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Master thesis

Proposer un workflow généraliste pour identifier les interactions protéine-protéine entre deux tissus. Exemple des PPIs entre le sécrétome et le surfaceome pour comprendre le dialogue entre tissus chez les mammifères et en particulier chez le bovin

Abstract : The prediction of the protein-protein interactions is studied in different domains. In particular, the interactions between surfaceome and secretome may strongly improved the understanding of inter-tissue crosstalk. This intership aims to develop a Snakemake-based workflow named Talkmine for the identification of the molecular dialogue between two biological tissues resulting from protein-protein interactions. The first objective was to identify and test some opensource tools known to predict proteins that belong to secretome or surfaceome. Publically available tools were classified according to three classes, i.e. peptide signal, subcellular location or topology prediction. Secondly, we developed the workflow. In brief, user gives a gene or protein identifiers list. g:Convert tool converts identifiers to a same format and then, Entrez-Direct tool generates a multi-fasta file. The protein sequences are then launched to the predictive tools. Finally, proteins tagged to secretome and surfaceome classes that are sent to PSICQUIC tool, which determines the protein-protein interactions. The user has access to the list of these interactions as well as to the intermediate results. The workflow Talkmine was initiated to be applied to Bos taurus to determine the interactions between muscle and fat tissue, and it could also be applied to other species and research purposes.
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https://hal.inrae.fr/hal-03332182
Contributor : Céline Boby <>
Submitted on : Thursday, September 2, 2021 - 3:07:51 PM
Last modification on : Wednesday, September 22, 2021 - 3:27:58 AM

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  • HAL Id : hal-03332182, version 1

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Manon Connault, Nadia Goué, Muriel Bonnet. Proposer un workflow généraliste pour identifier les interactions protéine-protéine entre deux tissus. Exemple des PPIs entre le sécrétome et le surfaceome pour comprendre le dialogue entre tissus chez les mammifères et en particulier chez le bovin. Bio-Informatique, Biologie Systémique [q-bio.QM]. 2021. ⟨hal-03332182⟩

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