|Public server:||ProteoRE Galaxy|
|Summary:||ProteoRE (Proteomics Research Environment)|
- "ProteoRE (Proteomics Research Environment) aims at centrally providing the proteomics community with an online research service enabling biologists/clinicians without programming expertise to annotate and interpret their proteomics data through the Web."
- ProteoRE currently comprises tools (including graphical display) for:
- Customary data manipulation (e.g. filtering, lists comparison, ID conversion…)
- Protein list annotation (e.g. information retrieval from public resources - human species)
- Functional analysis (e.g. GOterms frequencies, enrichment analysis) including graphical representation.
- Pathway analysis (e.g. Reactome)
- This version also includes Galaxy generic tools and some tools from the GalaxyP project that should be of great help for people who want to (re)process their MS-based proteomics data (e.g. peptide/protein identification).
- ProteoRE tools in the Galaxy Toolshed
- Help and support: email@example.com
- Tutorial: Annotating a protein list identified by LC-MS/MS experiments
- Tutorial: Biomarker candidate identification
- Unregistered user: allocated storage space is limited to 20 Mb and is not conserved between sessions.
- Registered user: up to 20 Gb per registered user
- Combes, F., Loux, V., & Vandenbrouck, Y. (2021). GO enrichment analysis for Differential Proteomics Using ProteoRE. In D. Cecconi (Ed.), Proteomics Data Analysis (pp. 179–196). Springer US. https://doi.org/10.1007/978-1-0716-1641-3_11
- Designing an In Silico Strategy to Select Tissue-Leakage Biomarkers Using the Galaxy Framework, Nguyen L., Brun V., Combes F., Loux V., Vandenbrouck Y. (2019) In: Brun V., Couté Y. (eds) Proteomics for Biomarker Discovery. Methods in Molecular Biology, vol 1959. Humana Press, New York, NY
- P17: ProteoRE, a Galaxy-based infrastructure for interpreting and exploring mass spectrometry-based proteomics data, GCC2017 poster presentation, Lien Nguyen, Maud Lacombe, Sandra Dérozier, Lisa Perus, Olivier Rué, Florence Combes, Christophe Caron, Virginie Brun, Valentin Loux, Yves Vandenbrouck
- ProteoRE tagged publications in the Galaxy Publication library