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. Author manuscript; available in PMC: 2009 Jul 9.
Published in final edited form as: Neurobiol Dis. 2007 Nov 28;29(3):515–528. doi: 10.1016/j.nbd.2007.11.008

Table 4.

Functional profiling of genes altered in nine-month-old transgenic α-syn mice.

GO annotation term % of regulated genes p value
protein binding 28.94% 6.81E-06
regulation of biological process 25.11% 3.05E-05
regulation of cellular process 21.70% 8.93E-04
regulation of metabolism 17.02% 0.0013
regulation of physiological process 21.28% 0.0013
transcriptional activator activity 3.40% 0.0014
biopolymer modification 12.77% 0.0018
regulation of cellular physiological process 20.43% 0.0018
transcription regulator activity 10.21% 0.0021
cytoskeletal protein binding 4.68% 0.0022
DNA binding 13.62% 0.0026
intracellular signaling cascade 8.94% 0.0031
biopolymer metabolism 17.45% 0.0034
transcription factor activity 8.09% 0.0035
regulation of transcription 14.89% 0.0039
protein modification 11.91% 0.0044
zinc ion binding 12.34% 0.0044
binding 48.09% 0.0045
regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism 14.89% 0.0047
transcription 14.89% 0.0064
regulation of transcription, DNA-dependent 14.04% 0.0064
regulation of cellular metabolism 15.32% 0.0076
transcription, DNA-dependent 14.04% 0.0082
cellular physiological process 48.94% 0.0099
cellular process 54.47% 0.012
enzyme linked receptor protein signaling pathway 3.40% 0.015
nucleic acid binding 17.87% 0.017
ubiquitin cycle 4.68% 0.021
GTPase regulator activity 3.40% 0.021
transition metal ion binding 13.19% 0.025
primary metabolism 34.47% 0.026
protein amino acid phosphorylation 5.53% 0.027
nucleobase, nucleoside, nucleotide and nucleic acid metabolism 18.30% 0.029
macromolecule metabolism 22.55% 0.035
negative regulation of biological process 6.38% 0.039
signal transduction 14.47% 0.040
enzyme regulator activity 5.11% 0.040
negative regulation of cellular process 5.96% 0.043
cell communication 15.32% 0.043

To determine functional categories associated with α-syn overexpression, we used the DAVID 2007 functional annotation tool (http://david.abcc.ncifcrf.gov/home.jsp), which classifies each probe into one or more functional categories using annotations from over 40 ontological databases and then determines which functional categories are represented in the data set more frequently than expected by chance alone. We limited the functional annotation chart generated by DAVID by classification of genes to functional categories defined by Gene Ontology Database annotations. Only probes with a q value ≤20% were used for the ontology analysis. We considered significant those categories with a p value ≤0.05 and contained at least 3% of the regulated genes. All molecular function and biological process annotation terms that fulfilled these criteria were included in the table regardless of how broad or narrow the annotation was. Therefore, we included broad categories, such as “binding,” as well as more specific and informative categories, such as “zinc ion binding.” The website QuickGO (http://www.ebi.ac.uk/ego) describes the GO annotation categories with their meanings and hierarchical relationships.

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