Visualization Tools and Workflows for Exploration and Interpretation of Results
iReport removes data-analysis challenges by providing novel tools and workflows for visualizing, querying, and filtering the results. These tools help researchers perform downstream analysis based on biological criteria, interrogate their data from multiple angles, and quickly identify compelling genes for further study.
The Summary Page in iReport features “Top Results by Experimental Keyword” and an interactive volcano plot (Figure 2) that enables the user to quickly identify expected, biologically relevant sets of gene-expression changes. Clicking on one of the top results (for example, “Antiviral Response”) lets the user drill down in the volcano plot to see which DEGs are associated with that process and takes the user directly to the experimentally demonstrated evidence that implicates those DEGs in that biological process.
These features accomplish two critical goals of microarray data interpretation: 1) biologists can quickly find a set of DEGs that anchor on a relevant biological process or phenotype, and 2) biologists can clarify the strength of this association by accessing the literature evidence and experimental context substantiating that association in the Publications and Findings panel in each chapter of iReport.
By reducing the effort required to find an expected, relevant result, iReport Summary Page enables researchers to move on to explore unexpected, potentially novel insights about their samples.
To facilitate this exploration, we built The Wheel, which enables biologists to focus on individual or sets of DEGs based on their biological properties (such as molecular function, fold change, subcellular location, etc.) and known biological associations (pathways, diseases, cellular functions, etc.). The Wheel uses a biologist-friendly hierarchy of topics to quickly expand the investigation from a very specific result (e.g., antiviral response, 10 DEGs) to a broader topic within that same theme (e.g., regulation of immune response, 32 DEGs) (Figure 3).