GO enrichment analysis using the hypergeometric statistical method with the Hochberg false discovery rate adjustment showed that many GO terms were overrespresented in the HLB response network. Among the overrepresented Inhibitors,Modulators,Libraries GO terms, the nodes belonging to the following six categories were color coded in the HLB response network, carbohydrate metabolic process, nitrogen Inhibitors,Modulators,Libraries and amino acid metabolic process, transport, defense response, hormone response and sig naling. The nodes for each of these six categories, to gether with the nodes belonging to some highly overrepresented GO terms such as response to stress, lipid metabolic process, cell wall and membrane part, were tomical structure size, regulation of cell size, and regulation of cellular component size.
In addition to these 13 GO terms, the minor hubs have 16 additional overrepresented GO terms, such as response to stimulus, response to stress, regulation Batimastat of biological quality and signal transduction. Analysis of the defense and hormone response subnetworks Given the importance of carbon and nitrogen metabol ism, transport, signaling, defense response and hormone response in the citrus response to the HLB bacterial in fection and in general plant defense response, the sub networks for these six categories were constructed by mapping the Probesets belonging to these categories into the HLB response network. The resulting edges were listed in Additional file 7. We first analyzed the HLB defense subnetwork. As shown in Figure 3A, the Probesets representing defense, hormone response and signaling were color coded.
Clearly, the large hubs belong to the categories of defense and hor monal responses but not signaling. Interestingly, several of the hormone response hubs are also defense response hubs as these hubs are involved Inhibitors,Modulators,Libraries in both responses. For example, the Probesets Cit. 11529. 1. S1 s at and Cit. 11530. 1. S1 at represent a transcription factor closest to the Arabidopsis At2G37630 encoded AS1, which is annotated as both response to fungus, virus, bacterium and salt stresses and response to hor mones such as auxin, GA, SA and JA. Interestingly, these hubs were connected to other large defense hubs such as Cit. 1194. 1. S1 s at, which represents a lipid trans porter closest to Arabidopsis DIR1, Cit. 3826. 1. S1 at, which represents a FER protein kinase like gene, and Cit. 10594. 1.
S1 at, which represents an EP3 like chitinase gene. Cit. Inhibitors,Modulators,Libraries 11529. 1. S1 s at, Cit. 11530. 1. S1, Cit. 1194. 1. S1 s at, and Cit. 3826. 1. S1 at were shown to be down regulated by the Las infections in two reports. Another example is Cit. 1923. 1. S1 s at, which represents a protein degradation component similar to Arabidopsis CSN5A and is assigned the GO terms of both auxin response and defense response. This hub is interconnected to at least two large defense hubs, Cit. 4216. 1. S1 s at and Cit. 2848. 1. S1 at. However, there is one hormone response hub, Cit. 4553. 1.