Arabidopsis bioinformatics: tools and strategies

Abstract

The sequencing of the Arabidopsis thaliana genome 21 years ago ushered in the genomics era for plant research. Since then, an incredible variety of bioinformatic tools permit easy access to large repositories of genomic, transcriptomic, proteomic, epigenomic and other '-omic' data. In this review, we cover some more recent tools (and highlight the 'classics') for exploring such data in order to help formulate quality, testable hypotheses, often without having to generate new experimental data. We cover tools for examining gene expression and co-expression patterns, undertaking promoter analyses and gene set enrichment analyses, and exploring protein-protein and protein-DNA interactions. We will touch on tools that integrate different data sets at the end of the article.

Recent progress in molecular genetics and omics-driven research in seed biology

“…Over the last decade, the development of high-throughput technologies has led to the establishment of useful resources for plant (epi)genomic, transcriptomic, or proteomic data. Bio-informatic tools have continuously been improved facilitating the access and use of these huge sets of "omics" data [21]. However, most of these "omics" approaches were initially implemented on whole seeds, that are comprised of several different tissues (seed coat, endosperm and embryo), with these tissues themselves encompass different cell types known to exhibit contrasting properties and fates.…”

“…Au cours de la dernière décennie, le développement des technologies à haut débit a conduit à l'établissement de ressources utiles pour les données (épi)génomiques, transcriptomiques ou protéomiques des plantes. Les outils bioinformatiques ont été continuellement améliorés pour faciliter l'accès et l'utilisation de ces immenses ensembles de données « omiques » [21]. Cependant, la plupart de ces approches « omiques » ont été initialement mises en oeuvre sur des graines entières, qui sont composées de différents tissus (téguments, albumen et embryon), qui englobent eux-mêmes plusieurs types de cellules connues pour présenter des propriétés et des destins contrastés.…”

Finding the LMA needle in the wheat proteome haystack

“…Multiple online tools exist to efficiently mine GO terms, however only a few cater for nonmodel species, let alone plants (148)(149)(150). When looking for relevant mining tools during our method development stage, we resorted to AgriGO online program which specifically focused on agricultural species and offered valuable illustrations to display enrichment sets (41).…”

Isolation and Comprehensive in Silico Characterisation of a New 3-Hydroxy-3-Methylglutaryl-Coenzyme A Reductase 4 (HMGR4) Gene Promoter from Salvia miltiorrhiza: Comparative Analyses of Plant HMGR Promoters

“…Due to its similarity to other plants, A. thaliana has become the starting point for studying numerous aspects of plant cell-, molecular- and system-biology [ 33 ]. The abundance of research conducted on A. thaliana has led to the creation of numerous clones, cloning vectors, mutant lines, seeds, databases and online tools containing genomic, epigenomic, transcriptomic and proteomic data [ 34 ].…”

“…The abundance of research conducted on A. thaliana has led to the creation of numerous clones, cloning vectors, mutant lines, seeds, databases and online tools containing genomic, epigenomic, transcriptomic and proteomic data [34].…”