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 symbolPFKM
Gene namephosphofructokinase, muscle
SynonymsATP-PFK|GSD7|PFK-1|PFK1|PFKA|PFKX|PPP1R122
CytomapUCSC genome browser: 12q13.3
Genomic locationchr12 :48513012-48540187
Type of geneprotein-coding
RefGenesNM_000289.5,
NM_001166686.1,NM_001166687.1,NM_001166688.1,
Ensembl idENSG00000152556
Description6-phosphofructo-1-kinase6-phosphofructokinase type A6-phosphofructokinase, muscle typeATP-PFKATP-dependent 6-phosphofructokinase, muscle typePFK-Aphosphofructo-1-kinase isozyme Aphosphofructokinase 1phosphofructokinase, polypeptide Xphosphofructo
Modification date20141207
dbXrefs MIM : 610681
HGNC : HGNC
Ensembl : ENSG00000152556
HPRD : 01988
Vega : OTTHUMG00000169898
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PFKM
BioGPS: 5213
Gene Expression Atlas: ENSG00000152556
The Human Protein Atlas: ENSG00000152556
PathwayNCI Pathway Interaction Database: PFKM
KEGG: PFKM
REACTOME: PFKM
ConsensusPathDB
Pathway Commons: PFKM
MetabolismMetaCyc: PFKM
HUMANCyc: PFKM
RegulationEnsembl's Regulation: ENSG00000152556
miRBase: chr12 :48,513,012-48,540,187
TargetScan: NM_000289
cisRED: ENSG00000152556
ContextiHOP: PFKM
cancer metabolism search in PubMed: PFKM
UCL Cancer Institute: PFKM
Assigned class in ccmGDBC

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Phenotypic Information for PFKM(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

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: PFKM
MedGen: PFKM (Human Medical Genetics with Condition)
ClinVar: PFKM
PhenotypeMGI: PFKM (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryPFKMchr124851878448518804PFKMchr124852030548520325
ovaryPFKMchr124853250748532527R3HDM2chr125766323457663254
ovaryPFKMchr124853445748534477chr125225395252253972
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 PFKM related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA077791TUBA1B199124952508049525178PFKM98502124853150348534653
DA368227PHLDA311001201438246201438345PFKM99570124853307448535735
BX537703PFKM1108124853535048535457PFKM1014630124853510848539887

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 # sample   2             
GAIN (# sample)   2             
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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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=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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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
chr12:48529111-48529111p.T294I2
chr12:48534513-48534513p.S400S2
chr12:48529142-48529142p.T304T2
chr12:48534587-48534587p.I425T2
chr12:48538878-48538878p.W686L2
chr12:48534623-48534623p.H437L2
chr12:48538894-48538894p.I691M2
chr12:48531547-48531547p.G327E2
chr12:48537853-48537853p.Y635Y2
chr12:48526792-48526792p.T127P2

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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 4151 1 11 372 137 8
# mutation 4171 1 11 372 137 12
nonsynonymous SNV 2 5  1 1  351 114 8
synonymous SNV 2121    1  21  23 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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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
chr12:48524199p.R47S,PFKM2
chr12:48536608p.R566L,PFKM2
chr12:48528749p.F66F1
chr12:48539356p.L388P,PFKM1
chr12:48534624p.G623G,PFKM1
chr12:48501950p.A8P,PFKM1
chr12:48536719p.G399G,PFKM1
chr12:48528758p.G648G,PFKM1
chr12:48539462p.S400S,PFKM1
chr12:48535119p.Q664L,PFKM1

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 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

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

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
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 PFKM
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
DB02726phosphofructokinase, muscleexperimental2-Phosphoglycolic Acid
DB04493phosphofructokinase, muscleexperimentalFructose-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



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