Figure 2

The multi-level nature of Reporter Features. A) Different Reporter Features can be calculated using different network representations of biological information, which will capture different but complementary aspects of the functionality of cellular machinery. Reporter GOs (marked in red tones in (a.)) are those Gene Ontology categories whose corresponding genes are most responsive to a perturbation than the background, and indicate which global functional groups within the cell are responding to the perturbation. Reporter TFs (b.), Reporter Proteins (c.), Reporter Complexes (d.) and Reporter Metabolites (e.) provide insights into more specific mechanistic aspects of the cellular response. For example, for the Reporter TFs network (b.), the transcription factor P1 is connected to all genes under its transcriptional regulation, i.e., transcripts of P2, P3, P4 an P5, this way depicting the regulatory network working through P1. B) For a series of related perturbations, Reporter Features allow the reconstruction of inferred regulatory maps that unify the perturbations under study via corresponding common regulatory mechanisms underlying them.