Identification of Transcription Factor Binding Sites in Promoter Regions by Modularity Analysis of the Motif Co-Occurrence Graph
A. P. Francisco,
Many algorithms have been proposed to date for the problem of finding biologically significant motifs in promoter regions. They can be classified into two large families: combinatorial methods and probabilistic methods. Probabilistic methods have been used more extensively, since they require less input from the user, and their output is easier to interpret. Combinatorial methods have the potential to identify hard to detect motifs, but their output is much harder to interpret, since it may consist of hundreds or thousands of motifs. In this work, we propose a method that processes the output of combinatorial motif finders in order to find groups of motifs that represent variations of the same motif, thus reducing the output to a manageable size. This processing is done by building a graph that represents the co-occurrences of motifs, and finding communities in this graph. We show that this innovative approach leads to a method that is as easy to use as a probabilistic motif finder, and as sensitive to low quorum motifs as a combinatorial motif finder. The method was integrated with two combinatorial motif finders, and made available on the Web, integrated in an application that can be used to analyze promoter regions in S. cerevisiae. Experiments performed using this system show that the method is effective in the identification of relevant binding sites.
Date: 2008-Jan-31 Time: 16:30:00 Room: 336
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Workshop “Metabolism and mathematical models: Two for a tango” – 2nd Edition
Title: Workshop Metabolism and mathematical models: Two for a tango – 2nd Edition
Dates: October 25-26, 2022
Location: This workshop will be held in a virtual way
The topic of this workshop is metabolism in general, with a special focus, although not exclusive, on parasitology. Besides an exploration of the biological, biochemical and biomedical aspects, the workshop will also aim at presenting some of the mathematical modelling, algorithmic theory and software development that have become crucial to explore such aspects.
This workshop is being organised in the context of two projects, both with the Inria European Team Erable. One of the projects involves a partnership with the University of São Paulo (USP), in São Paulo, Brazil, more specifically the Institute of Mathematics and Statistics (IME) and the Institute of Biomedical Sciences – Inria Associated Team Capoeira – and the other involves the Inesc-ID/IST in Portugal, ETH in Zürich and EMBL in Heidelberg – H2020 Twinning Project Olissipo.
The workshop is open to all members of these two projects but also, importantly, to the community in general.
The program and more details are available here.