Open AccessA versatile workflow to integrate RNA-seq genomic and transcriptomic data into mechanistic models of signaling pathways
Author(s) -
Martín GarridoRodríguez,
Daniel López-López,
Francisco Ortuño,
María PeñaChilet,
Eduardo Muñóz,
Marco A. Calzado,
Joaquı́n Dopazo
Publication year - 2021
Publication title -
plos computational biology/plos computational biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.628
H-Index - 182
eISSN - 1553-7358
pISSN - 1553-734X
DOI - 10.1371/journal.pcbi.1008748
Subject(s) - workflow , rna seq , computational biology , transcriptome , computer science , profiling (computer programming) , biology , gene , gene expression , genetics , database , operating system
MIGNON is a workflow for the analysis of RNA-Seq experiments, which not only efficiently manages the estimation of gene expression levels from raw sequencing reads, but also calls genomic variants present in the transcripts analyzed. Moreover, this is the first workflow that provides a framework for the integration of transcriptomic and genomic data based on a mechanistic model of signaling pathway activities that allows a detailed biological interpretation of the results, including a comprehensive functional profiling of cell activity. MIGNON covers the whole process, from reads to signaling circuit activity estimations, using state-of-the-art tools, it is easy to use and it is deployable in different computational environments, allowing an optimized use of the resources available.