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 USP11
Basic gene info.Gene symbolUSP11
Gene nameubiquitin specific peptidase 11
SynonymsUHX1
CytomapUCSC genome browser: Xp11.23
Genomic locationchrX :47092313-47107727
Type of geneprotein-coding
RefGenesNM_004651.3,
Ensembl idENSG00000102226
Descriptiondeubiquitinating enzyme 11ubiquitin carboxyl-terminal hydrolase 11ubiquitin carboxyl-terminal hydrolase, X-linkedubiquitin thioesterase 11ubiquitin thiolesterase 11ubiquitin-specific processing protease 11ubiquitin-specific-processing protease 11
Modification date20141207
dbXrefs MIM : 300050
HGNC : HGNC
Ensembl : ENSG00000102226
HPRD : 02081
Vega : OTTHUMG00000021437
ProteinUniProt: P51784
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_USP11
BioGPS: 8237
Gene Expression Atlas: ENSG00000102226
The Human Protein Atlas: ENSG00000102226
PathwayNCI Pathway Interaction Database: USP11
KEGG: USP11
REACTOME: USP11
ConsensusPathDB
Pathway Commons: USP11
MetabolismMetaCyc: USP11
HUMANCyc: USP11
RegulationEnsembl's Regulation: ENSG00000102226
miRBase: chrX :47,092,313-47,107,727
TargetScan: NM_004651
cisRED: ENSG00000102226
ContextiHOP: USP11
cancer metabolism search in PubMed: USP11
UCL Cancer Institute: USP11
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for USP11(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

check002.gifOthers
OMIM 300050; gene.
Orphanet
DiseaseKEGG Disease: USP11
MedGen: USP11 (Human Medical Genetics with Condition)
ClinVar: USP11
PhenotypeMGI: USP11 (International Mouse Phenotyping Consortium)
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.

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 USP11 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
N29021USP111167X4710733447107501SAV1164479145110201951111547
DA220924ASAP224174294848599491016USP11175494X4709242447098764
AI497670USP1122287X4710746247107727PRODH282345221891347518913538
T74731USP111189X4710735247107542SIRPA1774172019189061919143
CA312751USP1174331X4710701047107358DYNC2H131433711103336082103336206
AW955052USP11152X4710729847107349USP1151349X4710445147106621
AA322974USP11153X4710729847107350USP1152168X4710445147104850
AW849407USP111209X4709903747099245USP11203357X4710147847101632
T07607PRR14L1113223207888432078996USP11114324X4710429947104883
CD517199USP111108X4710658347106772USP11103280X4710446547106509

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=4

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check002.gifSomatic 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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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
chr23:47104414-47104414p.?3
chr23:47102831-47102831p.G583G3
chr23:47107095-47107095p.I917I2
chr23:47104863-47104863p.L794Q2
chr23:47101492-47101492p.Q440H2
chr23:47092392-47092392p.R27C2
chr23:47100031-47100031p.A286T2
chr23:47102906-47102906p.Y608Y2
chr23:47098522-47098522p.G120E2
chr23:47100994-47100994p.Q402*2

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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 34141 1 2 1862  67 12
# mutation 34131 1 2 1862  68 17
nonsynonymous SNV 1371 1 2 1642  66 7
synonymous SNV 216       22    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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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:47100031p.A286T2
chrX:47106541p.M774K1
chrX:47092372p.P177S1
chrX:47101537p.K447K1
chrX:47107299p.F570F1
chrX:47098812p.R780G1
chrX:47101911p.E180K1
chrX:47100744p.V455M1
chrX:47104264p.G583G1
chrX:47106620p.L824V1

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 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

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

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
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 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



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