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 PYGL

Basic gene info.	Gene symbol	PYGL
	Gene name	phosphorylase, glycogen, liver
	Synonyms	GSD6
	Cytomap	UCSC genome browser: 14q21-q22
	Genomic location	chr14 :51371934-51411248
	Type of gene	protein-coding
	RefGenes	NM_001163940.1, NM_002863.4,
	Ensembl id	ENSG00000100504
	Description	glycogen phosphorylase, liver form
	Modification date	20141219
dbXrefs	MIM : 613741
	HGNC : HGNC
	Ensembl : ENSG00000100504
	HPRD : 01987
	Vega : OTTHUMG00000166596
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PYGL
	BioGPS: 5836
	Gene Expression Atlas: ENSG00000100504
	The Human Protein Atlas: ENSG00000100504
Pathway	NCI Pathway Interaction Database: PYGL
	KEGG: PYGL
	REACTOME: PYGL
	ConsensusPathDB
	Pathway Commons: PYGL
Metabolism	MetaCyc: PYGL
	HUMANCyc: PYGL
Regulation	Ensembl's Regulation: ENSG00000100504
	miRBase: chr14 :51,371,934-51,411,248
	TargetScan: NM_001163940
	cisRED: ENSG00000100504
Context	iHOP: PYGL
	cancer metabolism search in PubMed: PYGL
	UCL Cancer Institute: PYGL
Assigned class in ccmGDB	C

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

Cancer 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/

Metabolic Pathway Description
KEGG_STARCH_AND_SUCROSE_METABOLISM REACTOME_METABOLISM_OF_CARBOHYDRATES REACTOME_GLUCOSE_METABOLISM

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

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 PYGL related fusion information.

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

AA147640

PYGL

258

51371938

51372197

STON1-GTF2A1L

253

417

48824707

48824871

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=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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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
chr14:51375596-51375597	p.S752fs*6	2
chr14:51382068-51382068	p.I463I	2
chr14:51382098-51382098	p.V453V	2
chr14:51378726-51378726	p.F599F	2
chr14:51378457-51378457	p.A654T	2
chr14:51387719-51387719	p.R243C	2
chr14:51398391-51398391	p.Q176H	2
chr14:51383415-51383415	p.A346E	2
chr14:51383825-51383825	p.?	2
chr14:51387288-51387288	p.I276V	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	2	2	1	10	1		5		2	1		6	3				10	9		9
# mutation	2	2	1	12	1		5		2	1		6	3				16	9		10
nonsynonymous SNV	1	2		7	1		3		2	1		6	2				9	8		8
synonymous SNV	1		1	5			2						1				7	1		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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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
chr14:51382068	p.I429I,PYGL	2
chr14:51376795	p.E89D	1
chr14:51383683	p.N793N,PYGL	1
chr14:51378963	p.G579R,PYGL	1
chr14:51390768	p.L461L,PYGL	1
chr14:51372175	p.V245I,PYGL	1
chr14:51381466	p.I69F,PYGL	1
chr14:51410917	p.N793D,PYGL	1
chr14:51376807	p.P567L,PYGL	1
chr14:51383714	p.R457S,PYGL	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 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

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


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

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 PYGL

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
DB00114	phosphorylase, glycogen, liver	nutraceutical	Pyridoxal Phosphate
DB00131	phosphorylase, glycogen, liver	approved; nutraceutical	Adenosine monophosphate
DB01696	phosphorylase, glycogen, liver	experimental	7,9-Dihydro-1h-Purine-2,6,8(3h)-Trione
DB02089	phosphorylase, glycogen, liver	experimental	CP-526423
DB02320	phosphorylase, glycogen, liver	experimental	1-N-Acetyl-Beta-D-Glucosamine
DB02379	phosphorylase, glycogen, liver	experimental	Beta-D-Glucose
DB03288	phosphorylase, glycogen, liver	experimental	5-Chloro-1h-Indole-2-Carboxylic Acid{[Cyclopentyl-(2-Hydroxy-Ethyl)-Carbamoyl]-Methyl}-Amide
DB03744	phosphorylase, glycogen, liver	experimental	Cp403700, (S)-1-{2-[(5-Chloro-1h-Indole-2-Carbonyl)-Amino]-3-Phenyl-Propionyl}-Azetidine-3-Carboxylate
DB04522	phosphorylase, glycogen, liver	experimental	Phosphonoserine
DB07315	phosphorylase, glycogen, liver	experimental	5-chloro-N-{4-[(1R)-1,2-dihydroxyethyl]phenyl}-1H-indole-2-carboxamide
DB07395	phosphorylase, glycogen, liver	experimental	4-[3-(2-Chloro-4,5-difluoro-benzoyl)ureido]-3-trifluoromethoxybenzoic acid
DB07396	phosphorylase, glycogen, liver	experimental	1-{2-[3-(2-Chloro-4,5-difluoro-benzoyl)-ureido]-4-fluoro-phenyl}-piperidine-4-carboxylic acid
DB07968	phosphorylase, glycogen, liver	experimental	N-(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