Genexpi: a toolset for identifying regulons and validating gene regulatory networks using time-course expression data

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388971%3A_____%2F18%3A00491992" target="_blank" >RIV/61388971:_____/18:00491992 - isvavai.cz</a>

Result on the web

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DOI - Digital Object Identifier

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Result language

angličtina

Original language name

Genexpi: a toolset for identifying regulons and validating gene regulatory networks using time-course expression data

Original language description

Background: Identifying regulons of sigma factors is a vital subtask of gene network inference. Integrating multiple sources of data is essential for correct identification of regulons and complete gene regulatory networks. Time series of expression data measured with microarrays or RNA-seq combined with static binding experiments (eg., ChIP-seq) or literature mining may be used for inference of sigma factor regulatory networks. nResults: We introduce Genexpi: a tool to identify sigma factors by combining candidates obtained from ChIP experiments or literature mining with time-course gene expression data. While Genexpi can be used to infer other types of regulatory interactions, it was designed and validated on real biological data from bacterial regulons. In this paper, we put primary focus on CyGenexpi: a plugin integrating Genexpi with the Cytoscape software for ease of use. As a part of this effort, a plugin for handling time series data in Cytoscape called CyDataseries has been developed and made available. Genexpi is also available as a standalone command Sine tool and an R package. nConclusions: Genexpi is a useful part of gene network inference toolbox it provides meaningful information about the composition of regulons and delivers biologically interpretable results.

Czech name

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Czech description

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Type

O - Miscellaneous

CEP classification

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OECD FORD branch

10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Project

<a href="/en/project/LM2015055" target="_blank" >LM2015055: Center for Systems Biology</a><br>

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year

2018

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů