A method to analyze time expression profiles demonstrated in a database of chili pepper fruit development

Abstract RNA-Seq experiments allow genome-wide estimation of relative gene expression. Estimation of gene expression at different time points generates time expression profiles of phenomena of interest, as for example fruit development. However, such profiles can be complex to analyze and interpret....

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Autores principales:	Christian Escoto-Sandoval, Alan Flores-Díaz, M. Humberto Reyes-Valdés, Neftalí Ochoa-Alejo, Octavio Martínez
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/5f492cd74b0b4a3ba29bad8f4190c86b
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spelling	oai:doaj.org-article:5f492cd74b0b4a3ba29bad8f4190c86b2021-12-02T16:07:03ZA method to analyze time expression profiles demonstrated in a database of chili pepper fruit development10.1038/s41598-021-92672-42045-2322https://doaj.org/article/5f492cd74b0b4a3ba29bad8f4190c86b2021-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-92672-4https://doaj.org/toc/2045-2322Abstract RNA-Seq experiments allow genome-wide estimation of relative gene expression. Estimation of gene expression at different time points generates time expression profiles of phenomena of interest, as for example fruit development. However, such profiles can be complex to analyze and interpret. We developed a methodology that transforms original RNA-Seq data from time course experiments into standardized expression profiles, which can be easily interpreted and analyzed. To exemplify this methodology we used RNA-Seq data obtained from 12 accessions of chili pepper (Capsicum annuum L.) during fruit development. All relevant data, as well as functions to perform analyses and interpretations from this experiment, were gathered into a publicly available R package: “Salsa”. Here we explain the rational of the methodology and exemplify the use of the package to obtain valuable insights into the multidimensional time expression changes that occur during chili pepper fruit development. We hope that this tool will be of interest for researchers studying fruit development in chili pepper as well as in other angiosperms.Christian Escoto-SandovalAlan Flores-DíazM. Humberto Reyes-ValdésNeftalí Ochoa-AlejoOctavio MartínezNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Christian Escoto-Sandoval Alan Flores-Díaz M. Humberto Reyes-Valdés Neftalí Ochoa-Alejo Octavio Martínez A method to analyze time expression profiles demonstrated in a database of chili pepper fruit development
description	Abstract RNA-Seq experiments allow genome-wide estimation of relative gene expression. Estimation of gene expression at different time points generates time expression profiles of phenomena of interest, as for example fruit development. However, such profiles can be complex to analyze and interpret. We developed a methodology that transforms original RNA-Seq data from time course experiments into standardized expression profiles, which can be easily interpreted and analyzed. To exemplify this methodology we used RNA-Seq data obtained from 12 accessions of chili pepper (Capsicum annuum L.) during fruit development. All relevant data, as well as functions to perform analyses and interpretations from this experiment, were gathered into a publicly available R package: “Salsa”. Here we explain the rational of the methodology and exemplify the use of the package to obtain valuable insights into the multidimensional time expression changes that occur during chili pepper fruit development. We hope that this tool will be of interest for researchers studying fruit development in chili pepper as well as in other angiosperms.
format	article
author	Christian Escoto-Sandoval Alan Flores-Díaz M. Humberto Reyes-Valdés Neftalí Ochoa-Alejo Octavio Martínez
author_facet	Christian Escoto-Sandoval Alan Flores-Díaz M. Humberto Reyes-Valdés Neftalí Ochoa-Alejo Octavio Martínez
author_sort	Christian Escoto-Sandoval
title	A method to analyze time expression profiles demonstrated in a database of chili pepper fruit development
title_short	A method to analyze time expression profiles demonstrated in a database of chili pepper fruit development
title_full	A method to analyze time expression profiles demonstrated in a database of chili pepper fruit development
title_fullStr	A method to analyze time expression profiles demonstrated in a database of chili pepper fruit development
title_full_unstemmed	A method to analyze time expression profiles demonstrated in a database of chili pepper fruit development
title_sort	method to analyze time expression profiles demonstrated in a database of chili pepper fruit development
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/5f492cd74b0b4a3ba29bad8f4190c86b
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A method to analyze time expression profiles demonstrated in a database of chili pepper fruit development

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