Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 PYGM
Basic gene info.Gene symbolPYGM
Gene namephosphorylase, glycogen, muscle
Synonyms-
CytomapUCSC genome browser: 11q12-q13.2
Genomic locationchr11 :64513860-64528187
Type of geneprotein-coding
RefGenesNM_001164716.1,
NM_005609.2,
Ensembl idENSG00000068976
Descriptionglycogen phosphorylase, muscle formmyophosphorylase
Modification date20141219
dbXrefs MIM : 608455
HGNC : HGNC
Ensembl : ENSG00000068976
HPRD : 01986
Vega : OTTHUMG00000066835
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PYGM
BioGPS: 5837
Gene Expression Atlas: ENSG00000068976
The Human Protein Atlas: ENSG00000068976
PathwayNCI Pathway Interaction Database: PYGM
KEGG: PYGM
REACTOME: PYGM
ConsensusPathDB
Pathway Commons: PYGM
MetabolismMetaCyc: PYGM
HUMANCyc: PYGM
RegulationEnsembl's Regulation: ENSG00000068976
miRBase: chr11 :64,513,860-64,528,187
TargetScan: NM_001164716
cisRED: ENSG00000068976
ContextiHOP: PYGM
cancer metabolism search in PubMed: PYGM
UCL Cancer Institute: PYGM
Assigned class in ccmGDBC

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

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

Mutations for PYGM
* 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
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 PYGM related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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=10

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=79)		Stat. for Synonymous SNVs
(# total SNVs=11)
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
chr11:64518938-64518938p.A610P10
chr11:64514214-64514214p.R816S4
chr11:64519471-64519471p.D565N2
chr11:64518013-64518013p.G671D2
chr11:64519106-64519106p.K597T2
chr11:64519513-64519513p.E551K2
chr11:64522183-64522183p.F327F2
chr11:64518818-64518818p.R650G2
chr11:64521017-64521017p.I459M2
chr11:64519396-64519396p.R590S2

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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
# sample532102 7 31 1073  1811111
# mutation532102 7 31 1173  2011113
nonsynonymous SNV332101 3 3  953  911 10
synonymous SNV2   1 4  1 22   11 13
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
chr11:64523005p.A57D,PYGM2
chr11:64525340p.E103Q,PYGM2
chr11:64521495p.D477N,PYGM2
chr11:64527201p.A277A,PYGM2
chr11:64519471p.T141M,PYGM2
chr11:64517855p.R82K1
chr11:64521023p.R728G,PYGM1
chr11:64525789p.P547L,PYGM1
chr11:64519106p.Y461H,PYGM1
chr11:64522219p.L269L,PYGM1

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 PYGM 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 PYGM

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

APOBEC2,ATP1B4,ATP2A1,C10orf71,MIR1-1HG,CACNA1S,CKM,
CSRP3,DHRS7C,KLHL41,MYH1,MYH6,MYH7,MYL1,
MYL2,MYLPF,NRAP,PYGM,TMOD4,TTN,UNC45B		ABRA,ACTN2,AGBL1,ASB10,C10orf71,CACNA1S,DHRS7C,
ENO3,FBP2,FBXO40,HFE2,LMOD3,MYF6,MYH4,
MYL3,MYO18B,MYOT,PYGM,TNNC1,TNNC2,UNC45B

ACTG2,ASB2,CNN1,DACT3,DES,GPM6A,HSPB8,
LDB3,LMOD1,LONRF2,MYH11,MYLK,PRIMA1,PSD,
PYGM,RBPMS2,SGCA,SORCS1,SYNM,SYNPO2,TCEAL2		ASIC1,ACTN1,AOC3,ATP1A2,BVES,CPXM2,CTXN1,
DACT3,FLNA,KCNH2,KY,LDB3,NPTXR,PDLIM7,
PLCD4,PNCK,PYGM,SLC2A4,SLC8A2,SMTN,TGFB1I1
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 PYGM
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
DB00114phosphorylase, glycogen, musclenutraceuticalPyridoxal Phosphate
DB01823phosphorylase, glycogen, muscleexperimentalBeta-D-Glucopyranose Spirohydantoin
DB01843phosphorylase, glycogen, muscleexperimental3-Amino-8,9,10-Trihydroxy-7-Hydroxymethyl-6-Oxa-1,3-Diaza-Spiro[4.5]Decane-2,4-Dione
DB02007phosphorylase, glycogen, muscleexperimentalAlpha-D-Glucose-6-Phosphate
DB02320phosphorylase, glycogen, muscleexperimental1-N-Acetyl-Beta-D-Glucosamine
DB02348phosphorylase, glycogen, muscleexperimentalFluoro-Phosphite Ion
DB02379phosphorylase, glycogen, muscleexperimentalBeta-D-Glucose
DB02447phosphorylase, glycogen, muscleexperimental3,8,9,10-Tetrahydroxy-7-Hydroxymethyl-6-Oxa-1,3-Diaza-Spiro[4.5]Decane-2,4-Dione
DB02471phosphorylase, glycogen, muscleexperimentalNojirimycine Tetrazole
DB02519phosphorylase, glycogen, muscleexperimentalIndirubin-5-Sulphonate
DB02604phosphorylase, glycogen, muscleexperimental2-Deoxy-Glucose-6-Phosphate
DB02719phosphorylase, glycogen, muscleexperimentalC-(1-Hydrogyl-Beta-D-Glucopyranosyl) Formamide
DB02720phosphorylase, glycogen, muscleexperimentalAlpha-D-Glucopyranosyl-2-Carboxylic Acid Amide
DB02843phosphorylase, glycogen, muscleexperimentalAlpha-D-Glucose-1-Phosphate
DB02964phosphorylase, glycogen, muscleexperimental8,9,10-Trihydroxy-7-Hydroxymethyl-2-Thioxo-6-Oxa-1,3-Diaza-Spiro[4.5]Decan-4-One
DB03067phosphorylase, glycogen, muscleexperimental4-{2,4-Bis[(3-Nitrobenzoyl)Amino]Phenoxy}Phthalic Acid
DB03133phosphorylase, glycogen, muscleexperimental2-(Beta-D-Glucopyranosyl)-5-Methyl-1,2,3-Benzimidazole
DB03218phosphorylase, glycogen, muscleexperimentalN-Acetyl-N'-Beta-D-Glucopyranosyl Urea
DB03250phosphorylase, glycogen, muscleexperimental2-(Beta-D-Glucopyranosyl)-5-Methyl-1,3,4-Benzothiazole
DB03286phosphorylase, glycogen, muscleexperimentalC-(1-Azido-Alpha-D-Glucopyranosyl) Formamide
DB03354phosphorylase, glycogen, muscleexperimental2-(Beta-D-Glucopyranosyl)-5-Methyl-1,3,4-Oxadiazole
DB03383phosphorylase, glycogen, muscleexperimental5-Chloro-1h-Indole-2-Carboxylic Acid [1-(4-Fluorobenzyl)-2-(4-Hydroxypiperidin-1yl)-2-Oxoethyl]Amide
DB03392phosphorylase, glycogen, muscleexperimental(3,4,5-Trihydroxy-6-Hydroxymethyl-Tetrahydro-Pyran-2-Yl)-Phosphoramidic Acid Dimethyl Ester
DB03479phosphorylase, glycogen, muscleexperimental8,9,10-Trihydroxy-7-Hydroxymethyl-3-Methyl-6-Oxa-1,3-Diaza-Spiro[4.5]Decane-2,4-Dione
DB03496phosphorylase, glycogen, muscleexperimental; investigationalFlavopiridol
DB03657phosphorylase, glycogen, muscleexperimental1-Deoxy-1-Methoxycarbamido-Beta-D-Glucopyranose
DB03835phosphorylase, glycogen, muscleexperimentalN-(8,9,10-Trihydroxy-7-Hydroxymethyl-2,4-Dioxo-6-Oxa-1,3-Diaza-Spiro[4.5]Dec-3-Yl-Acetamide
DB04013phosphorylase, glycogen, muscleexperimental1-Deoxy-1-Methoxycarbamido-Beta-D-Gluco-2-Heptulopyranosonamide
DB04044phosphorylase, glycogen, muscleexperimental4-{2-[(3-Nitrobenzoyl)Amino]Phenoxy}Phthalic Acid
DB04055phosphorylase, glycogen, muscleexperimental2,3-Dicarboxy-4-(2-Chloro-Phenyl)-1-Ethyl-5-Isopropoxycarbonyl-6-Methyl-Pyridinium
DB04083phosphorylase, glycogen, muscleexperimentalN'-Pyridoxyl-Lysine-5'-Monophosphate
DB04195phosphorylase, glycogen, muscleexperimentalHeptulose-2-Phosphate
DB04295phosphorylase, glycogen, muscleexperimentalN-Benzoyl-N'-Beta-D-Glucopyranosyl Urea
DB04522phosphorylase, glycogen, muscleexperimentalPhosphonoserine
DB04544phosphorylase, glycogen, muscleexperimental1-Deoxy-1-Acetylamino-Beta-D-Gluco-2-Heptulopyranosonamide
DB04566phosphorylase, glycogen, muscleexperimentalInosinic Acid
DB04642phosphorylase, glycogen, muscleexperimental7-{2,6-DICHLORO-4-[3-(2-CHLORO-BENZOYL)-UREIDO]-PHENOXY}-HEPTANOIC ACID
DB04643phosphorylase, glycogen, muscleexperimental4-{3-CHLORO-4-[3-(2,4-DICHLORO-BENZOYL)-UREIDO]-PHENOXY}-BUTYRIC ACID
DB04644phosphorylase, glycogen, muscleexperimental4-{4-[3-(2,4-DICHLORO-BENZOYL)-UREIDO]-2,3-DIMETHYL-PHENOXY}-BUTYRIC ACID
DB04645phosphorylase, glycogen, muscleexperimental5-{3-[3-(2,4-DICHLORO-BENZOYL)-UREIDO]-2-METHYL-PHENOXY}-PENTANOIC ACID
DB06986phosphorylase, glycogen, muscleexperimental2-CHLORO-N-[(1R,2R)-1-HYDROXY-2,3-DIHYDRO-1H-INDEN-2-YL]-6H-THIENO[2,3-B]PYRROLE-5-CARBOXAMIDE
DB07066phosphorylase, glycogen, muscleexperimental2-CHLORO-N-[(3R)-2-OXO-1,2,3,4-TETRAHYDROQUINOLIN-3-YL]-6H-THIENO[2,3-B]PYRROLE-5-CARBOXAMIDE
DB07792phosphorylase, glycogen, muscleexperimental(S)-2-CHLORO-N-(1-(2-(2-HYDROXYETHYLAMINO)-2-OXOETHYL)-2-OXO-1,2,3,4-TETRAHYDROQUINOLIN-3-YL)-6H-THIENO[2,3-B]PYRROLE-5-CARBOXAMIDE
DB07793phosphorylase, glycogen, muscleexperimental(2S)-N-[(3S)-1-(2-AMINO-2-OXOETHYL)-2-OXO-1,2,3,4-TETRAHYDROQUINOLIN-3-YL]-2-CHLORO-2H-THIENO[2,3-B]PYRROLE-5-CARBOXAMIDE
DB07807phosphorylase, glycogen, muscleexperimental(3R,4R,5R)-5-(HYDROXYMETHYL)-1-(3-PHENYLPROPYL)PIPERIDINE-3,4-DIOL
DB07949phosphorylase, glycogen, muscleexperimental({[(3E)-2'-OXO-2',7'-DIHYDRO-2,3'-BIINDOL-3(7H)-YLIDENE]AMINO}OXY)ACETIC ACID
DB08151phosphorylase, glycogen, muscleexperimental(5R,7R,8S,9S,10R)-7-(hydroxymethyl)-3-phenyl-1,6-dioxa-2-azaspiro[4.5]dec-2-ene-8,9,10-triol
DB08322phosphorylase, glycogen, muscleexperimental2-DEOXY-3,4-BIS-O-[3-(4-HYDROXYPHENYL)PROPANOYL]-L-THREO-PENTARIC ACID
DB08500phosphorylase, glycogen, muscleexperimental(3S,5R,7R,8S,9S,10R)-7-(hydroxymethyl)-3-(2-naphthyl)-1,6-dioxa-2-azaspiro[4.5]decane-8,9,10-triol
DB08503phosphorylase, glycogen, muscleexperimental(3S,5R,7R,8S,9S,10R)-7-(hydroxymethyl)-3-(4-methylphenyl)-1,6-dioxa-2-azaspiro[4.5]decane-8,9,10-triol
DB01076phosphorylase, glycogen, muscleapprovedAtorvastatin
DB00439phosphorylase, glycogen, musclewithdrawnCerivastatin
DB01095phosphorylase, glycogen, muscleapprovedFluvastatin
DB00175phosphorylase, glycogen, muscleapprovedPravastatin
DB01098phosphorylase, glycogen, muscleapprovedRosuvastatin
DB00641phosphorylase, glycogen, muscleapprovedSimvastatin


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Cross referenced IDs for PYGM
* 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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