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In this chapter, a step-by-step protocol linking these tools is designed to perform a functional annotation and GO-based enrichment analyses applied to a set of differentially expressed proteins as a use case. Analytical practices, guidelines as well as tips related to this strategy are also provided. Tools, datasets, and results are freely available at http//www.proteore.org , allowing researchers to reuse them.Downstream analysis of OMICS data requires interpretation of many molecular components considering current biological knowledge. M
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