Protein co-expression. proteome

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Proteomics (587)
Unknown (324)
Transcriptomics (91)
Genomics (43)
Other (4)
Metabolomics (4)

Organisms

Homo sapiens (328)
Mus musculus (121)
Rattus norvegicus (24)
Saccharomyces cerevisiae (17)
Bos taurus (7)
Xenopus laevis (4)
Canis lupus familiaris (4)
Streptomyces coelicolor (3)
Caenorhabditis elegans (3)
Mnemiopsis leidyi (1)
Fusarium fujikuroi (1)
Rhodococcus opacus (1)
Thermotoga maritima MSB8 (1)
Thalassiosira pseudonana CCMP1335 (1)
Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821 (1)
Colinus virginianus (1)
Roseburia inulinivorans DSM 16841 (1)
Thermoplasma acidophilum DSM 1728 (1)
Staphylococcus aureus subsp. aureus str. Newman (1)
Treponema denticola (1)
Streptomyces lividans (1)
Corynebacterium glutamicum (1)
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Entamoeba histolytica (1)
Porphyromonas gingivalis (1)
Schizosaccharomyces pombe (1)
Staphylococcus aureus (1)
Salmo salar (1)
Pseudomonas aeruginosa (1)
Actinoplanes sp. SE50/110 (1)

Organisms

Homo sapiens (10)
Mus musculus (6)
Saccharomyces cerevisiae (2)
Plasmodium falciparum (2)
Canis lupus familiaris (2)
Arabidopsis thaliana (2)
Drosophila melanogaster (2)
Streptomyces coelicolor (1)
Homo (1)
Ciona robusta (1)
Hericium erinaceus (1)
Caenorhabditis elegans (1)
Ovis aries (1)
Glycine max (1)
Rattus norvegicus (1)

Repository

pride (515)
biostudies-arrayexpress (75)
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geo (25)
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Tissue

Cell culture (133)
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Myocardial ischemia (2)
Pancreatic ductal adenocarcinoma (2)
Pancreatic ductal carcinoma (2)
Not Available (1)

Technology Type

Mass Spectrometry (515)
Shotgun proteomics (274)
Bottom-up proteomics (116)
Affinity purification coupled with mass spectrometry proteomics (86)
Data-dependent acquisition (64)
Data-independent acquisition (35)
Gel-based experiment (33)
SWATH MS (15)
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DiaPASEF (7)
Affinity proteomics (5)
Chemical cross-linking coupled with mass spectrometry proteomics (5)
Mass spectrometry (4)
SRM/MRM (4)
All-ion fragmentation (3)
HDMSE (2)
Mass spectrometry imaging (2)
Glycoproteomics (1)
PAcIFIC (1)
Proteogenomics (1)
Sodium dodecyl sulfate polyacrylamide gel electrophoresis (1)

Instrument Platform

Q Exactive (5)
Illumina NovaSeq 6000 (4)
Orbitrap Fusion (4)
Orbitrap Astral (3)
Orbitrap Fusion Lumos (3)
LTQ Velos (2)
Orbitrap Exploris 480 (2)
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NextSeq 2000 (1)
Illumina MiSeq (1)
Illumina HiSeq 2500 (1)
Illumina HiSeq 2000 (1)
Illumina HiSeq 4000 (1)
Instrument (1)
Autoflex II (1)
LTQ (1)
LTQ Orbitrap (1)
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LTQ XL (1)
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Q Exactive Plus (1)
Q-Exactive HF (QE) Quadrupole-Obitrap mass spectrometer (1)
Synapt G2 HDMS (1)
Thermo Q-Exactive HF (QE) Quadrupole-Obitrap mass spectrometer (1)
TimsTOF Pro (1)
TimsTOF fleX (1)
TripleTOF 5600 (1)
Diode array detection MS - - reverse phase (1)
GCT Premier (Waters) (1)

Publication Date

2022 (88)
2026 (79)
2023 (79)
2025 (77)
2024 (74)
2021 (53)
2020 (45)
2019 (32)
2018 (25)
2017 (21)
2016 (17)
2014 (16)
2015 (14)
2013 (13)
2010 (10)
2008 (7)
2011 (6)
2009 (6)
2012 (3)
2006 (1)

UNIPROT ID/AC

5811.TGME49_004050 (1)
5811.TGME49_005250 (1)
5811.TGME49_027920 (1)
5811.TGME49_044150 (1)
5811.TGME49_054560 (1)
5811.TGME49_094800 (1)
5811.TGME49_102050 (1)
5811.TGME49_119870 (1)
5811.TGME49_119920 (1)
A0A0F7UMP6_TOXGV (1)
A0A0F7UN03_TOXGV (1)
A0A0F7UNS9_TOXGV (1)
A0A0F7UNU4_TOXGV (1)
A0A0F7URF8_TOXGV (1)
A0A0F7US18_TOXGV (1)
A0A0F7USK4_TOXGV (1)
A0A0F7USU7_TOXGV (1)
A0A0F7UTC9_TOXGV (1)
A0A0F7UTQ6_TOXGV (1)
A0A0F7UTS9_TOXGV (1)
A0A0F7UU04_TOXGV (1)
A0A0F7UU07_TOXGV (1)
A0A0F7UUM4_TOXGV (1)
A0A0F7UVN4_TOXGV (1)
A0A0F7UWM4_TOXGV (1)
A0A0F7UXU1_TOXGV (1)
A0A0F7UXX2_TOXGV (1)
A0A0F7UY31_TOXGV (1)
A0A0F7UYG5_TOXGV (1)
A0A0F7UZH2_TOXGV (1)

CHEBI ID

CHEBI:15428 (3)
CHEBI:15741 (3)
CHEBI:15940 (3)
CHEBI:17521 (3)
CHEBI:30769 (3)
CHEBI:30915 (3)
CHEBI:32805 (3)
CHEBI:33508 (3)
CHEBI:14314 (2)
CHEBI:15603 (2)
CHEBI:15676 (2)
CHEBI:15756 (2)
CHEBI:15978 (2)
CHEBI:16010 (2)
CHEBI:16119 (2)
CHEBI:16235 (2)
CHEBI:16335 (2)
CHEBI:16414 (2)
CHEBI:16551 (2)
CHEBI:16704 (2)
CHEBI:16828 (2)
CHEBI:16857 (2)
CHEBI:16865 (2)
CHEBI:16958 (2)
CHEBI:16977 (2)
CHEBI:17053 (2)
CHEBI:17115 (2)
CHEBI:17148 (2)
CHEBI:17191 (2)
CHEBI:17268 (2)

Metabolite Name

Putrescine (2)
Sucrose (2)
(R)-pantothenate (1)
(S)-3-hydroxy-3-methylglutaryl-CoA (1)
1-Kestose (1)
1-deoxy-D-xylulose 5-phosphate (1)
1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate (1)
2,3-diphosphoglycerate (1)
2-C-methyl-D-erythritol 2,4-cyclodiphosphate (1)
2-C-methyl-D-erythritol 4-phosphate (1)
2-ketoglutarate (1)
2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol (1)
2-phospho-D-glycerate (1)
3-dehydroshikimate (1)
3-hydroxybutyryl-coenzyme A (1)
3-phospho-D-glycerate (1)
3beta-24-Methylenecycloartan-3-ol (1)
4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol (1)
4-aminobutanoate (1)
5-phospho-alpha-D-ribose 1-diphosphate (1)
ADP (1)
AMP (1)
ATP (1)
Aconitic acid, cis- (3TMS) (1)
Adenosine (1)
Alanine (2TMS) (1)
Alanine, 3-cyano-, L- (2TMS) (1)
Alanine, beta- (3TMS) (1)
Allantoin (1)
Alpha-Tocopherol (1)

First Public Date

2024 (9)
2023 (7)
2014 (5)
2025 (4)
2019 (3)
2026 (2)
2021 (2)
2018 (2)
2013 (2)
2022 (1)
2020 (1)
2016 (1)

Classification

protozoa (2)

Modification

2x(15)N labeled L-lysine (2)
N6-dimethyl-L-lysine (2)
-17.026549 (1)
15.994915 (1)
3x(2)H labeled N6-acetyl-L-lysine (1)
4-tetrahydrothiazine-3-carboxylic acid (1)
42.010565 (1)
47.036105 (1)
4x(15)N labeled L-arginine (1)
58.005479 (1)
ITRAQ4plex-117 (1)
MTRAQ heavy (1)
N6 (1)
Not available (1)

Study type

Transcription profiling by array (50)
RNA-seq of coding RNA (9)
Transcription profiling by SAGE (2)
Proteomic profiling by mass spectrometer (2)
Proteomic profiling by array (2)
RNA-seq of coding RNA from single cells (2)
RNA-seq of non coding RNA from single cells (1)
RIP-chip by array (1)
Transcription profiling by tiling array (1)
RIP-seq (1)
Other (1)
Single nucleus RNA sequencing (1)
Methylation profiling by high throughput sequencing (1)
RNA-seq of non coding RNA (1)

Release Date

2022 (39)
2025 (37)
2024 (35)
2023 (34)
2021 (29)
2020 (27)
2014 (24)
2015 (22)
2019 (21)
2018 (20)
2010 (16)
2016 (15)
2017 (14)
2009 (14)
2013 (13)
2012 (10)
2011 (10)
2026 (7)
2008 (7)
2006 (2)
2007 (2)
2005 (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 (8)
University of Vienna, Faculty of Chemistry, Department of Analytical Chemistry (6)
1 German Cancer Research Center (DKFZ), Heidelberg, Germany 2 Heidelberg University, Medical Faculty, Heidelberg, Germany (lab head) (3)
Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, Netherlands (3)
Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain (3)
Cornell University Department of Microbiology (3)
Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel (3)
Medical University of Vienna, Austria (3)
National Heart and Lung Institute, Imperial College London, London, UK (3)
1 German Cancer Research Center (DKFZ), Heidelberg, Germany 2 Heidelberg University, Medical Faculty, Heidelberg, Germany (2)
Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Australia (2)
CRG, UPF (2)
Centre de recherche du Centre Hospitalier Universitaire (CHU) de Quebec-Université Laval, Québec, QC, Canada Centre de recherche sur le cancer de l’Université Laval, Québec, QC, Canada PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, QC, Canada Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Québec, QC, Canada (2)
Department of Chemistry and Biotechnology Tallinn University of Technology Estonia (2)
Department of Laboratory Medicine, Wiita Lab, University of California, San Francisco, USA (2)
Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY (2)
Departments of Biochemistry and Neurology Emory University School of Medicine (2)
Dept. of Biochemistry & Molecular Biology, Complex Carbohydrate Research Center, Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602, Dept. of Biochemistry & Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104 USA (2)
Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center (2)
Harvard medical school (2)
Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China (2)
Leibniz Institute of Plant Biochemistry Research Group Head Proteome Biology of Plant Interactions (2)
Leibniz Institute of Plant Biochemistry, Department Biochemistry of Plant Interactions, Weinberg 3, 06120 Halle (Saale), Germany (2)
Leibniz Institute on Aging - Fritz Lipmann Institute (FLI) Beutenbergstraße 11 07745 Jena, Germany (2)
Moffitt Cancer Center Tampa, FL, USA (2)
National Heart and Lung Institute, Imperial College London, United Kingdom (2)
Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland (part of Philip Morris International group of companies) (2)
School of Biosciences Firth Court, Western Bank University of Sheffield Sheffield, S10 2TN United Kingdom (2)
Staff Scientist Biological Systems & Engineering Division Lawrence Berkeley National Laboratory Berkeley CA 94720 (2)
The University of Texas MD Anderson Cancer Center (MDACC), Houston, TX 77030, USA (2)

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Thermal Profiling Maps Multilayered Organization of the Mitochondrial Proteome

Mitochondria execute essential metabolic, biosynthetic, and signaling functions, yet the regulatory principles governing their proteome remain incompletely understood. Here, we develop a thermal proteome profiling (TPP) workflow applied directly to purified mitochondria, enabling systematic analy...

2025-12-08 | MTBLS7386 | MetaboLights

Dynamic profiling of the protein life cycle in response to pathogens (protein)

Protein expression is regulated by production and degradation of mRNAs and proteins, but their specific relationships remain unknown. We combine measurements of protein production and degradation and mRNA dynamics to build a quantitative genomic model of the differential regulation of gene expressio...

ORGANISM(S): Mus musculus

2015-03-06 | E-GEOD-59792 | biostudies-arrayexpress

Co-expression analysis of label-free proteomics data reveals prognostic biomarkers in pancreatic ductal adenocarcinoma

Despite extensive biological and clinical studies, including comprehensive genomics and transcriptomics analysis, pancreatic ductal adenocarcinoma (PDAC) remains a devastating disease, with poor survival and no effective therapies to date. Correlation networks are emerging as a powerful approach to ...

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

2024-11-15 | MSV000096427 | MassIVE

Proteome analysis of monocytes implicates altered mitochondrial biology in adults reporting adverse childhood experiences.

Not available

S-EPMC9889346 | biostudies-literature

Co-expression analysis of label-free proteomics data reveals prognostic biomarkers in pancreatic ductal adenocarcinoma

ORGANISM(S): Homo sapiens (Human)

2020-09-01 | PXD015744 | Pride

Metabolic switches and adaptations deduced from the proteomes of Streptomyces coelicolor wild type and phoP mutant grown in batch culture

Bacteria in the genus Streptomyces are soil dwelling oligotrophs and important producers of secondary metabolites. Previously we showed that global mRNA expression was subject to a series of metabolic and regulatory switches during the life time of a fermentor batch culture of S. coelicolor M145. He...

ORGANISM(S): Streptomyces coelicolor

2011-12-31 | E-GEOD-31068 | biostudies-arrayexpress

Treponema denticola gene expression during co-culture with Porphyromonas gingivalis

Porphyromonas gingivalis and Treponema denticola are periodontalpathogens that are associated with the severity and progression of periodontal diseases. this study investigates the gene expression of Treponema denticola during co-culture with Porphyromonas gingivalis.

ORGANISM(S): Treponema denticola

2014-03-31 | E-MTAB-2257 | biostudies-arrayexpress

Porphyromonas gingivalis gene expression during co-culture with Treponema denticola

Porphyromonas gingivalis and Treponema denticola are periodontalpathogens that are associated with the severity and progression of periodontal diseases. This study investigates the gene expression of Porphyromonas gingivalis during co-culture with Treponema denticola

ORGANISM(S): Porphyromonas gingivalis

2014-03-31 | E-MTAB-2214 | biostudies-arrayexpress

Comparative analysis of the human and mouse placental transcriptome and proteome

An important question for the use of the mouse as a model for studying human disease is the degree of functional conservation of genetic control pathways from human to mouse. The human and mouse placenta show structural similarities but there have been no systematic attempt to assess their molecular...

ORGANISM(S): Mus musculus

2009-06-29 | E-GEOD-13299 | biostudies-arrayexpress

A proteomic view on the cell biology of Staphylococcus aureus proteome

The genome sequence is the “blue-print of life”, but proteomics is required to relate this blue-print of life to the actual physiology of living cells. Because of their low complexity – only about 2.000 proteins make a Staphylococcus aureus cell viable – bacteria are excellent model systems to ident...

ORGANISM(S): Staphylococcus aureus

2009-11-11 | E-GEOD-15060 | biostudies-arrayexpress

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