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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doaj-5f492cd74b0b4a3ba29bad8f4190c86b2021-06-27T11:34:01ZengNature Publishing GroupScientific Reports2045-23222021-06-0111111210.1038/s41598-021-92672-4A method to analyze time expression profiles demonstrated in a database of chili pepper fruit developmentChristian Escoto-Sandoval0Alan Flores-Díaz1M. Humberto Reyes-Valdés2Neftalí Ochoa-Alejo3Octavio Martínez4Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Unidad de Genómica Avanzada (Langebio)Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Unidad de Genómica Avanzada (Langebio)Department of Plant Breeding, Universidad Autónoma Agraria Antonio NarroCentro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Departamento de Ingeniería Genética, Unidad IrapuatoCentro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Unidad de Genómica Avanzada (Langebio)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.https://doi.org/10.1038/s41598-021-92672-4 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Christian Escoto-Sandoval Alan Flores-Díaz M. Humberto Reyes-Valdés Neftalí Ochoa-Alejo Octavio Martínez |
spellingShingle |
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 Scientific Reports |
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 Publishing Group |
series |
Scientific Reports |
issn |
2045-2322 |
publishDate |
2021-06-01 |
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. |
url |
https://doi.org/10.1038/s41598-021-92672-4 |
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