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 TBL1X
Basic gene info.Gene symbolTBL1X
Gene nametransducin (beta)-like 1X-linked
SynonymsEBI|SMAP55|TBL1
CytomapUCSC genome browser: Xp22.3
Genomic locationchrX :9431334-9687780
Type of geneprotein-coding
RefGenesNM_001139466.1,
NM_001139467.1,NM_001139468.1,NM_005647.3,
Ensembl idENSG00000101849
DescriptionF-box-like/WD repeat-containing protein TBL1Xtransducin beta-like protein 1Xtransducin-beta-like protein 1, X-linked
Modification date20141207
dbXrefs MIM : 300196
HGNC : HGNC
Ensembl : ENSG00000101849
HPRD : 02183
Vega : OTTHUMG00000021117
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_TBL1X
BioGPS: 6907
Gene Expression Atlas: ENSG00000101849
The Human Protein Atlas: ENSG00000101849
PathwayNCI Pathway Interaction Database: TBL1X
KEGG: TBL1X
REACTOME: TBL1X
ConsensusPathDB
Pathway Commons: TBL1X
MetabolismMetaCyc: TBL1X
HUMANCyc: TBL1X
RegulationEnsembl's Regulation: ENSG00000101849
miRBase: chrX :9,431,334-9,687,780
TargetScan: NM_001139466
cisRED: ENSG00000101849
ContextiHOP: TBL1X
cancer metabolism search in PubMed: TBL1X
UCL Cancer Institute: TBL1X
Assigned class in ccmGDBC

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Phenotypic Information for TBL1X(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: TBL1X
Familial Cancer Database: TBL1X
* 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
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: TBL1X
MedGen: TBL1X (Human Medical Genetics with Condition)
ClinVar: TBL1X
PhenotypeMGI: TBL1X (International Mouse Phenotyping Consortium)
PhenomicDB: TBL1X

Mutations for TBL1X
* 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 TBL1X related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA634796NUCKS112281205719083205719310TBL1X224566X96520809656250
BQ436312MOSPD212170X1489157314891882TBL1X165859X96520799660291
BE827740CEP959305176253317662533965TBL1X304377X95094419509514
BE140570LAMB31831209789866209789948TBL1X82292X94852489485458
AW993932HEATR5B1346823724412637244584TBL1X451474X95968389596866
AW629132TBL1X10155X96876339687778PAFAH1B213848811117038809117039159
BQ774627TBL1X1897X96876999687778TBL1X91571X96869729687451
AI129599TBL1X1123X96867659686887TBL1X117417X96869459687245
M86146TBL1X174X96858539685926MPP575280146775152867751733

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

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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=37)
Stat. for Synonymous SNVs
(# total SNVs=21)
Stat. for Deletions
(# total SNVs=2)
Stat. for Insertions
(# total SNVs=0)
There's no inserted 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
chr23:9656197-9656197p.A166A3
chr23:9659627-9659627p.A209T2
chr23:9621720-9621720p.R32*2
chr23:9622285-9622285p.S45L2
chr23:9660265-9660265p.N288D2
chr23:9679795-9679795p.C528C2
chr23:9677345-9677345p.D432N1
chr23:9660219-9660219p.L272L1
chr23:9683003-9683003p.A556V1
chr23:9661249-9661249p.D318Y1

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 4 81 5 2  4    63 10
# mutation 4 71 5 2  4    63 15
nonsynonymous SNV 3 51 4 2  3    53 7
synonymous SNV 1 2  1    1    1  8
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
chrX:9679710p.T449K,TBL1X2
chrX:9679795p.C477C,TBL1X2
chrX:9660260p.A20V,TBL1X1
chrX:9677737p.D194N,TBL1X1
chrX:9652091p.N331Y,TBL1X1
chrX:9659627p.P46S,TBL1X1
chrX:9660274p.S198S,TBL1X1
chrX:9652149p.D381N,TBL1X1
chrX:9659655p.H23N,TBL1X1
chrX:9661244p.T219A,TBL1X1

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 TBL1X 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 TBL1X

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 TBL1X


There's no related Drug.
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Cross referenced IDs for TBL1X
* 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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