Genome-scale mechanistic modeling of signaling pathways made easy: A bioconductor/cytoscape/web server framework for the analysis of omic data
Por:
K. RIAN, M. HIDALGO, C. CUBUK, M. FALCO, C. LOUCERA, M. ESTEBAN-MEDINA, I. ALAMO-ALVAREZ, M. PENA-CHILET and J. DOPAZO
Publicada:
1 ene 2021
Ahead of Print:
1 may 2021
Resumen:
Genome-scale mechanistic models of pathways are gaining importance for genomic data interpretation because they provide a natural link between genotype measurements (transcriptomics or genomics data) and the phenotype of the cell (its functional behavior). Moreover, mechanistic models can be used to predict the potential effect of interventions, including drug inhibitions. Here, we present the implementation of a mechanistic model of cell signaling for the interpretation of transcriptomic data as an R/Bioconductor package, a Cytoscape plugin and a web tool with enhanced functionality which includes building interpretable predictors, estimation of the effect of perturbations and assessment of the effect of mutations in complex scenarios. (C) 2021 The Author(s). Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology.
Filiaciones:
K. RIAN:
Hosp Virgen Rocio, Fdn Progreso & Salud FPS, Clin Bioinformat Area, Seville 41013, Spain
Natl Sch Appl Sci Tangier, Lab Innovat Technol LTI, Tangier, Morocco
:
Ctr Invest Principe Felipe CIPF, Bioinformat & Biostat Unit, Valencia 46012, Spain
C. CUBUK:
Hosp Virgen Rocio, Fdn Progreso & Salud FPS, Clin Bioinformat Area, Seville 41013, Spain
Inst Canc Res, Div Genet & Epidemiol, London SW7 3RP, England
M. FALCO:
Hosp Virgen Rocio, Fdn Progreso & Salud FPS, Clin Bioinformat Area, Seville 41013, Spain
Ctr Invest Biomed Red Enfermedades Raras CIBERER, Bioinformat Rare Dis BiER, Seville 41013, Spain
Univ Helsinki Biomed, ONCOSYS Res Program, Helsinki 1 Haartmaninkatu 8, FI-00290 Helsinki, Finland
C. LOUCERA:
Hosp Virgen Rocio, Fdn Progreso & Salud FPS, Clin Bioinformat Area, Seville 41013, Spain
Inst Biomed Seville IBiS, Computat Syst Med, Seville 41013, Spain
M. ESTEBAN-MEDINA:
Hosp Virgen Rocio, Fdn Progreso & Salud FPS, Clin Bioinformat Area, Seville 41013, Spain
Inst Biomed Seville IBiS, Computat Syst Med, Seville 41013, Spain
I. ALAMO-ALVAREZ:
Hosp Virgen Rocio, Fdn Progreso & Salud FPS, Clin Bioinformat Area, Seville 41013, Spain
Inst Biomed Seville IBiS, Computat Syst Med, Seville 41013, Spain
M. PENA-CHILET:
Hosp Virgen Rocio, Fdn Progreso & Salud FPS, Clin Bioinformat Area, Seville 41013, Spain
Ctr Invest Biomed Red Enfermedades Raras CIBERER, Bioinformat Rare Dis BiER, Seville 41013, Spain
Inst Biomed Seville IBiS, Computat Syst Med, Seville 41013, Spain
:
Hosp Virgen Rocio, Fdn Progreso & Salud FPS, Clin Bioinformat Area, Seville 41013, Spain
Ctr Invest Biomed Red Enfermedades Raras CIBERER, Bioinformat Rare Dis BiER, Seville 41013, Spain
Inst Biomed Seville IBiS, Computat Syst Med, Seville 41013, Spain
Funct Genom Node INB ELIXIR, Seville, Spain
gold, Green Published
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