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 TXNRD1
Basic gene info.Gene symbolTXNRD1
Gene namethioredoxin reductase 1
SynonymsGRIM-12|TR|TR1|TRXR1|TXNR
CytomapUCSC genome browser: 12q23-q24.1
Genomic locationchr12 :104680726-104744062
Type of geneprotein-coding
RefGenesNM_001093771.2,
NM_001261445.1,NM_001261446.1,NM_003330.3,NM_182729.2,
NM_182742.2,NM_182743.2,
Ensembl idENSG00000198431
DescriptionKM-102-derived reductase-like factorgene associated with retinoic and IFN-induced mortality 12 proteingene associated with retinoic and interferon-induced mortality 12 proteinoxidoreductasethioredoxin reductase 1, cytoplasmicthioredoxin reductase GRI
Modification date20141222
dbXrefs MIM : 601112
HGNC : HGNC
Ensembl : ENSG00000198431
HPRD : 03068
Vega : OTTHUMG00000166481
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_TXNRD1
BioGPS: 7296
Gene Expression Atlas: ENSG00000198431
The Human Protein Atlas: ENSG00000198431
PathwayNCI Pathway Interaction Database: TXNRD1
KEGG: TXNRD1
REACTOME: TXNRD1
ConsensusPathDB
Pathway Commons: TXNRD1
MetabolismMetaCyc: TXNRD1
HUMANCyc: TXNRD1
RegulationEnsembl's Regulation: ENSG00000198431
miRBase: chr12 :104,680,726-104,744,062
TargetScan: NM_001093771
cisRED: ENSG00000198431
ContextiHOP: TXNRD1
cancer metabolism search in PubMed: TXNRD1
UCL Cancer Institute: TXNRD1
Assigned class in ccmGDBC

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Phenotypic Information for TXNRD1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: TXNRD1
Familial Cancer Database: TXNRD1
* 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_PYRIMIDINE_METABOLISM
REACTOME_METABOLISM_OF_NUCLEOTIDES
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: TXNRD1
MedGen: TXNRD1 (Human Medical Genetics with Condition)
ClinVar: TXNRD1
PhenotypeMGI: TXNRD1 (International Mouse Phenotyping Consortium)
PhenomicDB: TXNRD1

Mutations for TXNRD1
* 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
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryTXNRD1chr12104707287104707307KLHL33chr142090143020901450
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 TXNRD1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF801920TXNRD1712712104659393104659513LCN21173479130911776130912580
BP242040TXNRD1140112104709592104714927RNF185402574223155616531583080
BG231003MAP7D15913713664637236646450TXNRD113419812104659361104659425

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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=32)
Stat. for Synonymous SNVs
(# total SNVs=5)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=1)
There's no deleted 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
chr12:104725378-104725378p.E387Q3
chr12:104713335-104713335p.P171A2
chr12:104728050-104728050p.T412T2
chr12:104714974-104714974p.D215D2
chr12:104715041-104715041p.E238K2
chr12:104705135-104705135p.Y11C1
chr12:104719121-104719121p.Q258E1
chr12:104721449-104721449p.K364N1
chr12:104712748-104712748p.N113I1
chr12:104713330-104713330p.G169D1

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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=0

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample                    
# mutation                    
nonsynonymous SNV                    
synonymous SNV                    
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

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 TXNRD1 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 TXNRD1

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

ATP2A2,PARPBP,FAM91A1,GAS2L3,GCLM,IARS,NAA25,
PPP1CC,PPP3R1,PTPN11,PWP1,RACGAP1,SCYL2,SGOL1,
TDG,TMEM194A,TMPO,TXNRD1,UBQLN1,TBC1D31,XPOT
ANXA7,CALU,CLCN5,EPDR1,FAM98A,GPR155,ICMT,
IL12RB2,KPNA1,LOC100128164,PRRG1,PSMD1,SAMD4A,SETD7,
SGCB,SPPL2A,TTL,TXNRD1,USP14,USP9X,ZEB1

ATP2A2,BRI3BP,CAND1,CORO1C,EPT1,GAN,GTF2H3,
LARP4,LLPH,LRRC59,NAA50,NUP50,PGAM5,PLEKHB2,
PPP1CC,PPTC7,RAB35,RNF34,SCYL2,TMED2,TXNRD1
AMD1,APOBEC3A,BZW1,SPTSSA,C20orf24,C6orf211,CHUK,
DHRS9,DNAJB14,FGF3,HERC4,IDI1,NAPG,NQO1,
RP2,TMED7,TPMT,TWF1,TXNRD1,VPS26A,ZMPSTE24
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 TXNRD1
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
DB01169thioredoxin reductase 1approved; investigationalArsenic trioxide
DB02338thioredoxin reductase 1experimentalNadph Dihydro-Nicotinamide-Adenine-Dinucleotidephosphate
DB03147thioredoxin reductase 1experimentalFlavin-Adenine Dinucleotide
DB03566thioredoxin reductase 1experimentalSpermidine
DB04106thioredoxin reductase 1experimentalFotemustine


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Cross referenced IDs for TXNRD1
* 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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