Proteome data mining using ProteINSIDE online tool

Genomic and proteomic experiments are widely acknowledged to produce a huge amount of data to be analyzed. The challenge for scientist working on ruminant species is to extract meaningful biological context for proteins or genes to generate new hypothesis. This challenge is currently difficult because of the lack of an integrative workflow that hinders the efficiency and the robustness of data mining, thus scientists must use several tools often not designed for ruminant studies. We designed the online tool ProteINSIDE [1] that provides an overview of the biological information stored in public databases (NCBI and UniProt) or provided by annotations according to the Gene Ontology. It also predicts proteins that are secreted to search for proteins that mediate signalization between cells or tissues, and analyses protein-protein interactions to identify proteins contributing to a process or to visualize functional pathways. Using lists of proteins or genes as a unique input, ProteINSIDE is an original all-in-one tool to mine genomic and proteomic data from cattle, sheep, goat, human, rat, and mouse. A user-friendly web interface provides access to create analyzes and view results that can be sorted online or directly downloaded as several file formats (image, pdf, tabular, spreadsheet, fasta…). ProteINSIDE’s database collects and stores the biological information required to the efficient functioning of ProteINSIDE and is monthly updated to gather the last available knowledge. ProteINSIDE was successfully bench tested with 1000 protein identifiers from each species by comparison with DAVID, BioMyn, and AgBase designed for information retrieval and annotation, as well as with PrediSi, and Phobius that predict secreted proteins. ProteINSIDE is freely available using a simple internet browser at www.proteinside.org (an example of results is provided on the home page).