Screen-shot of the Multi-Experiment viewer (Use Case #1, Study 2).

Abstract

<p>(<b>A</b>) The matrix represent the genes (in columns) co-expressed with the query gene(s) in microarray experiments (in rows). The brightness of blue of the matrix element corresponds to the co-expression value of the gene in an experiment (Eq. 4). The genes and experiments are sorted by average Z-values of genes (Eqs. 1–3). The vertical and horizontal levers allow selecting the highest ranked genes and experiments for building regulatory modules (the selection is shown in a black square). Hovering over the genes and experiments brings up their short description. (<b>B–C</b>) Clicking on the experiment ID brings up the experiment properties and visualization of the expression data. (<b>D</b>) A word cloud that characterizes the found set of experiments described by keywords (ontology terms representing cell types, tissues, diseases, biological processes, etc.). Clicking on the term in the cloud highlights respective experiments. The ‘Recalculate’ button allows the user to recalculate the matrix choosing only the experiments containing selected terms.</p