The top-ranked IPA network of the PhosFox-processed case dataset of the qualitative phosphoproteomic case study example. The most significant network from the PhosFox-processed case dataset (426 proteins) associated with cellular assembly and organization, cellular compromise, cell death and survival. The red nodes are proteins found to be phosphorylated only in the case sample (included in the manually compiled 158 unique phosphoproteins), whereas the violet nodes are proteins that have both common phosphopeptides in the control and case sample, as well as unique phosphopeptides in the case sample identified by PhosFox. The white nodes are included in the network through the IPA knowledge database and not found in the sample, but known to be in the network. The signaling networks were supported by at least one curated annotation from the Ingenuity Pathways Knowledge Base (Ingenuity® Systems, http://www.ingenuity.com). Solid and dotted lines indicate direct and indirect molecular interactions, respectively. The shape of the nodes indicates the molecular class. The color coding of the edges are: pink, regulation of binding; green, expression; red, activation; violet, protein-protein interactions; black, inhibition; orange, molecular cleavage; blue, phosphorylation/activation; light blue, transcription.