Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

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 GYS1
Basic gene info.Gene symbolGYS1
Gene nameglycogen synthase 1 (muscle)
SynonymsGSY|GYS
CytomapUCSC genome browser: 19q13.3
Genomic locationchr19 :49471381-49496610
Type of geneprotein-coding
RefGenesNM_001161587.1,
NM_002103.4,NR_027763.1,
Ensembl idENSG00000104812
Descriptionglycogen [starch] synthase, muscle
Modification date20141207
dbXrefs MIM : 138570
HGNC : HGNC
Ensembl : ENSG00000104812
HPRD : 00721
Vega : OTTHUMG00000150723
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GYS1
BioGPS: 2997
Gene Expression Atlas: ENSG00000104812
The Human Protein Atlas: ENSG00000104812
PathwayNCI Pathway Interaction Database: GYS1
KEGG: GYS1
REACTOME: GYS1
ConsensusPathDB
Pathway Commons: GYS1
MetabolismMetaCyc: GYS1
HUMANCyc: GYS1
RegulationEnsembl's Regulation: ENSG00000104812
miRBase: chr19 :49,471,381-49,496,610
TargetScan: NM_001161587
cisRED: ENSG00000104812
ContextiHOP: GYS1
cancer metabolism search in PubMed: GYS1
UCL Cancer Institute: GYS1
Assigned class in ccmGDBC

Top
Phenotypic Information for GYS1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
KEGG_STARCH_AND_SUCROSE_METABOLISM
REACTOME_METABOLISM_OF_CARBOHYDRATES
REACTOME_GLUCOSE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: GYS1
MedGen: GYS1 (Human Medical Genetics with Condition)
ClinVar: GYS1
PhenotypeMGI: GYS1 (International Mouse Phenotyping Consortium)
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.

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 GYS1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AI091299GYS16211194947138749471592HSPA14207559101488463914885515
DA766946VPS26A1214107088394070892770GYS1209510194947425449481214
AI096400GYS11104194947138949471492CPXM1974542027763802776737
AI312670MYH71204142388195123883041GYS1200478194947215849472435
BU601594BRF1314214105716756105716895GYS1131197194947138749471453
AI332313MYH71204142388195123883041GYS1200477194947215849472435

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

Top
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.

Top
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

Top
check002.gifSomatic 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.

Top
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
chr19:49473096-49473096p.R609H2
chr19:49477527-49477527p.R498C2
chr19:49481193-49481193p.I432M2
chr19:49473876-49473876p.R579Q2
chr19:49481210-49481210p.M427V2
chr19:49489140-49489140p.A215A2
chr19:49477915-49477915p.R462G2
chr19:49494653-49494653p.T69M2
chr19:49473059-49473059p.F621F1
chr19:49481407-49481407p.A393T1

Top
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
# sample55 6  7 3  715  95113
# mutation55 6  7 4  715  95114
nonsynonymous SNV45 4  5 3  3 1  43 13
synonymous SNV1  2  2 1  414  5211
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])

Top
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
chr19:49473096p.R545H,GYS12
chr19:49481210p.S388F,GYS11
chr19:49494662p.P215P,GYS11
chr19:49485596p.P112P1
chr19:49472715p.F557F,GYS11
chr19:49477487p.P377S,GYS11
chr19:49489290p.T198T,GYS11
chr19:49481234p.R105C1
chr19:49494681p.A548A,GYS11
chr19:49485991p.I368M,GYS11

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 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]

Top
Gene Expression for GYS1

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))
Top
check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


Top
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

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
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

Top
check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top
Pharmacological Information for GYS1


There's no related Drug.
Top
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



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas