The workload descriptor consisted of modules labeled by attributes, and a list of values for these attributes was provided.
In total, we identified 20 modules, labeled by colors, with each containing at least 50 genes.
Unsupervised average linkage hierarchical clustering of all genes in this dataset resulted into 13 modules labeled by color and each comprised of mutually exclusive co-expressed genes.
In addition, we utilized high thresholds for module construction for further filtering, resulting in a final gene coexpression network comprising 26,030 genes, including 4,070 lncRNAs, which are distributed among 16 gene modules labeled by colors.
Using the same parameters for the clustering and branch detection, we found that two of the 12 modules (labeled by salmon and light-yellow color) in that work are not represented in the consensus modules.
Five gene coexpression modules, labeled by blue, dark gray, dark orange, light yellow, and yellow, were found to be significantly enriched with genes that were specifically duplicated in A. thaliana (fig. 2 B).
Signed networks were built using biweight midcorrelation as the correlation function, and a soft thresholding power of 12. WGCNA produces a set of modules (labeled by color), each containing a set of unique genes.
Here, a total of 46 coexpression modules (labeled numerically, e.g., M29, and by color, e.g., black, see Additional file 2) were obtained for Drosophila development.
The 23 gene co-expression modules are labeled by colors (e.g. the "palegreen" module), with pertinent functional characterizations taken from ref. [ 21].
Since modules are defined without respect to gene ontology information they are initially labelled by arbitrary integers and coded by colours.
