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

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Date

2021-02-11

Authors

Garrido-Rodriguez, Martín
Lopez-Lopez, Daniel
Ortuno, Francisco M.
Peña-Chilet, María
Muñoz, Eduardo
Calzado, Marco A.
Dopazo, Joaquin

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Public Library of Science
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Abstract

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.

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Medical Subject Headings::Phenomena and Processes::Mathematical Concepts::Algorithms
Medical Subject Headings::Anatomy::Cells::Cells, Cultured::Cell Line::Cell Line, Tumor
Medical Subject Headings::Disciplines and Occupations::Natural Science Disciplines::Biological Science Disciplines::Biology::Computational Biology
Medical Subject Headings::Information Science::Information Science::Information Storage and Retrieval::Databases as Topic::Databases, Factual
Medical Subject Headings::Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Genetic Techniques::Gene Expression Profiling
Medical Subject Headings::Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Genetic Techniques::Sequence Analysis::High-Throughput Nucleotide Sequencing
Medical Subject Headings::Organisms::Eukaryota::Animals::Chordata::Vertebrates::Mammals::Primates::Haplorhini::Catarrhini::Hominidae::Humans
Medical Subject Headings::Analytical, Diagnostic and Therapeutic Techniques and Equipment::Investigative Techniques::Models, Theoretical
Medical Subject Headings::Phenomena and Processes::Genetic Phenomena::Genetic Variation::Mutation
Medical Subject Headings::Information Science::Information Science::Computing Methodologies::Software
Medical Subject Headings::Phenomena and Processes::Chemical Phenomena::Biochemical Phenomena::Biochemical Processes::Transcription, Genetic::Transcriptome
Medical Subject Headings::Information Science::Information Science::Systems Analysis::Workflow
Medical Subject Headings::Disciplines and Occupations::Natural Science Disciplines::Biological Science Disciplines::Biology::Genetics::Genomics
Medical Subject Headings::Phenomena and Processes::Chemical Phenomena::Biochemical Phenomena::Biochemical Processes::Signal Transduction

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Keywords

Transcriptome, RNA massive sequencing, RNA-seq, Workflow, Signaling pathways, Transcriptoma, Flujo de trabajo, Secuenciación de escopeta completa del transcriptoma

Citation

Garrido-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):e1008748