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This tool is a major update of ProteINSIDE (link to the previous version)

Use this to cite ProteINSIDE:
  • 2015 - Kaspric N, Picard B, Reichstadt M, Tournayre J, and Bonnet M.
    ProteINSIDE to Easily Investigate Proteomics Data from Ruminants: Application to Mine Proteome of Adipose and Muscle Tissues in Bovine Foetuses.
    PLoS ONE 10(5): e0128086. doi:10.1371/journal.pone.0128086 -/- PubMed (PMID: 26000831)

Other article of ProteINSIDE:
  • 2015 - Nicolas Kaspric, Matthieu Reichstadt, Brigitte Picard, Jérémy Tournayre, and Muriel Bonnet
    Protein Function Easily Investigated by Genomics Data Mining Using the ProteINSIDE Online Tool.
    Genomics and Computational Biology, [S.l.], v. 1, n. 1, p. e16, sep. 2015. ISSN 2365-7154. Available at: PDF. Date accessed: 21 Sep. 2015.

Workflow of ProteINSIDE:
ToolReference
g:Profiler Uku Raudvere, Liis Kolberg, Ivan Kuzmin, Tambet Arak, Priit Adler, Hedi Peterson, Jaak Vilo: g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update) Nucleic Acids Research 2019; doi:10.1093/nar/gkz369 [PDF]
NCBI National Center for Biotechnology Information (NCBI)[Internet]. Bethesda (MD): National Library of Medicine (US), National Center for Biotechnology Information; [1988] – [cited 2017 Apr 06]. Available from: https://www.ncbi.nlm.nih.gov/
UniProt The UniProt Consortium UniProt: the universal protein knowledgebase in 2021 Nucleic Acids Res. 49:D1 (2021)
Cytoscape JS Franz M, Lopes CT, Huck G, Dong Y, Sumer O, Bader GD Bioinformatics (2016) 32 (2): 309-311 first published online September 28, 2015 doi:10.1093/bioinformatics/btv557 (PDF) PubMed abstract
AnimalQTLdb Zhi-Liang Hu, Carissa A. Park, and James M. Reecy (2019). Building a livestock genetic and genomic information knowledgebase through integrative developments of Animal QTLdb and CorrDB. Nucleic Acids Research, Volume 47, Issue D1, 8 January 2019, Pages D701–D710. DOI: 10.1093/nar/gky1084
PSICQUIC Aranda, B. et al. PSICQUIC and PSISCORE: accessing and scoring molecular interactions. Nat Meth 8, 528-529 (2011).doi:10.1038/nmeth.1637 http://www.nature.com/nmeth/journal/v8/n7/full/nmeth.1637.html
Tnet Opsahl T (2009). Structure and Evolution of Weighted Networks. University of London (Queen Mary College), London, UK. http://toreopsahl.com/publications/thesis/.
SignalP Predicting Secretory Proteins with SignalP
Henrik Nielsen
In Kihara, D (ed): Protein Function Prediction (Methods in Molecular Biology vol. 1611) pp. 59-73, Springer 2017.
doi: 10.1007/978-1-4939-7015-5_6
PMID: 28451972
TargetP Locating proteins in the cell using TargetP, SignalP, and related tools
Olof Emanuelsson, Soren Brunak, Gunnar von Heijne, Henrik Nielsen
Nature Protocols 2, 953-971 (2007).

ProteINSIDE contact: jeremy.tournayre@inrae.fr



Questions, bugs? Please contact jeremy.tournayre@inrae.fr