Ubiquitin specific protease

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Unknown (974)
Transcriptomics (289)
Proteomics (239)
Genomics (146)
Metabolomics (6)
Other (4)

Organisms

Homo sapiens (146)
Mus musculus (123)
Saccharomyces cerevisiae (22)
Drosophila melanogaster (21)
Rattus norvegicus (11)
Arabidopsis thaliana (11)
Caenorhabditis elegans (4)
Cryptococcus neoformans (4)
Schizosaccharomyces pombe (3)
Mycolicibacterium smegmatis MC2 155 (3)
Gallus gallus (3)
Sus scrofa (3)
Saccharomyces cerevisiae SK1 (2)
Corynebacterium glutamicum (2)
Citrus reticulata (2)
Chamaelirium luteum (1)
Mus musculus castaneus (1)
Tetrahymena thermophila (1)
Bacillus subtilis subsp. subtilis str. 168 (1)
Macaca mulatta (1)
Lepeophtheirus salmonis (1)
Entamoeba histolytica (1)
Apis mellifera (1)
Aedes aegypti (1)
Oncorhynchus mykiss (1)
Ovis aries (1)
Mycobacterium tuberculosis H37Rv (1)
Plasmodium falciparum (1)
Escherichia coli str. K-12 substr. MG1655 (1)
Danio rerio (1)

Organisms

Homo sapiens (34)
Mus musculus (21)
Arabidopsis thaliana (6)
Drosophila melanogaster (2)
Saccharomyces cerevisiae (2)
Citrus reticulata (1)
Zea mays (1)

Repository

biostudies-arrayexpress (290)
pride (195)
ENA (78)
geo (67)
MassIVE (22)
iProX (15)
MetaboLights (6)
EGA (4)
GPMDB (3)
jPOST (2)
PAXDB (2)
PanoramaPublic (1)

Tissue

Cell culture (74)
Epithelial cell (25)
Brain (12)
Permanent cell line cell (11)
Kidney (6)
Lung (6)
HeLa cell (5)
Bone marrow (4)
Fibroblast (4)
Whole body (4)
B cell (3)
Blood (3)
Blood cell (3)
Liver (3)
Macrophage (3)
Testis (3)
Colon (2)
Embryonic stem cell (2)
Epithelial cell of cervix (2)
HEK-293 cell (2)
Heart (2)
Hepatocyte (2)
Leaf (2)
Skeletal muscle (2)
Spleen (2)
T cell (2)
Bone cancer cell line (1)
Cell suspension culture (1)
Colonic epithelium (1)
Cytotoxic T-lymphocyte (1)

Disease

Cervix carcinoma (5)
Normal (4)
Colon cancer (4)
Breast cancer (3)
Not Available (3)
Amyotrophic lateral sclerosis (3)
Listeriosis (2)
Neuroblastoma (2)
Parkinson's disease (2)
Urinary bladder cancer (2)
Psoriasis vulgaris (1)
Liver cancer (1)
Bladder cancer (1)
Multiple myeloma (1)
Acute leukemia (1)
Adult hepatocellular carcinoma (1)
Anemia (1)
Arthrogryposis multiplex congenita-1 (1)
Bone osteosarcoma (1)
Cervical cancer (1)
Chronic lymphocytic leukemia (1)
Coronavirus infectious disease (1)
Diaphragm disease (1)
Fetal akinesia deformation sequence syndrome (1)
Frontotemporal dementia (1)
Hematopoietic system disease (1)
Herpes simplex (1)
Human cytomegalovirus infection (1)
Hypochromic anemia (1)
Kidney cancer (1)

Technology Type

Mass Spectrometry (195)
Shotgun proteomics (90)
Affinity purification coupled with mass spectrometry proteomics (49)
Bottom-up proteomics (41)
Data-dependent acquisition (27)
Data-independent acquisition (19)
Gel-based experiment (11)
SRM/MRM (8)
SWATH MS (6)
Top-down proteomics (5)
Chemical cross-linking coupled with mass spectrometry proteomics (4)
Mass spectrometry (3)
HDMSE (3)
MSE (3)
Mass spectrometry assay (2)
Affinity proteomics (2)
NMR spectroscopy (1)
DiaPASEF (1)

Instrument Platform

Illumina NovaSeq 6000 (29)
NextSeq 550 (11)
NextSeq 500 (7)
Illumina HiSeq 2500 (6)
Illumina HiSeq 2000 (4)
None (3)
Illumina HiSeq 4000 (3)
IEO HPC (2)
Element AVITI (2)
Sony SH800 (2)
BAS-5000 [FUJIFILM] (2)
Illumina Genome Analyzer IIx (2)
NextSeq 2000 (2)
Agilent TapeStation (1)
Eppendorf EpMotion 5073m pipetting robot (1)
NaN (1)
10x Genomics Chromium controller; Agilent 2100 Bioanalyzer and Qubit fluorometer (Thermo Fisher) for QC (1)
10x Genomics Chromium controller (GEM generation on Chromium Next GEM Chip G) (1)
BD FACSAria cell sorter (viable-cell sorting); Countess III cell counter (Thermo Fisher; viability check) (1)
Described in protocol (1)
Qubit instrument, DNA HS kit (1)
High Sensitivity DNA kit (1)
BioRad SureCell (1)
Unspecified (1)
454 GS FLX+ (1)
DNA Microarray Scanner BA [Agilent Technologies] (1)
ScanArray Express HT [PerkinElmer] (1)
Illumina NovaSeq X (1)
NA (1)
Illumina (1)

Publication Date

2025 (86)
2026 (46)
2024 (45)
2014 (43)
2023 (39)
2015 (36)
2013 (35)
2022 (31)
2011 (28)
2016 (24)
2021 (24)
2012 (23)
2019 (21)
2010 (20)
2018 (19)
2020 (18)
2008 (14)
2017 (13)
2007 (10)
2009 (8)
2006 (3)
2005 (2)
2004 (1)

UNIPROT ID/AC

5833.MAL13P1.267 (2)
5833.MAL13P1.269 (2)
5833.MAL13P1.325 (2)
5833.MAL13P1.334 (2)
5833.MAL7P1.78 (2)
5833.MAL8P1.208 (2)
5833.MAL8P1.320 (2)
5833.PF11_0033 (2)
5833.PF11_0263 (2)
5833.PF11_0512 (2)
5833.PF13_0305 (2)
5833.PF13_0321 (2)
5833.PF14_0001 (2)
5833.PF14_0009 (2)
5833.PF14_0173 (2)
5833.PF14_0734 (2)
5833.PF14_0751 (2)
5833.PF14_0756 (2)
5833.PF14_0759 (2)
5833.PFA0105w (2)
5833.PFA0120c (2)
5833.PFA0705c (2)
5833.PFB0050c (2)
5833.PFB0280w (2)
5833.PFB0925w (2)
5833.PFB0946c (2)
5833.PFC1011c (2)
5833.PFC1075w (2)
5833.PFD0075w (2)
5833.PFD0100c (2)

CHEBI ID

CHEBI:72961 (3)
CHEBI:16870 (3)
CHEBI:15428 (3)
CHEBI:16919 (3)
CHEBI:15354 (3)
CHEBI:136091 (2)
CHEBI:136137 (2)
CHEBI:136127 (2)
CHEBI:136135 (2)
CHEBI:134639 (2)
CHEBI:134541 (2)
CHEBI:133600 (2)
CHEBI:136281 (2)
CHEBI:136189 (2)
CHEBI:136133 (2)
CHEBI:86102 (2)
CHEBI:70966 (2)
CHEBI:75450 (2)
CHEBI:77096 (2)
CHEBI:136149 (2)
CHEBI:136081 (2)
CHEBI:136086 (2)
CHEBI:89482 (2)
CHEBI:17835 (2)
CHEBI:90470 (2)
CHEBI:136088 (2)
CHEBI:79207 (2)
CHEBI:79110 (2)
CHEBI:136071 (2)
CHEBI:90433 (2)

Metabolite Name

Serine (2)
Malate (2)
Glutamate (2)
Glucose (2)
Choline (2)
Creatine (2)
Glutamine (2)
Alanine (2)
Lactate (2)
Valine (2)
Isoleucine (2)
Leucine (2)
Glycine (2)
S-glutathionyl-L-cysteine (1)
1-18:0-2-18:3-phosphatidate (1)
1-(9Z-hexadecenoyl)-2-(11Z-octadecenoyl)-sn-glycero-3-phosphocholine (1)
1,2-di-(9Z,12Z-octadecadienoyl)-sn-glycero-3-phosphoserine (1)
L-alpha-Amino-gamma-oxalylaminobutyric acid (1)
1-heptadecanoyl-2-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-sn-glycero-3-phospho-(1'-rac-glycerol) (ammonium salt) (1)
Thr-Thr-Asp (1)
Ala-Leu-Asp-Asp (1)
Glu-Gln-Gln-Tyr (1)
1-16:0-2-18:3-phosphatidylinositol (1)
Ala-Asn-Asp-Pro (1)
Val-Ala-Gly (1)
Alpha-D-fructofuranose-beta-D-fructofuranose 1,2':1,2'-dianhydride (1)
Asn-Leu-Phe-Asp (1)
Ala-Thr-Ala-Pro (1)
1-hexadecanoyl-2-(9Z,12Z,15Z-octadecatrienoyl)-sn-glycero-3-phosphoethanolamine (1)
Met-Thr-Cys (1)

First Public Date

2024 (16)
2023 (12)
2025 (11)
2026 (9)
2022 (7)
2014 (5)
2020 (4)
2015 (4)
2021 (3)
2017 (3)
2019 (2)
2018 (1)
2016 (1)

Modification

2x(15)N labeled L-lysine (2)
4x(15)N labeled L-arginine (1)

Study type

Transcription profiling by array (115)
ChIP-seq (45)
RNA-seq of coding RNA (43)
RNA-seq of coding RNA from single cells (20)
Unknown experiment type (11)
ChIP-chip by tiling array (10)
ChIP-chip by array (7)
Comparative genomic hybridization by array (7)
Other (7)
Genotyping by array (3)
DNA-seq (3)
RIP-seq (2)
MicroRNA profiling by array (2)
Proteomic profiling by array (2)
CUT&RUN (2)
RNA-seq of total RNA (2)
RNA-seq of non coding RNA (2)
Transcription profiling by SAGE (1)
Cell line - One-color microarray (1)
Cell line - High-throughput sequencing (1)
Transcription profiling by tiling array (1)
Methylation profiling by array (1)
Methylation profiling by high throughput sequencing (1)

Release Date

2025 (152)
2022 (112)
2024 (110)
2023 (89)
2021 (76)
2015 (74)
2020 (73)
2016 (65)
2014 (60)
2019 (59)
2018 (53)
2013 (53)
2012 (50)
2011 (45)
2017 (43)
2010 (31)
2026 (29)
2008 (24)
2007 (19)
2009 (17)
2006 (14)
2005 (8)
2004 (4)
2001 (1)
2000 (1)
1999 (1)
1998 (1)

Lab affiliation

Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA., Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA (15)
Institute of Molecular Biology (IMB), Mainz, Germany (6)
Harvard Medical School (4)
CECAD, University of Cologne (2)
COI-NDM (University of Oxford) (2)
Cambridge Institute for Medical Research, University of Cambridge (2)
College of Pharmacy, Research Institute of Pharmaceutical Sciences, Kyungpook National University (2)
Department of Pathology and Cell Biology and Institute for Cancer Genetics Herbert Irving Comprehensive Cancer Vagelos College of Physicians & Surgeons Columbia University (2)
Erasmus MC (2)
Finley and Gygi lab Cell Biology Department Harvard Medical School US (2)
Institut Pasteur Unité des Interactions Bactéries-Cellules, Inserm U604, INRA USC2020 25 rue du Dr. Roux 75015 Paris France (2)
Institute of Biochemistry II, Faculty of Medicine, Goethe University, Theodor-Stern-Kai 7, D-60590 Frankfurt am Main, Germany (2)
Institute of Biochemistry II, University Hospital, Goethe University, Frankfurt, Germany (2)
Medical Research Council Protein Phosphorylation and Ubiquitylation Unit School of Life Sciences, University of Dundee, Dundee, Scotland (2)
Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, Collaborative Innovation Center of Hematology, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200000, China (2)
The University of Melbourne (2)
1. Center for Medical Biotechnology, VIB, Ghent, Belgium 2. Department for Biomolecular Medicine, Ghent University, Ghent, Belgium 3. VIB Proteomics Core, VIB, Ghent, Belgium (1)
1Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China. 2Analytical Instrumentation Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China. 3Center for Quantitative Biology, PKU-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China (1)
Aarhus University Department of Biomedicine DK-8000 Aarhus (1)
Acting Head of Proteomics (1)
Additional Professor, Department of Medical Oncology (Lab.), Dr B.R.A.I.R.C.H., AIIMS, New Delhi (1)
Affiliated Chuzhou Hospital of Anhui Medical University (1)
Army Medical University (Third Military Medical University) (1)
Assistant Professor, Department of Cell Biology Van Andel Institute (1)
Ben May Department for Cancer Research, the University of Chicago, Chicago, IL 60637, USA. (1)
Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Goettingen, Germany (1)
Biology Department, University of Massachusetts Boston, Boston, MA, USA (1)
Biotechnology Center, National Chung-Hsing University, Taichung 402, Taiwan (1)
Bowling Green State University (1)
CABIMER (1)

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Urinary Ubiquitin-Specific Protease 2 (USP2) as a Diagnostic Biomarker for Chronic Kidney Disease: An Integrated Multi-Omics and Network Analysis

Urinary USP2 is elevated in chronic kidney disease and shows strong diagnostic performance. Integrated metabolomics and proteomics analyses identified cortisol and prostaglandin A3 as candidate mediators and linked USP2 to lipid metabolism and ferroptosis-related pathways.

2026-05-05 | MTBLS14426 | MetaboLights

Proximity-dependent biotinylation reveals an interaction between ubiquitin-specific peptidase 46 and centrosome-related proteins

To characterize the protein interaction network of USP46, BioID analysis was conducted on a knock-in cell line that expresses USP46 and biotin ligase fusion protein stably.

ORGANISM(S): Mus Musculus (mouse)

2025-03-25 | PXD053674 | JPOST Repository

Structural basis of ubiquitin recognition by the deubiquitinating protease USP2.

Not available

S-EPMC7126176 | biostudies-literature

β-Lapachone Antagonizes Ubiquitin-Specific Protease 18 Activity to Elicit Anti-Neoplastic Effects

PRJNA1416776 | ENA

Post-transcriptional fine-tuning of COP9 signalosome subunit biosynthesis is regulated by the c-Myc/Lin28B/let-7 pathway

The COP9 signalosome (CSN) is a conserved protein complex occurring in all eukaryotes. The mammalian CSN consists of eight subunits (CSN1 – CSN8) and possesses an intrinsic metalloprotease JAMM motif localised to CSN5. In addition, it is associated with kinases such as protein kinase CK2 and D and t...

ORGANISM(S): Homo sapiens

2011-10-26 | E-GEOD-19085 | biostudies-arrayexpress

Ubiquitin-specific protease 4 is inhibited by its ubiquitin-like domain.

Not available

S-EPMC3077250 | biostudies-literature

DOT4/dot4 null, UBP8/ubp8 null transcript arrays

Comparison of DOT4/dot4 null cells, UBP8/ubp8 null cells, and DOT4UBP8/dot4ubp8 null cells in YEPD.

ORGANISM(S): Saccharomyces cerevisiae

2010-06-10 | E-GEOD-2329 | biostudies-arrayexpress

Ubiquitin-specific protease 7 is a regulator of ubiquitin-conjugating enzyme UbE2E1.

Not available

S-EPMC3675629 | biostudies-literature