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National audience; 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).

International audience; Nowadays, genomic and proteomic studies produce vast amounts of data. To get the biological meaning of these data and to generate testable new hypothesis, scientists must use several tools often not designed for ruminant studies. Here we present ProteINSIDE: an online tool to analyse lists of protein or gene identifiers from well-annotated species (human, rat, and mouse) and ruminants (cow, sheep, and goat). The aims of ProteINSIDE modules are to gather biological information stores in well-updated public databases, to proceed to annotations according to the Gene Ontology consortium, to predict potentially secreted proteins, and to search for proteins interactions. ProteINSIDE provides results from several software and databases in a single query. From a list of identifiers, ProteINSIDE uses orthologs or homologs to extend analyses and biological information retrieval. As a tutorial, we presented how to launch, to recover, to view, and to interpret the results provided by the two types of analysis available with ProteINSIDE (basic and custom analyses). ProteINSIDE is freely available using a simple internet browser at www.proteinside.org. The results of this article are provided on the home page of ProteINSIDE website as the example of an analysis results.

International audience; Genomics experiments are widely acknowledged to produce a huge amount of data to be analysed. The challenge is to extract meaningful biological context for proteins or genes which is currently difficult because of the lack of an integrative workflow that hinders the efficiency and the robustness of data mining performed by biologists working on ruminants. Thus, we designed ProteINSIDE, a free web service (www.proteinside.org) that (I) provides an overview of the biological information stored in public databases or provided by annotations according to the Gene Ontology, (II) predicts proteins that are secreted to search for proteins that mediate signalisation between cells or tissues, and (III) 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 that merges data from these searches to present a fast overview and integrative analysis of genomic and proteomic data from Bovine, Ovine, Caprine, Human, Rat, and Murine species. ProteINSIDE was bench tested with 1000 proteins identifiers from each species by comparison with DAVID, BioMyn, AgBase, PrediSi, and Phobius. Compared to DAVID or BioMyn, identifications and annotations provided by ProteINSIDE were similar from monogastric proteins but more numerous and relevant for ruminants proteins. ProteINSIDE, thanks to SignalP, listed less proteins potentially secreted with a signal peptide than PrediSi and Phobius, in agreement with the low false positive rate of SignalP. In addition ProteINSIDE is the only resource that predicts proteins secreted by cellular processes that do not involve a signal peptide. Lastly, we reported the usefulness of ProteINSIDE to bring new biological hypotheses of research from proteomics data: the biological meaning of the uptake of adiponectin by the foetal muscle and a role for autophagy during ontogenesis of adipose and muscle tissues.

International audience; Nowadays, genomic and proteomic studies produce vast amounts of data. To get the biological meaning of these data and to generate testable new hypothesis, scientists must use several tools often not designed for ruminant studies. Here we present ProteINSIDE: an online tool to analyse lists of protein or gene identifiers from well-annotated species (human, rat, and mouse) and ruminants (cow, sheep, and goat). The aims of ProteINSIDE modules are to gather biological information stores in well-updated public databases, to proceed to annotations according to the Gene Ontology consortium, to predict potentially secreted proteins, and to search for proteins interactions. ProteINSIDE provides results from several software and databases in a single query. From a list of identifiers, ProteINSIDE uses orthologs or homologs to extend analyses and biological information retrieval. As a tutorial, we presented how to launch, to recover, to view, and to interpret the results provided by the two types of analysis available with ProteINSIDE (basic and custom analyses). ProteINSIDE is freely available using a simple internet browser at www.proteinside.org. The results of this article are provided on the home page of ProteINSIDE website as the example of an analysis results.

International audience; Genomics experiments are widely acknowledged to produce a huge amount of data to be analysed. The challenge is to extract meaningful biological context for proteins or genes which is currently difficult because of the lack of an integrative workflow that hinders the efficiency and the robustness of data mining performed by biologists working on ruminants. Thus, we designed ProteINSIDE, a free web service (www.proteinside.org) that (I) provides an overview of the biological information stored in public databases or provided by annotations according to the Gene Ontology, (II) predicts proteins that are secreted to search for proteins that mediate signalisation between cells or tissues, and (III) 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 that merges data from these searches to present a fast overview and integrative analysis of genomic and proteomic data from Bovine, Ovine, Caprine, Human, Rat, and Murine species. ProteINSIDE was bench tested with 1000 proteins identifiers from each species by comparison with DAVID, BioMyn, AgBase, PrediSi, and Phobius. Compared to DAVID or BioMyn, identifications and annotations provided by ProteINSIDE were similar from monogastric proteins but more numerous and relevant for ruminants proteins. ProteINSIDE, thanks to SignalP, listed less proteins potentially secreted with a signal peptide than PrediSi and Phobius, in agreement with the low false positive rate of SignalP. In addition ProteINSIDE is the only resource that predicts proteins secreted by cellular processes that do not involve a signal peptide. Lastly, we reported the usefulness of ProteINSIDE to bring new biological hypotheses of research from proteomics data: the biological meaning of the uptake of adiponectin by the foetal muscle and a role for autophagy during ontogenesis of adipose and muscle tissues.

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).