An "Electronic Fluorescent Pictograph" browser for exploring and analyzing large-scale biological data sets

Abstract

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.

Figure 1. Representation of eFP Browser implementation.

A. Schematic of browser inputs showing from top to bottom on the left the input image that forms the basis for the output, the XML control file, the identifier to probe set lookup, and the expression database. These are used by the eFP Browser to generate the output image upon user input. B. Snippet of the XML control file with significant tags highlighted.

Figure 2. Expression pattern of ABI3 – ABSCISIC ACID INSENSITIVE 3.

ABI3, At3g24650, is expressed strongly in Stage 8–10 seeds. Features and control options of the Arabidopsis eFP Browser are also shown.

Figure 3. Relative and Compare Modes of the Arabidopsis eFP Browser.

A. Expression of RGL2, At3g03450, in Relative Expression mode, showing stronger expression relative to its median expression level in imbibed seeds and flower parts, as described in the literature. B. Expression of the ethylene receptors ERS1, At2g40940 versus ETR1, At1g66340 as visualized in the Compare Mode, showing stronger expression (yellow-green) of ERS1 in earlier stages of seed development and stronger expression (red) of ETR1 in later stages of seed development.

Figure 4. Abiotic stress response for the cold-inducible transcription factor gene C-BOX BINDING FACTOR 1, At4g25490, as viewed with the Arabidopsis eFP Browser.

Figure 5. Tissue-specific expression patterns for At5g43350, AtPT1/Pht1;1.

This gene encodes an inorganic phosphate transporter known to be strongly expressed in the roots. Tissues where values from replicate samples exhibit a high standard deviation are coloured grey – the standard deviation filtering feature of the Arabidopsis eFP Browser was activated during output generation.

Figure 6. Absolute and relative expression patterns of expression for DHS1, At4g39980, and DHS2, At4g33510.

DHS1 is strongly induced by UV light treatment, while DHS2 is diurnally responsive but not UV-inducible per se, see boxed timepoints.

Figure 7. A section of the Arabidopsis eFP Browser Biotic Stress output.

Induction of a pathogen-inducible gene, PR1, At2g14610, upon Pseudomonas syringae attack, is clearly evident 24 hours after inoculation.

Figure 8. An exemplary Arabidopsis Cell eFP Browser output image.

The subcellular localisation pattern of At3g26520, encoding Tonoplast Intrinsic Protein 2, false coloured according to degree of support for a given location based on both measured and predicted subcellular localizations from the SUBA database.

Figure 9. An exemplary Mouse eFP Browser output image.

The expression level for myosin (XM_126201.1) is strongest in skeletal muscle and a couple of other areas, such as the trachea, as denoted by the strong red colouration there.