Mouse Brain Case Study

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3.1 Analysis of MPS VII mouse whole brain 3.1.1 Identification of dysregulated proteins by 2D PAGE and LC-MS/MS To identify dysregulated proteins in MPS VII mice compared to wildtype mice (n=3 each group, 5-month old), brains were collected and subjected to 2D-PAGE combined with nanoLC-MS/MS. From the 2D PAGE gels, a total of 2,055 spots were compared (Figure 1). Spots that had a fold-change >1.5 and a p-value <0.05 between MPS VII and control mice were deemed significant and subjected to in-gel trypic digestion. NanoLC-MS/MS analysis of the differentially expressed spots led to the identification of 43 individual proteins that were either upregulated or downregulated in MPS VII (Table 1). These proteins were identified by submitting the…show more content…
The whole network was analyzed by NetworkAnalyzer, which computes complex network parameters such as node degrees, average clustering coefficients, topological coefficients, and shortest path lengths. In the PPI network the nodes with high degree defined as hub proteins and the nodes with high betweenness defined as bottleneck proteins, which both play a fundamental role in the network [16]. Therefore, the degree and betweenness of each node are calculated, leading to identification of hub and bottleneck proteins (Table 5). The top 15 hub and bottleneck proteins are mainly those associated with ubiquitin, cytoskeleton and molecular chaperones. Hub and bottleneck proteins with their interacting proteins or chemicals were predicted from STICH web server and illustrated in Figure 3. More importantly, hub and bottleneck proteins within the network have been demonstrated to be potential therapeutic targets [17-19]. By submitting these hub and bottleneck proteins as drug targets in Drugbank database, potential drugs to treat MPS VII disease were predicted (Table 6). To provide more specific and detailed information about the PPI network, subnetworks were identified, which represented protein complexes or functional modules. A total of 5 subnetworks were identified using the MCODE plug-in and illustrated in Figure 4. The parameters of each subnetwork, including seed proteins, are listed in Table 7. Most of the hub
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