Cancer Cell Metabolism Gene Database

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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 TBL1XR1
Basic gene info.Gene symbolTBL1XR1
Gene nametransducin (beta)-like 1 X-linked receptor 1
SynonymsC21|DC42|IRA1|TBLR1
CytomapUCSC genome browser: 3q26.32
Genomic locationchr3 :176738541-176915048
Type of geneprotein-coding
RefGenesNM_024665.4,
Ensembl idENSG00000177565
DescriptionF-box-like/WD repeat-containing protein TBL1XR1TBL1-related protein 1nuclear receptor co-repressor/HDAC3 complex subunitnuclear receptor corepressor/HDAC3 complex subunit TBLR1transducin beta-like 1X-related protein 1
Modification date20141222
dbXrefs MIM : 608628
HGNC : HGNC
Ensembl : ENSG00000177565
HPRD : 15476
Vega : OTTHUMG00000157140
ProteinUniProt: Q9BZK7
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_TBL1XR1
BioGPS: 79718
Gene Expression Atlas: ENSG00000177565
The Human Protein Atlas: ENSG00000177565
PathwayNCI Pathway Interaction Database: TBL1XR1
KEGG: TBL1XR1
REACTOME: TBL1XR1
ConsensusPathDB
Pathway Commons: TBL1XR1
MetabolismMetaCyc: TBL1XR1
HUMANCyc: TBL1XR1
RegulationEnsembl's Regulation: ENSG00000177565
miRBase: chr3 :176,738,541-176,915,048
TargetScan: NM_024665
cisRED: ENSG00000177565
ContextiHOP: TBL1XR1
cancer metabolism search in PubMed: TBL1XR1
UCL Cancer Institute: TBL1XR1
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for TBL1XR1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: TBL1XR1
Familial Cancer Database: TBL1XR1
* 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 BRCA 6, UCEC 7, STAD 8,

Therapeutic Vulnerabilities in Cancer9

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,
6 http://www.nature.com/nature/journal/v490/n7418/full/nature11412.html,
7 http://www.nature.com/nature/journal/v497/n7447/full/nature12113.html,
8 http://www.nature.com/nature/journal/v513/n7517/full/nature13480.html,
9Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM 608628; gene.
Orphanet
DiseaseKEGG Disease: TBL1XR1
MedGen: TBL1XR1 (Human Medical Genetics with Condition)
ClinVar: TBL1XR1
PhenotypeMGI: TBL1XR1 (International Mouse Phenotyping Consortium)
PhenomicDB: TBL1XR1

Mutations for TBL1XR1
* 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
ovaryTBL1XR1chr3176756394176756414TBL1XR1chr3176823581176823601
ovaryTBL1XR1chr3176782070176782090chr3175564466175564486
ovaryTBL1XR1chr3176792478176792498TBL1XR1chr3176793293176793313
ovaryTBL1XR1chr3176806208176806228TBL1XR1chr3176830861176830881
ovaryTBL1XR1chr3176811624176811644TBL1XR1chr3176832855176832875
ovaryTBL1XR1chr3176815851176815871TBL1XR1chr3176808970176808990
ovaryTBL1XR1chr3176816154176816174chr144602973746029757
ovaryTBL1XR1chr3176817396176817416TBL1XR1chr3176898534176898554
ovaryTBL1XR1chr3176824517176824537TBL1XR1chr3176894263176894283
ovaryTBL1XR1chr3176824850176824870chr3176979266176979286
ovaryTBL1XR1chr3176825233176825253TBL1XR1chr3176866483176866503
ovaryTBL1XR1chr3176830246176830266ZBBXchr3167011994167012014
ovaryTBL1XR1chr3176831899176831919TBL1XR1chr3176830432176830452
ovaryTBL1XR1chr3176832143176832163HDAC2chr6114289185114289205
ovaryTBL1XR1chr3176835071176835091chr3176955439176955459
ovaryTBL1XR1chr3176840191176840211TBL1XR1chr3176809643176809663
ovaryTBL1XR1chr3176853835176853855TBL1XR1chr3176858766176858786
ovaryTBL1XR1chr3176868448176868468TBL1XR1chr3176874166176874186
ovaryTBL1XR1chr3176873093176873113TBL1XR1chr3176879302176879322
ovaryTBL1XR1chr3176876046176876066chr3176961776176961796
ovaryTBL1XR1chr3176893440176893460TBL1XR1chr3176894828176894848
ovaryTBL1XR1chr3176901690176901710TBL1XR1chr3176903608176903628
pancreasTBL1XR1chr3176888675176888695chr39402375494023774
prostateTBL1XR1chr3176764643176764643TBL1XR1chr3176913694176913694
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 TBL1XR1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF083294TPM421353191619990916212249TBL1XR13455553176807601176807811
BU859760TBL1XR112223176914909176915130RGS172208106153332781153365181
AJ707222TBL1XR1201433176792513176792636ZBTB41383961773771697377427
BQ447327GRIP12440126713069867131135TBL1XR14347143176817152176817432
AK022268TBL1XR1115323176902489176904018ENPP2153022568120643145120643871

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 # sample91    14 3 7 1 1  
GAIN (# sample)81      3 7      
LOSS (# sample)1     14     1 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=66)		Stat. for Synonymous SNVs
(# total SNVs=8)
Stat. for Deletions
(# total SNVs=5)		Stat. for Insertions
(# total SNVs=7)

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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
chr3:176769295-176769296p.A142fs*13
chr3:176752059-176752059p.E393*3
chr3:176769382-176769382p.A113S2
chr3:176767841-176767841p.R216*2
chr3:176744219-176744219p.F487S2
chr3:176769438-176769438p.T94R2
chr3:176767902-176767902p.I195M2
chr3:176751986-176751986p.S417N2
chr3:176756101-176756101p.T349T2
chr3:176769342-176769342p.N126fs*162

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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
# sample22112  2 31 541  22 10
# mutation22113  2 31 541  22 16
nonsynonymous SNV22111  2 31 521  11 13
synonymous SNV   2        2   11 3
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
chr3:176769438p.T94I2
chr3:176756101p.T349T2
chr3:176767804p.Q264L1
chr3:176768330p.G122E1
chr3:176744174p.F487S1
chr3:176756102p.D255Y1
chr3:176769466p.S119N1
chr3:176767807p.Y395H1
chr3:176768359p.G243V1
chr3:176744217p.A113T1

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 TBL1XR1 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 TBL1XR1

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

ACAP2,ATP13A3,DCUN1D1,DLG1,FBXO45,FXR1,FYTTD1,
KLHL24,LMLN,LPP,MFN1,OPA1,PAK2,PDCD10,
PHC3,RNF168,SENP2,TBL1XR1,TOR1AIP2,UBXN7,VPS8		BET1,C5orf51,CGGBP1,DCUN1D4,FAM172A,FAM8A1,GABPA,
GDAP2,RAB33B,SREK1IP1,SIKE1,SLC30A5,SMAD2,SMAD5,
TAF9B,TBL1XR1,TCEA1,TMEM106B,TNPO1,TROVE2,VAMP4

ARMC8,CCNK,DCUN1D1,DLG1,GFM1,KLF5,MPP5,
OPA1,PAK2,PAPOLA,PDIK1L,PPIL4,PRKCI,RC3H1,
RSRC1,SNX4,TBL1XR1,THUMPD1,YY1,ZNF148,ZNF639		ACAP2,CAMK2D,CD2AP,CMAS,CNOT2,FAM126B,FMR1,
GDAP2,GPBP1,C2CD5,OPN3,PLOD2,RAB14,SLC20A1,
SLC38A9,SP3,TBL1XR1,TMEM65,VCPIP1,YME1L1,ZNF654
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 TBL1XR1


There's no related Drug.
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Cross referenced IDs for TBL1XR1
* 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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