Figure 2

Computational pathway analysis of brain proteomic profiling. (A) IPA showing decreased and increased biological functions in NR1^neo−/− mouse brain regions. Depicted are functions with an activation score (z-score) >1 (increased activation) or < −1 (decreased activation) with their corresponding log₂ (P) (right graph, the dotted line represents the 0.05 P value threshold) as well as the five most-significantly dysregulated non-directionally (z-score > −1, <1, or not predicted) affected pathways (in the middle of the bar plots). (B) Identified IPA networks in the data set by global pathway analysis using the Ingenuity Pathways Knowledge Database (IPKB) software. All significantly altered proteins in the frontal cortex and hippocampus from the model were used for the network analysis based on criteria annotated in the IPKB database, which contains molecular information available in the scientific literature. Networks were generated algorithmically on the basis of the connectivity derived from molecular interaction information, scored according to the significant number of focus proteins and assigned associated biological functions (see network descriptions) by overlaying the network molecules onto predefined maps of functional or pathway information in the IPKB database. Proteins are indicated by their gene names. Red and green symbols/text indicate increased and decreased proteins, respectively. Blue symbols indicate predicted inhibition, orange lines indicate predicted activation. Yellow lines indicate inconsistencies with the states of the downstream molecules. Lines ending with arrows indicate activation, lines without arrows indicate interaction/binding.