ArticleScientific reports2021
A method to analyze time expression profiles demonstrated in a database of chili pepper fruit development.
Article in Scientific reports, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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5 citing papers in PubMed, 8 citations in OpenAlex.
- The Transcription Factor CaNAC81 Is Involved in the Carotenoid Accumulation in Chili Pepper Fruits.Plants (Basel, Switzerland) · 2025Article
- Estimating Transcriptome Diversity and Specialization inPlants (Basel, Switzerland) · 2024Article
- Gene Functional Networks from Time Expression Profiles: A Constructive Approach Demonstrated in Chili Pepper (Plants (Basel, Switzerland) · 2023Article
- Putative Transcription Factor Genes Associated with Regulation of Carotenoid Biosynthesis in Chili Pepper Fruits Revealed by RNA-Seq Coexpression Analysis.International journal of molecular sciences · 2022Article
- Inheritance of gene expression throughout fruit development in chili pepper.Scientific reports · 2021Article
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Authors and funding
5 authors at 2 institutions in 1 country.
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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.
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