The Pathway Tools cellular overview diagram and Omics Viewer - PubMed (original) (raw)

The Pathway Tools cellular overview diagram and Omics Viewer

Suzanne M Paley et al. Nucleic Acids Res. 2006.

Abstract

The Pathway Tools cellular overview diagram is a visual representation of the biochemical network of an organism. The overview is automatically created from a Pathway/Genome Database describing that organism. The cellular overview includes metabolic, transport and signaling pathways, and other membrane and periplasmic proteins. Pathway Tools supports interrogation and exploration of cellular biochemical networks through the overview diagram. Furthermore, a software component called the Omics Viewer provides visual analysis of whole-organism datasets using the overview diagram as an organizing framework. For example, gene expression and metabolomics measurements, alone or in combination, can be painted onto the overview, as can computed whole-organism datasets, such as predicted reaction-flux values. The cellular overview and Omics Viewer provide a mechanism whereby biologists can apply the pattern-recognition capabilities of the human visual system to analyze large-scale datasets in a biologically meaningful context. SRI's BioCyc.org website provides overview diagrams for more than 200 organisms. This article describes enhancements to the overview made since a 1999 publication, including the automatic layout capability, expansion of the cellular machinery that it includes, new semantic zooming and poster-generating capabilities, and extension of the Omics Viewer to support painting of metabolites, animations and zooming to individual pathway diagrams.

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Figures

Figure 1

Figure 1

The cellular overview diagram for Escherichia coli K-12, from the EcoCyc database.

Figure 2

Figure 2

A portion of the cellular overview diagram for E.coli. The pathway in the center of the image is ketogluconate metabolism. The diagram shows all connections from metabolites in this pathway to other pathways or reactions. This pathway is regulated by three transcription factors—the regulon for each of these transcription factors is highlighted in a different color, as shown in the key.

Figure 3

Figure 3

The cellular overview diagram for E.coli overlaid with data from a gene expression experiment, showing a magnified view of the gluconeogenesis pathway. Notice that in this magnified view, isozymes are distinguished as parallel lines within one reaction arrow, and gene names and their corresponding data values are drawn in the color for that data value.

Figure 4

Figure 4

A portion of a table of E.coli pathways that are significantly up- or down-regulated as measured by a gene expression experiment. The pathway diagram shows all genes with an expression log ratio >1 in red, and all those with a ratio less than −1 in yellow. The column on the right lists each enzyme in the pathway, its associated genes and, where available, its cellular location.

References

    1. Karp P.D., Paley S., Romero P. The Pathway Tools Software. Bioinformatics. 2002;18:S225–S232. - PubMed
    1. Karp P.D., Ouzounis C.A., Moore-Kochlacs C., Goldovsky L., Kaipa P., Ahren D., Tsoka S., Darzentas N., Kunin V., Lopez-Bigas N. Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res. 2005;33:6083–6089. - PMC - PubMed
    1. Karp P., Krummenacker M., Paley S., Wagg J. Integrated pathway/genome databases and their role in drug discovery. Trend. Biotechnol. 1999;17:275–281. - PubMed
    1. Saraiya P., North C., Duca K. Visualizing biological pathways: requirements analysis, systems evaluation and research agenda. Inform. Visualiz. 2005;4:191–205.
    1. Michal G. Biochemical Pathways Wall Chart. Boehringer Mannheim GmbH Biochemica; 1982.

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