Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

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	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 symbol	TBL1X
	Gene name	transducin (beta)-like 1X-linked
	Synonyms	EBI\|SMAP55\|TBL1
	Cytomap	UCSC genome browser: Xp22.3
	Genomic location	chrX :9431334-9687780
	Type of gene	protein-coding
	RefGenes	NM_001139466.1, NM_001139467.1,NM_001139468.1,NM_005647.3,
	Ensembl id	ENSG00000101849
	Description	F-box-like/WD repeat-containing protein TBL1Xtransducin beta-like protein 1Xtransducin-beta-like protein 1, X-linked
	Modification date	20141207
dbXrefs	MIM : 300196
	HGNC : HGNC
	Ensembl : ENSG00000101849
	HPRD : 02183
	Vega : OTTHUMG00000021117
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_TBL1X
	BioGPS: 6907
	Gene Expression Atlas: ENSG00000101849
	The Human Protein Atlas: ENSG00000101849
Pathway	NCI Pathway Interaction Database: TBL1X
	KEGG: TBL1X
	REACTOME: TBL1X
	ConsensusPathDB
	Pathway Commons: TBL1X
Metabolism	MetaCyc: TBL1X
	HUMANCyc: TBL1X
Regulation	Ensembl's Regulation: ENSG00000101849
	miRBase: chrX :9,431,334-9,687,780
	TargetScan: NM_001139466
	cisRED: ENSG00000101849
Context	iHOP: TBL1X
	cancer metabolism search in PubMed: TBL1X
	UCL Cancer Institute: TBL1X
Assigned class in ccmGDB	C

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Phenotypic Information for TBL1X(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: TBL1X
	MedGen: TBL1X (Human Medical Genetics with Condition)
	ClinVar: TBL1X
Phenotype	MGI: TBL1X (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

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

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows TBL1X related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
DA634796	NUCKS1	1	228	1	205719083	205719310	TBL1X	224	566	X	9652080	9656250
BQ436312	MOSPD2	12	170	X	14891573	14891882	TBL1X	165	859	X	9652079	9660291
BE827740	CEP95	9	305	17	62533176	62533965	TBL1X	304	377	X	9509441	9509514
BE140570	LAMB3	1	83	1	209789866	209789948	TBL1X	82	292	X	9485248	9485458
AW993932	HEATR5B	13	468	2	37244126	37244584	TBL1X	451	474	X	9596838	9596866
AW629132	TBL1X	10	155	X	9687633	9687778	PAFAH1B2	138	488	11	117038809	117039159
BQ774627	TBL1X	18	97	X	9687699	9687778	TBL1X	91	571	X	9686972	9687451
AI129599	TBL1X	1	123	X	9686765	9686887	TBL1X	117	417	X	9686945	9687245
M86146	TBL1X	1	74	X	9685853	9685926	MPP5	75	280	14	67751528	67751733

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy 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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SNV 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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Somatic 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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Top 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 position	Mutation(aa)	Unique sampleID count
chr23:9656197-9656197	p.A166A	3
chr23:9660265-9660265	p.N288D	2
chr23:9679795-9679795	p.C528C	2
chr23:9659627-9659627	p.A209T	2
chr23:9621720-9621720	p.R32*	2
chr23:9622285-9622285	p.S45L	2
chr23:9683031-9683031	p.A565A	1
chr23:9622289-9622289	p.P46P	1
chr23:9660253-9660253	p.D284N	1
chr23:9661422-9661422	p.R339Q	1

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample		4		8	1		5		2			4					6	3		10
# mutation		4		7	1		5		2			4					6	3		15
nonsynonymous SNV		3		5	1		4		2			3					5	3		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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Top 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 Position	Mutation(aa)	Unique sampleID count
chrX:9679795	p.T449K,TBL1X	2
chrX:9679710	p.C477C,TBL1X	2
chrX:9656079	p.G507V,TBL1X	1
chrX:9679769	p.A142V,TBL1X	1
chrX:9659735	p.T265M,TBL1X	1
chrX:9661417	p.S513R,TBL1X	1
chrX:9656230	p.R150R,TBL1X	1
chrX:9659749	p.D267Y,TBL1X	1
chrX:9661422	p.S515S,TBL1X	1
chrX:9656242	p.N156N,TBL1X	1

Other 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

Copy 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

Gene 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.

Differential 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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CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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