L421L	1
chr3:48563099	p.G46D	1

Other 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

Copy 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

Gene 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.

Differential 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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CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB04395	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4	experimental	Phosphoaminophosphonic Acid-Adenylate Ester
DB04493	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4	experimental	Fructose-6-Phosphate
DB00515	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4	approved	Cisplatin

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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