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 PFKM

Basic gene info.	Gene symbol	PFKM
	Gene name	phosphofructokinase, muscle
	Synonyms	ATP-PFK\|GSD7\|PFK-1\|PFK1\|PFKA\|PFKX\|PPP1R122
	Cytomap	UCSC genome browser: 12q13.3
	Genomic location	chr12 :48513012-48540187
	Type of gene	protein-coding
	RefGenes	NM_000289.5, NM_001166686.1,NM_001166687.1,NM_001166688.1,
	Ensembl id	ENSG00000152556
	Description	6-phosphofructo-1-kinase6-phosphofructokinase type A6-phosphofructokinase, muscle typeATP-PFKATP-dependent 6-phosphofructokinase, muscle typePFK-Aphosphofructo-1-kinase isozyme Aphosphofructokinase 1phosphofructokinase, polypeptide Xphosphofructo
	Modification date	20141207
dbXrefs	MIM : 610681
	HGNC : HGNC
	Ensembl : ENSG00000152556
	HPRD : 01988
	Vega : OTTHUMG00000169898
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PFKM
	BioGPS: 5213
	Gene Expression Atlas: ENSG00000152556
	The Human Protein Atlas: ENSG00000152556
Pathway	NCI Pathway Interaction Database: PFKM
	KEGG: PFKM
	REACTOME: PFKM
	ConsensusPathDB
	Pathway Commons: PFKM
Metabolism	MetaCyc: PFKM
	HUMANCyc: PFKM
Regulation	Ensembl's Regulation: ENSG00000152556
	miRBase: chr12 :48,513,012-48,540,187
	TargetScan: NM_000289
	cisRED: ENSG00000152556
Context	iHOP: PFKM
	cancer metabolism search in PubMed: PFKM
	UCL Cancer Institute: PFKM
Assigned class in ccmGDB	C

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

Cancer Description
Cancer	CGAP: PFKM
	Familial Cancer Database: PFKM

* 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: PFKM
	MedGen: PFKM (Human Medical Genetics with Condition)
	ClinVar: PFKM
Phenotype	MGI: PFKM (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PFKM

Mutations for PFKM

* 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

There's no inter-chromosomal structural variation.

- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	PFKM	chr12	48518784	48518804	PFKM	chr12	48520305	48520325
ovary	PFKM	chr12	48532507	48532527	R3HDM2	chr12	57663234	57663254
ovary	PFKM	chr12	48534457	48534477		chr12	52253952	52253972

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 PFKM 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
DA077791	TUBA1B	1	99	12	49525080	49525178	PFKM	98	502	12	48531503	48534653
DA368227	PHLDA3	1	100	1	201438246	201438345	PFKM	99	570	12	48533074	48535735
BX537703	PFKM	1	108	12	48535350	48535457	PFKM	101	4630	12	48535108	48539887

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=53)	Stat. for Synonymous SNVs (# total SNVs=23)

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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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
chr12:48529111-48529111	p.T294I	2
chr12:48534513-48534513	p.S400S	2
chr12:48529142-48529142	p.T304T	2
chr12:48534587-48534587	p.I425T	2
chr12:48538878-48538878	p.W686L	2
chr12:48534623-48534623	p.H437L	2
chr12:48538894-48538894	p.I691M	2
chr12:48531547-48531547	p.G327E	2
chr12:48537853-48537853	p.Y635Y	2
chr12:48526792-48526792	p.T127P	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		4	1	5	1		1		1	1		3	7	2		1	3	7		8
# mutation		4	1	7	1		1		1	1		3	7	2		1	3	7		12
nonsynonymous SNV		2		5			1		1			3	5	1		1	1	4		8
synonymous SNV		2	1	2	1					1			2	1			2	3		4

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
chr12:48524199	p.R47S,PFKM	2
chr12:48536608	p.R566L,PFKM	2
chr12:48501950	p.A8P,PFKM	1
chr12:48536719	p.G399G,PFKM	1
chr12:48528758	p.G648G,PFKM	1
chr12:48539462	p.S400S,PFKM	1
chr12:48535119	p.Q664L,PFKM	1
chr12:48501970	p.R98Q,PFKM	1
chr12:48537586	p.A413T,PFKM	1
chr12:48528785	p.R673M,PFKM	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 PFKM 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 PFKM

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


ABCA2,ARF3,BRSK1,KANSL2,CHD4,DDX23,GDF11, GPR173,MAP3K12,KMT2B___KMT2D,NCDN,PFKM,PLCD4,RAB39B, RNF41,SALL2,SENP1,SYNGAP1,TMEM106C,ZNF516,ZSWIM5	RBFOX1,ANKRD23,ASB12,ASB16,CACNG1,CALML6,CMYA5, DUSP26,FEM1A,JPH1,KLHL38,MYADML2,MYOM3,OBSCN, PEBP4,PFKM,RYR1,SRPK3,TMEM38A,TRIM54,UCP3

C10orf2,CDK4,CS,DDN,DDX55,ESPL1,HSPD1, LDHB,LRPPRC,MARS2,MGC14436,NAA25,NOLC1,PA2G4, PDCD11,PFKM,POLR1B,PUS1,SCLY,TRAP1,XPOT	ABI2,APBB1,CD81,DCBLD2,DIP2C,KANK1,KCTD15, TP73-AS1,LPPR2,MID2,PDE2A,PDZRN3,PFKM,PHC1, RBFOX2,SEMA4C,SLC29A1,STAT5B,TACC1,TMEM43,ZBTB4

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 PFKM

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
DB02726	phosphofructokinase, muscle	experimental	2-Phosphoglycolic Acid
DB04493	phosphofructokinase, muscle	experimental	Fructose-6-Phosphate

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Cross referenced IDs for PFKM

* 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