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 USP11

Basic gene info.	Gene symbol	USP11
	Gene name	ubiquitin specific peptidase 11
	Synonyms	UHX1
	Cytomap	UCSC genome browser: Xp11.23
	Genomic location	chrX :47092313-47107727
	Type of gene	protein-coding
	RefGenes	NM_004651.3,
	Ensembl id	ENSG00000102226
	Description	deubiquitinating enzyme 11ubiquitin carboxyl-terminal hydrolase 11ubiquitin carboxyl-terminal hydrolase, X-linkedubiquitin thioesterase 11ubiquitin thiolesterase 11ubiquitin-specific processing protease 11ubiquitin-specific-processing protease 11
	Modification date	20141207
dbXrefs	MIM : 300050
	HGNC : HGNC
	Ensembl : ENSG00000102226
	HPRD : 02081
	Vega : OTTHUMG00000021437
Protein	UniProt: P51784 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_USP11
	BioGPS: 8237
	Gene Expression Atlas: ENSG00000102226
	The Human Protein Atlas: ENSG00000102226
Pathway	NCI Pathway Interaction Database: USP11
	KEGG: USP11
	REACTOME: USP11
	ConsensusPathDB
	Pathway Commons: USP11
Metabolism	MetaCyc: USP11
	HUMANCyc: USP11
Regulation	Ensembl's Regulation: ENSG00000102226
	miRBase: chrX :47,092,313-47,107,727
	TargetScan: NM_004651
	cisRED: ENSG00000102226
Context	iHOP: USP11
	cancer metabolism search in PubMed: USP11
	UCL Cancer Institute: USP11
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for USP11(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: USP11
	Familial Cancer Database: USP11

* 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_PROTEINS

Others
OMIM	300050; gene.
Orphanet
Disease	KEGG Disease: USP11
	MedGen: USP11 (Human Medical Genetics with Condition)
	ClinVar: USP11
Phenotype	MGI: USP11 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: USP11

Mutations for USP11

* 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 USP11 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
N29021	USP11	1	167	X	47107334	47107501	SAV1	164	479	14	51102019	51111547
DA220924	ASAP2	24	174	2	9484859	9491016	USP11	175	494	X	47092424	47098764
AI497670	USP11	22	287	X	47107462	47107727	PRODH	282	345	22	18913475	18913538
T74731	USP11	1	189	X	47107352	47107542	SIRPA	177	417	20	1918906	1919143
CA312751	USP11	74	331	X	47107010	47107358	DYNC2H1	314	337	11	103336082	103336206
AW955052	USP11	1	52	X	47107298	47107349	USP11	51	349	X	47104451	47106621
AA322974	USP11	1	53	X	47107298	47107350	USP11	52	168	X	47104451	47104850
AW849407	USP11	1	209	X	47099037	47099245	USP11	203	357	X	47101478	47101632
T07607	PRR14L	1	113	22	32078884	32078996	USP11	114	324	X	47104299	47104883
CD517199	USP11	1	108	X	47106583	47106772	USP11	103	280	X	47104465	47106509

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=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=72)	Stat. for Synonymous SNVs (# total SNVs=35)

Stat. for Deletions (# total SNVs=1)	Stat. for Insertions (# total SNVs=1)

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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
chr23:47104414-47104414	p.?	3
chr23:47102831-47102831	p.G583G	3
chr23:47107095-47107095	p.I917I	2
chr23:47104863-47104863	p.L794Q	2
chr23:47101492-47101492	p.Q440H	2
chr23:47092392-47092392	p.R27C	2
chr23:47100031-47100031	p.A286T	2
chr23:47102906-47102906	p.Y608Y	2
chr23:47098522-47098522	p.G120E	2
chr23:47100994-47100994	p.Q402*	2

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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		3	4	14	1		1		2		1	8	6	2			6	7		12
# mutation		3	4	13	1		1		2		1	8	6	2			6	8		17
nonsynonymous SNV		1	3	7	1		1		2		1	6	4	2			6	6		7
synonymous SNV		2	1	6								2	2					2		10

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:47100031	p.A286T	2
chrX:47106541	p.M774K	1
chrX:47092372	p.P177S	1
chrX:47101537	p.K447K	1
chrX:47107299	p.F570F	1
chrX:47098812	p.R780G	1
chrX:47101911	p.E180K	1
chrX:47100744	p.V455M	1
chrX:47104264	p.G583G	1
chrX:47106620	p.L824V	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 USP11 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 USP11

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


ARAF,CDK16,CLIP2,ELK1,FGD1,FTSJ1,GPKOW, GPR173,GRIPAP1,HDAC6,LAMC3,LOC401588,OTUD5,PAGE4, SPON2,TBC1D25,TFE3,UBA1,USP11,WDR45,KRBOX4	CCDC8,CCDC97,CLSTN1,CSRP1,D4S234E,DTX3,GGT7, IL4R,LAMB3,MKL1,MPP2,NKPD1,PAK6,PAQR7, PVRL1,RIPK4,SLC4A3,SNAP47,ST5,TRIM29,USP11

APBB1,CHD6,DTX3,DYRK1B,GDI1,GPRASP2,KIF3C, MAGED2,MARK4,MECP2,MED29,NCKAP5L,OTUD5,TBC1D25, TIGD7,TMEM185A,TSPYL2,USP11,USP51,ZMYM3,ZNF275	VSTM4,ENO2,FAM65A,GPR124,ISLR,KIF3C,LTBP3, MAGEE1,MAPK8IP1,PALM2-AKAP2,PCDHB4,SCRN1,SLC16A2,SLC22A17, STAT5B,TCF4,TIMP2,USP11,USP27X,WFS1,ZKSCAN2

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 USP11

There's no related Drug.

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Cross referenced IDs for USP11

* 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