TissGDB

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	TissGeneSummary
	TissGeneExp
	TissGene-miRNA
	TissGeneMut: TissGeneSNV, TissGeneCNV, and TissGeneFusions
	TissGeneNet
	TissGeneProg
	TissGeneClin: TissGeneDrug and TissGeneDisease

TissGeneSummary for USP1

Gene summary

Basic gene information	Gene symbol	USP1
	Gene name	ubiquitin specific peptidase 1
	Synonyms	UBP
	Cytomap	UCSC genome browser: 1p31.3
	Type of gene	protein-coding
	RefGenes	NM_001017415.1, NM_001017416.1,NM_003368.4,
	Description	deubiquitinating enzyme 1hUBPubiquitin carboxyl terminal hydrolase 1ubiquitin carboxyl-terminal hydrolase 1ubiquitin specific processing protease 1ubiquitin specific protease 1ubiquitin thioesterase 1ubiquitin thiolesterase 1ubiquitin-specific-pro
	Modification date	20141207
dbXrefs	MIM : 603478
	HGNC : HGNC
	Ensembl : ENSG00000162607
	HPRD : 04593
	Vega : OTTHUMG00000008972
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_USP1
	BioGPS: 7398
Pathway	NCI Pathway Interaction Database: USP1
	KEGG: USP1
	REACTOME: USP1
	Pathway Commons: USP1
Context	iHOP: USP1
	ligand binding site mutation search in PubMed: USP1
	UCL Cancer Institute: USP1
Assigned class in TissGDB*	C
Included tissue-specific gene expression resources	TiGER,GTEx
Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx)	BladderTestis
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)	BLCATGCT
Reference showing the relevant tissue of USP1
Description by TissGene annotations	Cancer gene Have significant anti-correlated miRNA TissgsLTS

* Class A consists of genes with literature evidence and is part of the cTissGenes. Class B consists of only cTissGenes without additional evidence. The remaining genes belong to Class C.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez

GO ID	GO term	PubMed ID
GO:0006282	regulation of DNA repair	18082604
GO:0009411	response to UV	18082604
GO:0016579	protein deubiquitination	18082604
GO:0006282	regulation of DNA repair	18082604
GO:0009411	response to UV	18082604
GO:0016579	protein deubiquitination	18082604

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TissGeneExp for USP1

Gene expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)

Gene isoform expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA pan-cancer tcga_rsem_isoform_tpm, version 2016-09-01)

Gene expressions across normal tissues of GTEx data
(GTEx GTEx_Analysis_v6_RNA-seq_RNA-SeQCv1.1.8_gene_rpkm.gct)
- Here, we shows the matched tissue types only among our 28 cancer types.

Different expressions across 14 cancer types with more than 10 samples between matched tumors and normals (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)

- Significantly differentially expressed cancer types and information. (|Fold change|>1 and FDR<0.05)

Cancer type

Mean(exp) in tumor

Mean(exp) in matched normal

Log2FC

P-val.

FDR

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TissGene-miRNA for USP1

Significantly anti-correlated miRNAs of TissGene across 28 cancer types
(Gene-miRNA relations from TargetScanHuman Relsease 7.1, Conserved_Site_Context_Scores.txt.zip, 06.01.2016)
(TCGA IlluminaHiSeq_miRNASeq, log2(RPM+1) data, version 2016-11-21)
(TCGA IlluminaHiSeq_RNASeqV2, log2(normalized_count+1) data, version 2016-08-16)
(Spearman’s Rank Correlation (p-value<0.05 and coefficient<-0.25))

Cancer type	miRNA id	miRNA accession	P-val.	Coeff.	# samples
LUAD	hsa-miR-215-5p	MIMAT0000272	0.0096	-0.33	60

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TissGeneMut for USP1

TissGeneSNV for USP1

nsSNV counts per each loci.
Different colors of circles represent different cancer types. Circle size denotes number of samples.
(TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25)
* Click on the image to enlarge it in a new window.

Somatic nucleotide variants of TissGene across 28 cancer types
(X-axis: cancer type and Y-axis: % of mutated samples)
The numbers in parentheses are numbers of samples with mutation (nsSNVs).
(TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25)

- nsSNVs sorted by frequency.

AAchange	Cancer type	# samples
p.N725T	UCEC	1
p.H238D	CESC	1
p.R439C	STAD	1
p.Q454*	HNSC	1
p.S323C	BLCA	1
p.L627F	BRCA	1
p.C506R	LIHC	1
p.E168G	LUAD	1
p.S445G	LIHC	1
p.E744D	BLCA	1
p.M618I	LUSC	1
p.N166K	UCS	1
p.S335L	HNSC	1
p.Y91C	ESCA	1
p.G393R	KIRC	1
p.E234K	SKCM	1
p.Q216*	BRCA	1
p.D199A	UCEC	1
p.Q617*	SKCM	1
p.S292*	LUAD	1
p.A676T	COAD	1
p.S766F	BLCA	1
p.N84D	LUAD	1
p.E221K	LIHC	1
p.E262D	STAD	1
p.K623Q	LIHC	1
p.G667A	LUAD	1
p.S248I	CESC	1
p.L208F	PRAD	1
p.E742G	COAD	1
p.F39L	HNSC	1
p.K224E	BRCA	1
p.K343T	STAD	1
p.F542V	READ	1
p.P777L	CESC	1
p.S475Y	UCEC	1
p.E607G	UCEC	1
p.D502N	SKCM	1
p.D543N	LUAD	1
p.E469Q	BLCA	1
p.K26T	COAD	1
p.E235*	UCEC	1
p.E625K	LGG	1
p.Q297H	SKCM	1
p.Q297H	BLCA	1
p.C506S	BRCA	1
p.N612S	HNSC	1
p.Q212E	LUAD	1
p.E121K	CESC	1
p.P265L	ESCA	1
p.N765K	TGCT	1
p.S605C	LUAD	1
p.S734L	HNSC	1
p.S575R	OV	1
p.K30N	READ	1
p.Q177H	THYM	1
p.K673T	COAD	1

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TissGeneCNV for USP1

Copy number variations of TissGene across 28 cancer types (X-axis: cancer type and Y-axis: % of CNV samples)
(TCGA Gistic2_CopyNumber_Gistic2_all_data_by_genes, Gistic2 copy number data, version 2016-08-16)

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TissGeneFusions for USP1

Fusion genes including TissGene
(ChimerDB 3.0, 2016-12-01 and TCGA fusion Portal 2015-12-01)

Database	Src	Cancer type	Sample	Fusion gene	ORF	5'-gene BP	3'-gene BP
Chimerdb3.0	ChiTaRs	NA	BG291031	USP1-USP1		chr1:62916702	chr1:62917055
TCGAfusionPortal	PRADA	BRCA	TCGA-AR-A24S-01A	USP1-SGIP1	Out-of-frame	Chr1:62914337	Chr1:67091530
TCGAfusionPortal	PRADA	PRAD	TCGA-J9-A8CK-01A	USP1-EFCAB7	5UTR-CDS	Chr1:62903071	Chr1:64027380

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TissGeneNet for USP1

Co-expressed gene networks based on protein-protein interaction data (CePIN)
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(PINA2 ppi data)

BRCA (tumor)	BRCA (normal)
USP1, UBC, SUMO2, EZR, ANXA2, WDR48, KRT17, PCNA, UBA52, ATAD5, UBB, HSPB1, PHLPP1, DSC1, FANCD2, PHLPP2, DSG1, FLG, ALDH16A1, TAGLN2, PKP1 (tumor)	USP1, UBC, SUMO2, EZR, KPNA1, WDR48, PCNA, UBA52, LYZ, PSME1, ATAD5, UBB, HSPB1, PHLPP1, DSC1, FANCD2, PHLPP2, DSG1, ALDH16A1, PKP1, CALML3 (normal)

COAD (tumor)	COAD (normal)
USP1, UBC, SUMO2, EZR, PCNA, MYH9, UBA52, ID2, LYZ, PSME1, ATAD5, USP4, PHLPP1, CALML5, KRT4, FANCD2, PHLPP2, DSG1, ALDH16A1, PKP1, CALML3 (tumor)	USP1, UBC, KPNA1, ANXA2, LGALS7, WDR48, KRT17, PCNA, UBA52, ID2, LYZ, ATAD5, UBB, HSPB1, PHLPP1, KRT4, FANCD2, PHLPP2, FLG, ALDH16A1, PKP1 (normal)

HNSC (tumor)	HNSC (normal)
USP1, UBC, SUMO2, EZR, KPNA1, ANXA2, WDR48, PCNA, UBA52, ID2, ATAD5, USP4, UBB, PHLPP1, DSC1, KRT4, FANCD2, DSG1, FLG, TAGLN2, PKP1 (tumor)	USP1, UBC, KPNA1, ANXA2, LGALS7, WDR48, KRT17, PCNA, UBA52, ID2, ATAD5, USP4, HSPB1, PHLPP1, DSC1, FANCD2, PHLPP2, DSG1, FLG, LGALS7B, CALML3 (normal)

KICH (tumor)	KICH (normal)
USP1, SUMO2, KPNA1, ANXA2, WDR48, KRT17, ID2, ATAD5, USP4, UBB, DSC1, CALML5, KRT4, FANCD2, PHLPP2, DSG1, FLG, ALDH16A1, TAGLN2, LGALS7B, CALML3 (tumor)	USP1, UBC, EZR, KPNA1, ANXA2, LGALS7, WDR48, PCNA, MYH9, ID2, LYZ, PSME1, ATAD5, USP4, UBB, HSPB1, FANCD2, PHLPP2, DSG1, FLG, ALDH16A1 (normal)

KIRC (tumor)	KIRC (normal)
USP1, SUMO2, EZR, KPNA1, ANXA2, WDR48, PCNA, UBA52, ID2, ATAD5, USP4, UBB, HSPB1, KRT4, FANCD2, PHLPP2, DSG1, FLG, ALDH16A1, TAGLN2, CALML3 (tumor)	USP1, UBC, KPNA1, ANXA2, LGALS7, WDR48, KRT17, PCNA, MYH9, UBA52, LYZ, PSME1, ATAD5, UBB, HSPB1, PHLPP1, PHLPP2, ALDH16A1, TAGLN2, LGALS7B, CALML3 (normal)

KIRP (tumor)	KIRP (normal)
USP1, SUMO2, EZR, ANXA2, LGALS7, WDR48, PCNA, ID2, PSME1, ATAD5, USP4, UBB, CALML5, KRT4, FANCD2, PHLPP2, DSG1, ALDH16A1, TAGLN2, PKP1, CALML3 (tumor)	USP1, UBC, KPNA1, WDR48, KRT17, PCNA, MYH9, UBA52, ID2, LYZ, PSME1, ATAD5, UBB, HSPB1, PHLPP1, FANCD2, PHLPP2, DSG1, FLG, ALDH16A1, PKP1 (normal)

LIHC (tumor)	LIHC (normal)
USP1, SUMO2, KPNA1, WDR48, PCNA, MYH9, UBA52, LYZ, PSME1, ATAD5, USP4, UBB, HSPB1, DSC1, FANCD2, PHLPP2, DSG1, FLG, ALDH16A1, PKP1, CALML3 (tumor)	USP1, UBC, SUMO2, EZR, KPNA1, WDR48, KRT17, PCNA, MYH9, UBA52, PSME1, ATAD5, USP4, UBB, HSPB1, KRT4, FANCD2, PHLPP2, DSG1, FLG, ALDH16A1 (normal)

LUAD (tumor)	LUAD (normal)
USP1, UBC, SUMO2, KPNA1, ANXA2, LGALS7, WDR48, PCNA, MYH9, ID2, PSME1, ATAD5, USP4, UBB, HSPB1, KRT4, FANCD2, FLG, ALDH16A1, LGALS7B, PKP1 (tumor)	USP1, UBC, SUMO2, EZR, KPNA1, ANXA2, WDR48, PCNA, UBA52, ATAD5, UBB, HSPB1, PHLPP1, DSC1, CALML5, FANCD2, PHLPP2, DSG1, ALDH16A1, TAGLN2, PKP1 (normal)

LUSC (tumor)	LUSC (normal)
USP1, UBC, SUMO2, EZR, LGALS7, WDR48, KRT17, PCNA, MYH9, LYZ, PSME1, ATAD5, USP4, UBB, HSPB1, DSC1, KRT4, FLG, ALDH16A1, PKP1, CALML3 (tumor)	USP1, UBC, SUMO2, EZR, ANXA2, LGALS7, WDR48, KRT17, PCNA, MYH9, ID2, ATAD5, UBB, HSPB1, KRT4, FANCD2, PHLPP2, FLG, ALDH16A1, PKP1, CALML3 (normal)

PRAD (tumor)	PRAD (normal)
USP1, UBC, SUMO2, EZR, KPNA1, WDR48, KRT17, MYH9, UBA52, LYZ, ATAD5, USP4, HSPB1, DSC1, KRT4, FANCD2, PHLPP2, DSG1, FLG, ALDH16A1, TAGLN2 (tumor)	USP1, UBC, KPNA1, LGALS7, WDR48, MYH9, UBA52, LYZ, PSME1, ATAD5, USP4, UBB, HSPB1, PHLPP1, DSC1, FANCD2, PHLPP2, DSG1, FLG, ALDH16A1, LGALS7B (normal)

STAD (tumor)	STAD (normal)
USP1, UBC, SUMO2, EZR, KPNA1, ANXA2, LGALS7, WDR48, MYH9, LYZ, PSME1, ATAD5, USP4, UBB, HSPB1, DSC1, PHLPP2, FLG, ALDH16A1, TAGLN2, CALML3 (tumor)	USP1, UBC, SUMO2, EZR, KPNA1, LGALS7, WDR48, PCNA, MYH9, UBA52, LYZ, ATAD5, USP4, UBB, HSPB1, PHLPP1, FANCD2, PHLPP2, ALDH16A1, TAGLN2, PKP1 (normal)

THCA (tumor)	THCA (normal)
USP1, UBC, SUMO2, KPNA1, ANXA2, WDR48, PCNA, MYH9, UBA52, ID2, PSME1, ATAD5, USP4, UBB, HSPB1, PHLPP1, PHLPP2, DSG1, FLG, ALDH16A1, TAGLN2 (tumor)	USP1, UBC, SUMO2, KPNA1, LGALS7, WDR48, MYH9, UBA52, LYZ, PSME1, ATAD5, USP4, UBB, HSPB1, DSC1, FANCD2, PHLPP2, FLG, ALDH16A1, LGALS7B, PKP1 (normal)

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TissGeneProg for USP1

Kaplan-Meier plots with logrank tests of overall survival (OS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)
* Click on the image to enlarge it in a new window.

Kaplan-Meier plots with logrank test of relapse free survival (RFS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)
* Click on the image enlarge it in a new window.

Forest plot of Cox proportional hazard ratio (HR) and 95% CI of overall survival (OS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)
* Click on the image enlarge it in a new window.

Forest plot of Cox proportional hazard ratio (HR) and 95% CI of relapse free survival (RFS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)
* Click on the image enlarge it in a new window.

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TissGeneClin for USP1

TissGeneDrug for USP1

Drug information targeting TissGene
(DrugBank Version 5.0.6, 2017-04-01)

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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TissGeneDisease for USP1

Disease information associated with TissGene
(DisGeNet, 2016-06-01)

Disease ID	Disease name	# pubmeds	Source
umls:C0015625	Fanconi Anemia	5	BeFree,LHGDN
umls:C3469521	FANCONI ANEMIA, COMPLEMENTATION GROUP A (disorder)	5	BeFree
umls:C0006142	Malignant neoplasm of breast	1	GAD
umls:C0007131	Non-Small Cell Lung Carcinoma	1	BeFree
umls:C0007134	Renal Cell Carcinoma	1	BeFree
umls:C0008626	Congenital chromosomal disease	1	BeFree
umls:C0009402	Colorectal Carcinoma	1	BeFree
umls:C0023418	leukemia	1	BeFree
umls:C0030567	Parkinson Disease	1	BeFree
umls:C0037286	Skin Neoplasms	1	BeFree
umls:C0242379	Malignant neoplasm of lung	1	BeFree
umls:C0376358	Malignant neoplasm of prostate	1	BeFree
umls:C0600139	Prostate carcinoma	1	BeFree
umls:C0678213	Complete hydatidiform mole	1	BeFree
umls:C0684249	Carcinoma of lung	1	BeFree
umls:C0751688	Malignant Squamous Cell Neoplasm	1	BeFree
umls:C1527249	Colorectal Cancer	1	BeFree