An “Electronic Fluorescent Pictograph” Browser for Exploring and Analyzing Large-Scale Biological Data Sets

By D. Winter, Ben Vinegar, Hardeep Nahal, R. Ammar, Greg V. Wilson, Nicholas J. Provart. PLoS ONE, 2007

2,624 citations recorded by the source corpus.

Background The exploration of microarray data and data from other high-throughput projects for hypothesis generation has become a vital aspect of post-genomic research. For the non-bioinformatics specialist, however, many of the currently available tools provide overwhelming amounts of data that are presented in a non-intuitive way. Methodology/Principal Findings In order to facilitate the interpretation and analysis of microarray data and data from other large-scale data sets, we have developed a tool, which we have dubbed the electronic Fluorescent Pictograph – or eFP – Browser, available at http://www.bar.utoronto.ca/, for exploring microarray and other data for hypothesis generation. This eFP Browser engine paints data from large-scale data sets onto pictographic representations of the experimental samples used to generate the data sets. We give examples of using the tool to present Arabidopsis gene expression data from the AtGenExpress Consortium (Arabidopsis eFP Browser), data for subcellular localization of Arabidopsis proteins (Cell eFP Browser), and mouse tissue atlas microarray data (Mouse eFP Browser). Conclusions/Significance The eFP Browser software is easily adaptable to microarray or other large-scale data sets from any organism and thus should prove useful to a wide community for visualizing and interpreting these data sets for hypothesis generation.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/f83f76c648359efd9b70171ba1ae69065cc1aaf4

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Citations in the corpus

Flavonoids: new roles for old molecules. (2010, methodology): “These expression analyses were confirmed by the “electronic fluorescent pictograph” browser available at http://bbc.botany.utoronto.ca/efp/cgi-bin/efpWeb.cgi (Winter et al. 2007).”
Abscisic Acid Synthesis and Response (2013, background): “However, two Arabidopsis PIPs (AtPIP1;4: AT4G00430 and AtPIP2;5: AT3G54820) are induced by drought and are highly expressed in guard cells (Alexandersson et al., 2005; Winter et al., 2007; Yang et al., 2008), which could facilitate stomatal closure.”
ORS1, an H2O2-Responsive NAC Transcription Factor, Controls Senescence in Arabidopsis thaliana (2011, methodology): “For computational analyses, the online tools of GENEVESTIGATOR (www.genevestigator.com; Zimmermann et al., 2004), eFP browser (www.bar.utoronto.ca/efp/cgi-bin/efpWeb.cgi; Winter et al., 2007) and the Plant Transcription Factor Database (http:// plntfdb.bio.uni-potsdam.de/v3.”
The Salt Overly Sensitive (SOS) pathway: established and emerging roles. (2013, methodology): “The cell type- and section-specific microarray data were obtained and processed using the eFP browser (Winter et al., 2007), using ATH1 microarray data.”
PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update (2009, background): “The protein summary page now provides dynamic links to further external resources, such as Aramemnon (18), eFP browser (19), co-expression networks ATTED-II (20), subcellular localization (21) and other more general protein information at the GABI Primary Database (22).”
First off the mark: early seed germination. (2011, methodology): “D) Arabidopsis transcriptome analysis available via the seed-specific eFP-browser at www.bar.utoronto.ca (Winter et al., 2007; Bassel et al., 2008) based on experiments for non-dormant, non-stratified after-ripened wild-type seeds (Nakabayashi et al., 2005; Preston et al., 2009), cold-stratified…”
Comprehending crystalline β-carotene accumulation by comparing engineered cell models and the natural carotenoid-rich system of citrus (2011, positive): “This is in agreement with expression data published in the developmental map of the Arabidopsis eFP browser (Winter et al., 2007), which indicates that expression is exclusively in developing seeds.”
The AtGenExpress hormone and chemical treatment data set: experimental design, data evaluation, model data analysis and data access. (2008, background): “The Botany Array Resource provides electronic Northerns (Touﬁghi et al. , 2005), electronic ﬂuorescent pictographs (Winter et al. , 2007) and other tools by means of a user-friendly interface that presents gene expression patterns in a visually appealing manner.”
The heat‐shock protein/chaperone network and multiple stress resistance (2017, background): “The latter is represented by DREB (dehydration response element binding) TFs. HSFA3 is a target of DREB2A (Yoshida et al., 2008), which is induced by multiple stresses such as drought, salt, heat and cold and to a lesser extent by oxidative stress, UV-B light and wounding (Winter et al., 2007).”