A versatile workflow to integrate RNA-seq genomic and transcriptomic data into mechanistic models of signaling pathways

Garrido-Rodriguez, MartínLopez-Lopez, DanielOrtuno, Francisco M.Peña-Chilet, MaríaMuñoz, EduardoCalzado, Marco A.Dopazo, Joaquin2022-10-042022-10-042021-02-11Garrido-Rodriguez M, Lopez-Lopez D, Ortuno FM, Peña-Chilet M, Muñoz E, Calzado MA, et al. A versatile workflow to integrate RNA-seq genomic and transcriptomic data into mechanistic models of signaling pathways. PLoS Comput Biol. 2021 Feb 11;17(2):e1008748http://hdl.handle.net/10668/4220MIGNON 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.enAtribución 4.0 InternacionalAtribución 4.0 Internacionalhttp://creativecommons.org/licenses/by/4.0/TranscriptomeRNA massive sequencingRNA-seqWorkflowSignaling pathwaysTranscriptomaFlujo de trabajoSecuenciación de escopeta completa del transcriptomaMedical Subject Headings::Phenomena and Processes::Mathematical Concepts::AlgorithmsMedical Subject Headings::Anatomy::Cells::Cells, Cultured::Cell Line::Cell Line, TumorMedical Subject Headings::Disciplines and Occupations::Natural Science Disciplines::Biological Science Disciplines::Biology::Computational BiologyMedical Subject Headings::Information Science::Information Science::Information Storage and Retrieval::Databases as Topic::Databases, FactualMedical Subject Headings::Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Genetic Techniques::Gene Expression ProfilingMedical Subject Headings::Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Genetic Techniques::Sequence Analysis::High-Throughput Nucleotide SequencingMedical Subject Headings::Organisms::Eukaryota::Animals::Chordata::Vertebrates::Mammals::Primates::Haplorhini::Catarrhini::Hominidae::HumansMedical Subject Headings::Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Models, TheoreticalMedical Subject Headings::Phenomena and Processes::Genetic Phenomena::Genetic Variation::MutationMedical Subject Headings::Information Science::Information Science::Computing Methodologies::SoftwareMedical Subject Headings::Phenomena and Processes::Chemical Phenomena::Biochemical Phenomena::Biochemical Processes::Transcription, Genetic::TranscriptomeMedical Subject Headings::Information Science::Information Science::Systems Analysis::WorkflowMedical Subject Headings::Disciplines and Occupations::Natural Science Disciplines::Biological Science Disciplines::Biology::Genetics::GenomicsMedical Subject Headings::Phenomena and Processes::Chemical Phenomena::Biochemical Phenomena::Biochemical Processes::Signal TransductionA versatile workflow to integrate RNA-seq genomic and transcriptomic data into mechanistic models of signaling pathwaysresearch article33571195open access10.1371/journal.pcbi.10087481553-7358PMC7904194