OmicScope: da proteômica quantitativa à biologia de sistemas

Author(s)

Guilherme Reis de Oliveira

• Document type: Doctoral Thesis
• Press: Campinas, SP.
• Institution: Universidade Estadual de Campinas (UNICAMP). Instituto de Biologia
• Defense date: 2024-03-18

Examining board members

Daniel Martins de Souza; Helder Takashi Imoto Nakaya; Mariana Lima Boroni Martins; Paulo Costa Carvalho; Thiago Verano Braga

• Advisor: Daniel Martins de Souza; Alessandro dos Santos Farias

Abstract

The large-scale analysis of proteins has significantly advanced our understanding of biological phenomena, ranging from the search for biomarkers to discovery of new biochemical mechanisms. In this context, mass-spectrometry-based proteomics stands out as the primary approach for quantitatively analyzing proteins in biological systems. Despite its intrinsic advantage in generating data, analyzing this data presents challenges, such as the expressive investment of time to carry out differential proteomics and enrichment analysis, exploring protein-protein interactions, integrating data with independent results, and other applications. This thesis introduces OmicScope, a package developed for downstream data analysis following the protein identification and quantitation process. OmicScope is divided into three major components to perform, respectively, differential proteomics, enrichment analysis, and meta-analysis. Each mode offers a range of functions, including the generation of publication quality figures and networks, facilitating systems-level data analysis. In addition to its distribution as a Python package, OmicScope is also available as a web app at https://omicscope.ib.unicamp.br/. To showcase the enhancements brought by OmicScope to our laboratory, two original articles developed by our group are included, exemplifying the advancements in our data analysis pipeline and the presentation of results both before and during the tool's development (AU)

• FAPESP's process: 18/01410-1 - Evaluating the effects of clozapine on immune system cells
• Grantee: Guilherme Reis-De-Oliveira
• Support Opportunities: Scholarships in Brazil - Doctorate (Direct)