| Title: | gcProfileMakeR: An R Package for Automatic Classification of Constitutive and Non-Constitutive Metabolites |
| Author(s): | Perez-Sanz F; Ruiz-Hernandez V; Terry MI; Arce-Gallego S; Weiss J; Navarro PJ; Egea-Cortines M; |
| Address: | "Instituto Murciano de Investigaciones Biomedicas El Palmar, 30120 Murcia, Spain. Department of Biosciences, University Salzburg, 5020 Salzburg, Austria. Genetica Molecular, Instituto de Biotecnologia Vegetal, Edificio I+D+I, Plaza del Hospital s/n, Universidad Politecnica de Cartagena, 30202 Cartagena, Spain. Vall d'Hebron Institute of Oncology, 08035 Barcelona, Spain. DSIE Cuartel de Antiguones, Plaza del Hospital s/n, Universidad Politecnica de Cartagena, 30202 Cartagena, Spain" |
| ISSN/ISBN: | 2218-1989 (Print) 2218-1989 (Electronic) 2218-1989 (Linking) |
| Abstract: | "Metabolomes comprise constitutive and non-constitutive metabolites produced due to physiological, genetic or environmental effects. However, finding constitutive metabolites and non-constitutive metabolites in large datasets is technically challenging. We developed gcProfileMakeR, an R package using standard Excel output files from an Agilent Chemstation GC-MS for automatic data analysis using CAS numbers. gcProfileMakeR has two filters for data preprocessing removing contaminants and low-quality peaks. The first function NormalizeWithinFiles, samples assigning retention times to CAS. The second function NormalizeBetweenFiles, reaches a consensus between files where compounds in close retention times are grouped together. The third function getGroups, establishes what is considered as Constitutive Profile, Non-constitutive by Frequency i.e., not present in all samples and Non-constitutive by Quality. Results can be plotted with the plotGroup function. We used it to analyse floral scent emissions in four snapdragon genotypes. These included a wild type, Deficiens nicotianoides and compacta affecting floral identity and RNAi:AmLHY targeting a circadian clock gene. We identified differences in scent constitutive and non-constitutive profiles as well as in timing of emission. gcProfileMakeR is a very useful tool to define constitutive and non-constitutive scent profiles. It also allows to analyse genotypes and circadian datasets to identify differing metabolites" |
| Keywords: | R package automatic classification circadian clock constitutive metabolome floral organ identity gcProfileMakeR machine learning non-constitutive metabolome; |
| Notes: | "PubMed-not-MEDLINEPerez-Sanz, Fernando Ruiz-Hernandez, Victoria Terry, Marta I Arce-Gallego, Sara Weiss, Julia Navarro, Pedro J Egea-Cortines, Marcos eng BFU2017-88300-C2-1R/Ministerio de Ciencia, Innovacion y Universidades/ BFU2017-88300-C2-2R/Ministerio de Ciencia, Innovacion y Universidades/ FPU13/03606/Ministerio de Educacion, Cultura y Deporte/ Switzerland 2021/04/04 Metabolites. 2021 Mar 31; 11(4):211. doi: 10.3390/metabo11040211" |
