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 PFKP

Basic gene info.	Gene symbol	PFKP
	Gene name	phosphofructokinase, platelet
	Synonyms	ATP-PFK\|PFK-C\|PFK-P\|PFKF
	Cytomap	UCSC genome browser: 10p15.3-p15.2
	Genomic location	chr10 :3110818-3178997
	Type of gene	protein-coding
	RefGenes	NM_001242339.1, NM_002627.4,
	Ensembl id	ENSG00000067057
	Description	6-phosphofructokinase type C6-phosphofructokinase, platelet typeATP-PFKATP-dependent 6-phosphofructokinase, platelet typePhosphofructokinase, platelet typephosphofructo-1-kinase isozyme Cphosphofructokinase 1phosphohexokinase
	Modification date	20141207
dbXrefs	MIM : 171840
	HGNC : HGNC
	Ensembl : ENSG00000067057
	HPRD : 01384
	Vega : OTTHUMG00000017556
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PFKP
	BioGPS: 5214
	Gene Expression Atlas: ENSG00000067057
	The Human Protein Atlas: ENSG00000067057
Pathway	NCI Pathway Interaction Database: PFKP
	KEGG: PFKP
	REACTOME: PFKP
	ConsensusPathDB
	Pathway Commons: PFKP
Metabolism	MetaCyc: PFKP
	HUMANCyc: PFKP
Regulation	Ensembl's Regulation: ENSG00000067057
	miRBase: chr10 :3,110,818-3,178,997
	TargetScan: NM_001242339
	cisRED: ENSG00000067057
Context	iHOP: PFKP
	cancer metabolism search in PubMed: PFKP
	UCL Cancer Institute: PFKP
Assigned class in ccmGDB	C

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

Cancer 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/

Metabolic Pathway Description
KEGG_GLYCOLYSIS_GLUCONEOGENESIS KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM KEGG_GALACTOSE_METABOLISM REACTOME_METABOLISM_OF_CARBOHYDRATES REACTOME_GLUCOSE_METABOLISM

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

Structural Variants in COSMIC : go to COSMIC mutation histogram

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

Related fusion transcripts : go to Chitars2.0

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

ID	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
AA350049	MARK1	1	110	1	220837603	220837712	PFKP	105	292	10	3170511	3170698
DB459081	LYPLA1	1	270	8	55013468	55014552	PFKP	270	370	10	3154477	3154577
BP431482	PFKP	4	269	10	3178690	3178956	STRAP	258	333	12	16055870	16055944
U33818	PFKP	1	119	10	3170203	3170322	PABPC4	118	2394	1	40026502	40041659
BI005429	TG	1	275	8	134125702	134144076	PFKP	266	420	10	3149421	3150966

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

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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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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=3

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Somatic 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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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
chr10:3149418-3149418	p.R265fs*2	4
chr10:3176752-3176752	p.K700N	3
chr10:3154433-3154433	p.A370V	2
chr10:3178031-3178032	p.?	2
chr10:3155620-3155620	p.A427A	2
chr10:3150932-3150932	p.I304V	2
chr10:3155348-3155348	p.A398P	2
chr10:3145973-3145973	p.Q153K	2
chr10:3150973-3150973	p.F317F	2
chr10:3155672-3155672	p.A445T	2

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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		3		12	1		3		1			5	2	2	1	1		10	2	9
# mutation		3		11	1		3		1			6	3	2	1	1		10	2	10
nonsynonymous SNV		2		9	1		3					3	2	2	1	1		8	2	7
synonymous SNV		1		2					1			3	1					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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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
chr10:3151612	p.N667N,PFKP	2
chr10:3175485	p.R48C,PFKP	2
chr10:3155602	p.C343C,PFKP	2
chr10:3124609	p.P421P,PFKP	2
chr10:3174604	p.D648N,PFKP	1
chr10:3141502	p.N151N,PFKP	1
chr10:3178006	p.N426S,PFKP	1
chr10:3150944	p.V429I,PFKP	1
chr10:3155656	p.N667Y,PFKP	1
chr10:3175425	p.A158V,PFKP	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 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

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


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

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 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