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The studies in this dissertation investigate neurodegenerative conditions of the central and peripheral nervous system utilizing bioinformatics and systems biology approaches. Various neurodegenerative conditions are associated with neuroinflammation or the inflammation of nervous tissue. We utilized Parkinson’s disease as our system for neuroinflammation in the central nervous system and diabetic peripheral neuropathy for the peripheral nervous system. Parkinson’s disease is associated with loss of dopaminergic neurons in the substantia nigra and consequent loss of dopamine signaling in the striatum of the central nervous system. Characteristics of Parkinson’s Disease include symptoms such as shaking, rigidity, slowness of movement, difficulty walking, dementia, depression, anxiety, sleeping disorders, and hallmark formation of misfolded α-synuclein aggregates called Lewy bodies. Diabetic peripheral neuropathy is a microvascular complication associated with diabetes mellitus. Degeneration of the peripheral nervous system in diabetes presents as neuropathic pain in the periphery with eventual loss of sensation in a stocking and glove like pattern. The loss of sensation is an underlying cause of diabetic foot syndrome which is the leading cause of lower limb amputations. This dissertation consists of three studies. The first study compared multiple murine models of diabetic peripheral neuropathy at different stages of the disease against human subjects in effort to identify an underlying cause of disease using publicly available microarray transcriptomic data. Pathway and network analysis were performed in conjunction on differentially expressed genes identified by comparing healthy controls to diabetic mice and progressive to non-progressive human subjects with diabetic peripheral neuropathy. Clusters of pathways in this network were related to inflammation, degradation, apoptosis, as well as kinase and immune signaling, as conserved changes across multiple time points, models, and species of DPN. These observed pathways, commonly disrupted across progression, species, and various murine models of the disease, are likely the key responses associated with diabetic peripheral neuropathy. The second study further investigated a single high dose streptozotocin model of type 1 diabetes mellitus by comparing tissues related to diabetic peripheral neuropathy (sciatic nerve and dorsal root ganglia) and diabetic nephropathy (renal glomerulus and cortex). RNA-sequencing identified differentially expressed genes in each complication-prone tissue between healthy controls and streptozotocin-treated mice. Genes with a conserved directional change were analysed using network and pathway analysis. Clusters related to DNA-damage response, oxidative stress, and immune response were represented in shared genes between diabeticnephropathy and diabetic peripheral neuropathy tissue experiencing a common directional change. These cluster themes are likely key conserved disruptions in microvascular complication-prone tissue. The third study explored neuroinflammation of the central nervous system utilizing mice overexpressing α-synuclein under the mouse thymidine1 promoter as an animal model of Parkinson’s disease. This murine model exhibits parkinsonian motor and non-motor symptoms as well as α-synuclein aggregation pathology. Early activation of microglia, the resident innate immune cells of the brain, and an inflammatory response can be measured in the brains of these animals as early as one month of age. RNA and DNA were extracted from microglia isolated from these animals at 3 and 13 months of age for RNA-sequencing and reduced representation bisulfite sequencing, respectively. The time points for tissue collection involve the beginning of motor symptoms at 3 months and 13 months is immediately prior to a loss of 40% of dopamine signaling which occurs at 14 months of age. The overexpression of α-synuclein-induced both genomic methylation and gene expression changes that are indicative of an immunologically activated M1 state of microglia. Correlation between gene expression and a change in methylation status were investigated but only intronic CG rich sites held a significant correlation with observed gene expression (r=-0.15, p=0.008). Profiling the changes induced by α-synuclein provides valuable insight into the systems contributing to disease progression. Overall, these results warrant further investigation into the role inflammation plays on the progression of neurodegenerative diseases. Our wide range of models and techniques lends strength to the notion of common immune activation pathways induced by a variety of disease insults in both the central and peripheral nervous systems.