The Rat Genome Database pathway portal

Abstract

The set of interacting molecules collectively referred to as a pathway or network represents a fundamental structural unit, the building block of the larger, highly integrated networks of biological systems. The scientific community's interest in understanding the fine details of how pathways work, communicate with each other and synergize, and how alterations in one or several pathways may converge into a disease phenotype, places heightened demands on pathway data and information providers. To meet such demands, the Rat Genome Database [(RGD) http://rgd.mcw.edu] has adopted a multitiered approach to pathway data acquisition and presentation. Resources and tools are continuously added or expanded to offer more comprehensive pathway data sets as well as enhanced pathway data manipulation, exploration and visualization capabilities. At RGD, users can easily identify genes in pathways, see how pathways relate to each other and visualize pathways in a dynamic and integrated manner. They can access these and other components from several entry points and effortlessly navigate between them and they can download the data of interest. The Pathway Portal resources at RGD are presented, and future directions are discussed. Database URL: http://rgd.mcw.edu.

Figure 1.

Shows a partial view of RGD's home page with the main entry points, video tutorials, rotating banner and the Latest News sections, with an arrow pointing to the Pathways entry (A) and the top portion of RGD's Pathway Resource page the Pathway entry brings, housing the interactive pathway diagram pages and pathway suites and physiological pathway diagrams with an arrow pointing to the ‘testosterone biosynthetic pathway’ (B).

Figure 2.

Shows a partial view of the interactive diagram page for the ‘androgen signaling pathway’ (A) and for the ‘prostate cancer pathway’ with the inset showing the list of miRNAs of potential interest in prostate cancer which can be accessed by clicking on the functional class icon (B).

Figure 3.

Shows the Prostate Cancer Pathway Suite.

Figure 4.

Shows a partial view of the Ontology Report page for the ‘glucagon signaling pathway’ (A) and the path(s) to the ‘glucagon signaling pathway’ term within the ontology (B).