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 PYGL
Basic gene info.Gene symbolPYGL
Gene namephosphorylase, glycogen, liver
SynonymsGSD6
CytomapUCSC genome browser: 14q21-q22
Genomic locationchr14 :51371934-51411248
Type of geneprotein-coding
RefGenesNM_001163940.1,
NM_002863.4,
Ensembl idENSG00000100504
Descriptionglycogen phosphorylase, liver form
Modification date20141219
dbXrefs MIM : 613741
HGNC : HGNC
Ensembl : ENSG00000100504
HPRD : 01987
Vega : OTTHUMG00000166596
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PYGL
BioGPS: 5836
Gene Expression Atlas: ENSG00000100504
The Human Protein Atlas: ENSG00000100504
PathwayNCI Pathway Interaction Database: PYGL
KEGG: PYGL
REACTOME: PYGL
ConsensusPathDB
Pathway Commons: PYGL
MetabolismMetaCyc: PYGL
HUMANCyc: PYGL
RegulationEnsembl's Regulation: ENSG00000100504
miRBase: chr14 :51,371,934-51,411,248
TargetScan: NM_001163940
cisRED: ENSG00000100504
ContextiHOP: PYGL
cancer metabolism search in PubMed: PYGL
UCL Cancer Institute: PYGL
Assigned class in ccmGDBC

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Phenotypic Information for PYGL(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PYGL
Familial Cancer Database: PYGL
* 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: PYGL
MedGen: PYGL (Human Medical Genetics with Condition)
ClinVar: PYGL
PhenotypeMGI: PYGL (International Mouse Phenotyping Consortium)
PhenomicDB: PYGL

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

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PYGL related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AA147640PYGL1258145137193851372197STON1-GTF2A1L25341724882470748824871

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 # sample2                
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=60)
Stat. for Synonymous SNVs
(# total SNVs=24)
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
chr14:51383415-51383415p.A346E2
chr14:51398391-51398391p.Q176H2
chr14:51383825-51383825p.?2
chr14:51387288-51387288p.I276V2
chr14:51387292-51387292p.E274E2
chr14:51375596-51375596p.S752Y2
chr14:51378988-51378988p.T552S2
chr14:51376786-51376786p.S668S2
chr14:51375596-51375597p.S752fs*62
chr14:51382068-51382068p.I463I2

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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
# sample221101 5 21 63   109 9
# mutation221121 5 21 63   169 10
nonsynonymous SNV12 71 3 21 62   98 8
synonymous SNV1 15  2     1   71 2
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
chr14:51382068p.I429I,PYGL2
chr14:51375597p.K690N,PYGL1
chr14:51382154p.N525S,PYGL1
chr14:51411117p.V382V,PYGL1
chr14:51378580p.A146P,PYGL1
chr14:51387279p.I682M,PYGL1
chr14:51379780p.L516L,PYGL1
chr14:51398410p.F339L,PYGL1
chr14:51375642p.W141L,PYGL1
chr14:51382199p.F676L,PYGL1

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 PYGL 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 PYGL

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

ATP6V1D,CGRRF1,ELL2,FAM120AOS,FAM162A,GPC5,HHEX,
HSDL2,KCNS3,KLHDC2,KTN1,PDE4A,PIGH,PTPLAD2,
PYGL,STON2,TMX1,TPST2,TRIM9,ZAK,ZNF385D
ACO1,AOC3,CLMP,ASPH,BHMT2,MTURN,CAV1,
DHDDS,DMGDH,GCOM1,GLYAT,ITGB1BP1,MRAS,PALMD,
PYGL,SORBS1,TK2,TLN2,TNS1,TSPAN3,VKORC1L1

AIF1L,AKT1,ANO1,CCDC109B,FAM115C,FNTB,GOLGA5,
HPSE,KCNK1,LOC152225,LY6E,MAP6D1,MARK3,NIN,
PARP2,PYGL,RGS10,SAV1,TMX1,TRIB2,WDHD1
ABHD12B,ASTL,CCNJ,CKAP4,DMRT2,EXOC3L2,FGFRL1,
GPAT2,IL1RL2,LRFN4,MTNR1A,NOX1,NSUN7,PITX1,
PPM1H,PREP,PYGL,RHOV,TMEM44,XRRA1,ZDHHC16
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 PYGL
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, livernutraceuticalPyridoxal Phosphate
DB00131phosphorylase, glycogen, liverapproved; nutraceuticalAdenosine monophosphate
DB01696phosphorylase, glycogen, liverexperimental7,9-Dihydro-1h-Purine-2,6,8(3h)-Trione
DB02089phosphorylase, glycogen, liverexperimentalCP-526423
DB02320phosphorylase, glycogen, liverexperimental1-N-Acetyl-Beta-D-Glucosamine
DB02379phosphorylase, glycogen, liverexperimentalBeta-D-Glucose
DB03288phosphorylase, glycogen, liverexperimental5-Chloro-1h-Indole-2-Carboxylic Acid{[Cyclopentyl-(2-Hydroxy-Ethyl)-Carbamoyl]-Methyl}-Amide
DB03744phosphorylase, glycogen, liverexperimentalCp403700, (S)-1-{2-[(5-Chloro-1h-Indole-2-Carbonyl)-Amino]-3-Phenyl-Propionyl}-Azetidine-3-Carboxylate
DB04522phosphorylase, glycogen, liverexperimentalPhosphonoserine
DB07315phosphorylase, glycogen, liverexperimental5-chloro-N-{4-[(1R)-1,2-dihydroxyethyl]phenyl}-1H-indole-2-carboxamide
DB07395phosphorylase, glycogen, liverexperimental4-[3-(2-Chloro-4,5-difluoro-benzoyl)ureido]-3-trifluoromethoxybenzoic acid
DB07396phosphorylase, glycogen, liverexperimental1-{2-[3-(2-Chloro-4,5-difluoro-benzoyl)-ureido]-4-fluoro-phenyl}-piperidine-4-carboxylic acid
DB07968phosphorylase, glycogen, liverexperimentalN-(2-CHLORO-4-FLUOROBENZOYL)-N'-(5-HYDROXY-2-METHOXYPHENYL)UREA


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Cross referenced IDs for PYGL
* 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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