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 GSR
Basic gene info.Gene symbolGSR
Gene nameglutathione reductase
SynonymsHEL-75
CytomapUCSC genome browser: 8p21.1
Genomic locationchr8 :30535579-30585486
Type of geneprotein-coding
RefGenesNM_000637.3,
NM_001195102.1,NM_001195103.1,NM_001195104.1,
Ensembl idENSG00000104687
DescriptionGRGRaseepididymis luminal protein 75glutathione reductase, mitochondrial
Modification date20141207
dbXrefs MIM : 138300
HGNC : HGNC
Ensembl : ENSG00000104687
HPRD : 00704
Vega : OTTHUMG00000163946
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GSR
BioGPS: 2936
Gene Expression Atlas: ENSG00000104687
The Human Protein Atlas: ENSG00000104687
PathwayNCI Pathway Interaction Database: GSR
KEGG: GSR
REACTOME: GSR
ConsensusPathDB
Pathway Commons: GSR
MetabolismMetaCyc: GSR
HUMANCyc: GSR
RegulationEnsembl's Regulation: ENSG00000104687
miRBase: chr8 :30,535,579-30,585,486
TargetScan: NM_000637
cisRED: ENSG00000104687
ContextiHOP: GSR
cancer metabolism search in PubMed: GSR
UCL Cancer Institute: GSR
Assigned class in ccmGDBC

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Phenotypic Information for GSR(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GSR
Familial Cancer Database: GSR
* 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_GLUTATHIONE_METABOLISM
REACTOME_METABOLISM_OF_NUCLEOTIDES

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

Mutations for GSR
* 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
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryGSRchr83054076830540788GSRchr83055693830556958
ovaryGSRchr83057725230577272C12orf42chr12103752262103752282
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 GSR 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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample          1      
GAIN (# sample)                 
LOSS (# sample)          1      
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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=38)
Stat. for Synonymous SNVs
(# total SNVs=12)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=1)

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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
chr8:30553994-30553994p.R233H3
chr8:30541669-30541669p.Q363H2
chr8:30538562-30538562p.?2
chr8:30554006-30554006p.?2
chr8:30539537-30539537p.E399Q2
chr8:30537051-30537051p.V519F2
chr8:30553940-30553940p.S251*2
chr8:30541660-30541660p.N366N2
chr8:30557645-30557645p.S216S2
chr8:30537081-30537081p.A509T2

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample31 5  2 2  651  47 5
# mutation31 5  2 2  651  68 6
nonsynonymous SNV2  3    2  541  35 5
synonymous SNV11 2  2    11   33 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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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
chr8:30557645p.S216S,GSR3
chr8:30560722p.F176F,GSR2
chr8:30546804p.R147W,GSR1
chr8:30537159p.P367Q,GSR1
chr8:30560645p.P285S,GSR1
chr8:30539537p.N139S,GSR1
chr8:30550507p.P367T,GSR1
chr8:30537169p.L276L,GSR1
chr8:30560691p.P132T,GSR1
chr8:30541674p.E356K,GSR1

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 GSR 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 GSR

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

BNIP3L,CCDC25,DOPEY2,EIF2AK3,GSR,GTF2E2,HMBOX1,
IDE,KIAA1244,PPP2CB,PRRC1,SCARB2,SEC16A,SEC24A,
SH2D4A,SLC35F5,SPTLC2,TRIP11,UBR1,UBXN8,WRN
AHCY,ARSH,ASTN2,CENPO,CXCL6,FAM83A,FBN2,
GSR,HIST1H2BH,HOXC10,HS6ST2,KCNJ13,KDM4A,LPAR3,
MCM4,MUC6,PFKFB2,PRPS2,RACGAP1,SLC39A11,TIMELESS

AGPAT5,TTI2,CCDC25,DCTN6,ELP3,ERI1,ESCO2,
FUT10,GSR,GTF2E2,INTS10,INTS9,LEPROTL1,MAK16,
PBK,PPP2CB,PPP2R2A,SARAF,TNFRSF10A,UBXN8,XPO7
ACP1,AGR3,ARFIP2,C1orf131,CCDC125,GSR,H2AFY,
JTB,KRTCAP3,MAPKAPK5,MGST2,NECAP1,NT5DC1,NUDT5,
PDSS1,PI4K2B,SS18L2,TMEM106C,TOM1L1,TXNDC12,ZNF468
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 GSR
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
DB00143glutathione reductaseapproved; nutraceuticalGlutathione
DB00157glutathione reductaseapproved; nutraceuticalNADH
DB00262glutathione reductaseapprovedCarmustine
DB01644glutathione reductaseexperimental3,6-Dihydroxy-Xanthene-9-Propionic Acid
DB01907glutathione reductaseexperimentalNicotinamide-Adenine-Dinucleotide
DB02153glutathione reductaseexperimental3-Sulfinoalanine
DB02553glutathione reductaseexperimentalGlutathionylspermidine Disulfide
DB02895glutathione reductaseexperimental3-(Prop-2-Ene-1-Sulfinyl)-Propene-1-Thiol
DB03147glutathione reductaseexperimentalFlavin-Adenine Dinucleotide
DB03310glutathione reductaseexperimentalOxidized Glutathione Disulfide
DB03867glutathione reductaseexperimentalMeta-Nitro-Tyrosine
DB07393glutathione reductaseexperimental2-(2-PHENYL-3-PYRIDIN-2-YL-4,5,6,7-TETRAHYDRO-2H-ISOPHOSPHINDOL-1-YL)PYRIDINE
DB07714glutathione reductaseexperimental6-(3-METHYL-1,4-DIOXO-1,4-DIHYDRONAPHTHALEN-2-YL)HEXANOIC ACID
DB00515glutathione reductaseapprovedCisplatin


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Cross referenced IDs for GSR
* 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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