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Development of a computational tool for gene co-expression analyses and its application in systems biology

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Author(s):
Pedro de Sa Tavares Russo
Total Authors: 1
Document type: Doctoral Thesis
Press: São Paulo.
Institution: Universidade de São Paulo (USP). Instituto de Matemática e Estatística (IME/SBI)
Defense date:
Examining board members:
Helder Takashi Imoto Nakaya; Diego Mauricio Riaño Pachón; Eduardo Moraes Rego Reis; Ana Carolina Quirino Simões
Advisor: Helder Takashi Imoto Nakaya
Abstract

System biology methods provide a holistic view of biological processes, integrating the several intracellular molecular components via the use of highly complex networks. In particular, co-expression networks have allowed for an increasing understanding of biological systems and the complex molecular mechanisms driving them. On the other hand, previously described tools for the analysis of biological networks are in general relatively difficult to use for life and health scientists given their high mathematical and computational demand. Therefore, in order to provide at the same time a relevant and easy-to-use analysis, we have developed the CEMiTool package, which aims to identify gene coexpression modules in an automatic, easy and intuitive way for users with little to no prior computational expertise. We applied CEMiTool to over 1000 transcriptomics studies and used the results to create a new gene coexpression database, which allows users to integrate information across analyses. Moreover, to further facilitate analyses we developed an online version of the tool named webCEMiTool, which permits users to run coexpression analysis easily via browser. Finally, we also developed annotator, a package for automatically determining experimental groups based on sample annotation string similarity. All code is freely available to the community. (AU)

FAPESP's process: 17/05762-7 - ConsensusGraph: identifying consensus gene networks
Grantee:Pedro de Sá Tavares Russo
Support Opportunities: Scholarships in Brazil - Doctorate (Direct)