dc.contributor | Vall d'Hebron Barcelona Hospital Campus |
dc.contributor.author | Pérez Sanz, Fernando |
dc.contributor.author | Ruiz-Hernández, Victoria |
dc.contributor.author | Terry, Marta I. |
dc.contributor.author | Arce Gallego, Sara |
dc.contributor.author | Weiss, Julia |
dc.contributor.author | Navarro Lorente, Pedro Javier |
dc.contributor.author | Egea-Cortines, Marcos |
dc.date.accessioned | 2022-06-08T09:52:11Z |
dc.date.available | 2022-06-08T09:52:11Z |
dc.date.issued | 2021-04 |
dc.identifier.citation | Perez-Sanz F, Ruiz-Hernández V, Terry MI, Arce-Gallego S, Weiss J, Navarro PJ, et al. gcProfileMakeR: An R Package for Automatic Classification of Constitutive and Non-Constitutive Metabolites. Metabolites. 2021 Abr;11(4):211. |
dc.identifier.issn | 2218-1989 |
dc.identifier.uri | https://hdl.handle.net/11351/7642 |
dc.description | Circadian clock; Constitutive metabolome; Machine learning |
dc.description.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. |
dc.language.iso | eng |
dc.publisher | MDPI |
dc.relation.ispartofseries | Metabolites;11(4) |
dc.rights | Attribution 4.0 International |
dc.rights.uri | http://creativecommons.org/licenses/by/4.0/ |
dc.source | Scientia |
dc.subject | Metabolòmica |
dc.subject | ADN - Bancs de dades |
dc.subject | Genètica molecular |
dc.subject.mesh | Molecular Sequence Data |
dc.subject.mesh | Metabolome |
dc.subject.mesh | Molecular Biology |
dc.title | gcProfileMakeR: An R Package for Automatic Classification of Constitutive and Non-Constitutive Metabolites |
dc.type | info:eu-repo/semantics/article |
dc.identifier.doi | 10.3390/metabo11040211 |
dc.subject.decs | datos de secuencia molecular |
dc.subject.decs | metaboloma |
dc.subject.decs | biología molecular |
dc.relation.publishversion | https://doi.org/10.3390/metabo11040211 |
dc.type.version | info:eu-repo/semantics/publishedVersion |
dc.audience | Professionals |
dc.contributor.organismes | Institut Català de la Salut |
dc.contributor.authoraffiliation | [Perez-Sanz F] Instituto Murciano de Investigaciones Biomédicas El Palmar, 30120 Murcia, Spain. [Ruiz-Hernández V] Department of Biosciences, University Salzburg, 5020 Salzburg, Austria. [Terry MI, Weiss J, Egea-Cortines M] Genética Molecular, Instituto de Biotecnología Vegetal, Edificio I+D+I, Universidad Politécnica de Cartagena, 30202 Cartagena, Spain. [Arce-Gallego S] Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain. [Navarro PJ] DSIE Cuartel de Antiguones, Universidad Politécnica de Cartagena, 30202 Cartagena, Spain |
dc.identifier.pmid | 33807334 |
dc.identifier.wos | 000643265800001 |
dc.rights.accessrights | info:eu-repo/semantics/openAccess |