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 GYS1

Basic gene info.	Gene symbol	GYS1
	Gene name	glycogen synthase 1 (muscle)
	Synonyms	GSY\|GYS
	Cytomap	UCSC genome browser: 19q13.3
	Genomic location	chr19 :49471381-49496610
	Type of gene	protein-coding
	RefGenes	NM_001161587.1, NM_002103.4,NR_027763.1,
	Ensembl id	ENSG00000104812
	Description	glycogen [starch] synthase, muscle
	Modification date	20141207
dbXrefs	MIM : 138570
	HGNC : HGNC
	Ensembl : ENSG00000104812
	HPRD : 00721
	Vega : OTTHUMG00000150723
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GYS1
	BioGPS: 2997
	Gene Expression Atlas: ENSG00000104812
	The Human Protein Atlas: ENSG00000104812
Pathway	NCI Pathway Interaction Database: GYS1
	KEGG: GYS1
	REACTOME: GYS1
	ConsensusPathDB
	Pathway Commons: GYS1
Metabolism	MetaCyc: GYS1
	HUMANCyc: GYS1
Regulation	Ensembl's Regulation: ENSG00000104812
	miRBase: chr19 :49,471,381-49,496,610
	TargetScan: NM_001161587
	cisRED: ENSG00000104812
Context	iHOP: GYS1
	cancer metabolism search in PubMed: GYS1
	UCL Cancer Institute: GYS1
Assigned class in ccmGDB	C

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Phenotypic Information for GYS1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: GYS1
	Familial Cancer Database: GYS1

* 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: GYS1
	MedGen: GYS1 (Human Medical Genetics with Condition)
	ClinVar: GYS1
Phenotype	MGI: GYS1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: GYS1

Mutations for GYS1

* 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 GYS1 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
AI091299	GYS1	6	211	19	49471387	49471592	HSPA14	207	559	10	14884639	14885515
DA766946	VPS26A	1	214	10	70883940	70892770	GYS1	209	510	19	49474254	49481214
AI096400	GYS1	1	104	19	49471389	49471492	CPXM1	97	454	20	2776380	2776737
AI312670	MYH7	1	204	14	23881951	23883041	GYS1	200	478	19	49472158	49472435
BU601594	BRF1	3	142	14	105716756	105716895	GYS1	131	197	19	49471387	49471453
AI332313	MYH7	1	204	14	23881951	23883041	GYS1	200	477	19	49472158	49472435

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

There's no copy number variation information in COSMIC data for this gene.

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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=45)	Stat. for Synonymous SNVs (# total SNVs=15)

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
chr19:49473096-49473096	p.R609H	2
chr19:49477527-49477527	p.R498C	2
chr19:49481193-49481193	p.I432M	2
chr19:49473876-49473876	p.R579Q	2
chr19:49481210-49481210	p.M427V	2
chr19:49489140-49489140	p.A215A	2
chr19:49477915-49477915	p.R462G	2
chr19:49494653-49494653	p.T69M	2
chr19:49473059-49473059	p.F621F	1
chr19:49481407-49481407	p.A393T	1

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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	5	5		6			7		3			7	1	5			9	5	1	13
# mutation	5	5		6			7		4			7	1	5			9	5	1	14
nonsynonymous SNV	4	5		4			5		3			3		1			4	3		13
synonymous SNV	1			2			2		1			4	1	4			5	2	1	1

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
chr19:49473096	p.R545H,GYS1	2
chr19:49481210	p.S388F,GYS1	1
chr19:49494662	p.P215P,GYS1	1
chr19:49485596	p.P112P	1
chr19:49472715	p.F557F,GYS1	1
chr19:49477487	p.P377S,GYS1	1
chr19:49489290	p.T198T,GYS1	1
chr19:49481234	p.R105C	1
chr19:49494681	p.A548A,GYS1	1
chr19:49485991	p.I368M,GYS1	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 GYS1 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 GYS1

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


AKT1S1,ALDH16A1,AP2A1,AP2S1,BCL2L12,EMC10,CLPTM1, GPI,GRWD1,GYS1,IRF3,KDELR1,NUCB1,PPFIA3, PPP2R1A,PRMT1,RUVBL2,SCAF1,STRN4,TEAD2,TRPM4	ADSSL1,BIN1,CFL2,CKMT2,CLTCL1,COQ9,FAM166B, FXR1,GYS1,KLHL33,MAPK12,MYOM1,NDUFS1,PITX3, PPAPDC3,SCN4A,SLC25A34,SPTB,TMEM143,TMEM52,TRIM55

AKT1S1,ALDH16A1,BCAT2,CALM3,GPI,GRWD1,GYS1, MGC2752,NACC1,NUP62,PNKP,PPP5C,PRPF31,RDH13, PPP6R1,SARS2,TRIM28,UBE2M,ZNF526,ZNF784,ZNF787	ARID1A,PRRC2A,CABIN1,CAMTA2,CEP250,CHERP,CIC, DHX38,DIDO1,FLII,GTF3C1,GYS1,HCFC1,INPPL1, INTS1,MEGF8,MTOR,NCOR2,SCAF1,SETD1A,SMARCA4

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 GYS1

There's no related Drug.

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Cross referenced IDs for GYS1

* 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