Illustration of the Reporter Features algorithm. The algorithm takes as input gene expression data (significance of change for pair-wise comparisons or correlation for multi-dimensional datasets) and the topology of bio-molecular interaction networks (either physical or functional interactions) represented as a graph. The bio-molecular network should be of the type "feature j - gene i", where feature j is any biological feature of interest (e.g., a GO term, a transcription factor, a protein or a metabolite) associated with the gene i. Gene expression in the form of z-score is then mapped onto the "gene nodes" of the graph. Finally, the score of each feature can be calculated based on the score of its neighbors "gene nodes" (see Methods). Reporter Features are those features with a z-score above a selected cut-off. The example in the grey boxes was selected from the Reporter TFs for the Δgrr1 dataset.