See Supplemental Experimental Procedures for details on tissue collection, RNA isolation,
array hybridization, and preprocessing. Probe” refers to a single probe on the array. GS measurements were computed for each probe. In many cases, multiple probes for a single “gene,” e.g., FOXP2, were present on the array ( Figure S5, Table S2). There were 20,104 probes in the network, 16,448 of which were annotated with a gene symbol at the time of analysis (February 2011, see http://songbirdtranscriptome.net for up-to-date annotations). Since many genes were represented by > 1 probe, only 8,015 annotations were unique. Of these 8,015 LY294002 manufacturer unique genes, there were 2,496 unique annotations in the five singing-related modules. When we report GS.motifs.X for a gene, that value is the average GS.motifs.X score of all probes
for that gene unless otherwise noted. The area X coexpression network was constructed using probes; thus when we report the number of genes in a module we are referring to the number of unique gene annotations found for probes in that module. Due to sources of natural and experimental variability, different probes to the same gene were sometimes assigned to different, though usually similar, modules during network construction, e.g., probes made to different regions of the same gene may bind to alternatively spliced transcript variants with varying levels of efficiency. Many methods exist for analyzing gene expression microarray data. We chose WGCNA because of its biological relevance and other advantages EPZ-6438 supplier (Supplemental Experimental Procedures). All WGCNA computations were done in the free statistical software
R (http://www.r-project.org/) using functions in the WGCNA library (Langfelder and Horvath, 2008), available via R’s package installer. After preprocessing the raw microarray data to remove outliers, normalize, and filter the data from 42,921 to 20,104 probes (Supplemental Experimental Procedures), the correlation matrix was obtained by computing the signed pairwise Pearson correlations between all probes across all birds. The correlation matrix was transformed using a power function ((1 + correlation) / 2)β) to form the adjacency matrix, a matrix of network connection strengths. β was determined empirically using the scale-free topology criterion (signed network: β = 14; Bay 11-7085 unsigned: β = 6; Zhang and Horvath, 2005). The network is “weighted” because connection strengths can take on any value between 0 and 1, in contrast to “unweighted” networks where connections are binary. Connectivity (k) is defined for each probe as the sum of its connections to all other probes. The intramodular connectivity (kIN, Table S2) of each probe is the sum of its connections to other probes in its module. Intramodular connectivity in VSP (kIN.V) was computed based on the coexpression relationships in VSP of probes grouped by their area X module assignments.