Genome2D: a visualization tool for the rapid analysis of bacterial transcriptome data

Abstract

Genome2D is a Windows-based software tool for visualization of bacterial transcriptome and customized datasets on linear chromosome maps constructed from annotated genome sequences. Genome2D facilitates the analysis of transcriptome data by using different color ranges to depict differences in gene-expression levels on a genome map. Such output format enables visual inspection of the transcriptome data, and will quickly reveal transcriptional units, without prior knowledge of expression level cutoff values. The compiled version of Genome2D is freely available for academic or non-profit use from http://molgen.biol.rug.nl/molgen/research/molgensoftware.php.

Figure 1

Genome2D visualization of the genomic organization of L. lactis IL1403 (GenBank annotation: AE0051576). The figure displays a partial, detailed view in which putative terminators, determined using the TIGR software package TransTerm, are shown as stem-loop structures [11,46]. Predicted promoter elements (-35 boxes in green; -10 boxes in blue) and cre-boxes (in red) are shown. See text for more details.

Figure 2

Demonstration of the power of visualization in transcriptome analyses. The dataset used is from Hamoen and colleagues [24]. The strength of up- or downregulation is depicted by the intensity of the color. Stem-loop structures indicate annotated terminators. (a,b) Probable cases of low-level activation. Genes are colored on the basis of expression ratios from DNA macroarray experiments [24], without applying a stringent cutoff. Red shades indicate ComK-dependent activation, whereas green shows downregulation. Gray shades indicate ratios of around 1. Stem-loop structures are used to depict annotated terminators. K-boxes are shown by vertical red lines. (c,d) Putative cases of transcriptional readthrough. Red shades indicate significant ComK-dependent expression. K-boxes are depicted by vertical green lines. Gray genes are not significantly ComK-dependent. (e,f) Probable cases in which antisense RNA has a role (colors and symbols identical to (c) and (d)).