The remaining genes, when analyzed using the Database for Annotation, Visualization, and Integrated Discovery (DAVID [33], fell into four clusters of categories: oxidoreductases, taurine and sulfur metabolism associated genes, membrane proteins, and flagellar and chemotactic genes.
The responses were converted into importance-based clusters of categories (low- (1 2), medium- (3 5), and high- (6 7) importance categories).
We divided the clustering into eight distinct clusters of categories, labeled A H, each contributing significant information to the overall interpretation of results.
Another challenge presented with the integration of the published and grey literature rather than keeping these two sets of literature separate for categorizing and clustering of categories into themes.
Cluster analysis of categories of genes demonstrated that genes involved in transcriptional regulation, signal transduction, and cytoskeleton were highly represented (Figure 3 and Supplemental Tables S1, S2, S3, S4 and S5).
Furthermore, we found consistently (with thresholds ranging from 25%to85%5%) the cluster of gene categories: "response to glucose stimulus", "collagen type VI", "muscle organ development", and "sarcolema".
To determine whether there were differences in the functional categories in each cluster, the distribution of categories within each cluster was compared with the total distribution of the same cluster within all the annotated genes using independent χ tests.
Additional file 1: Table S1 contains full tables with all of the GO categories and clusters of GO categories enriched.
Using inductive qualitative content analysis [ 20], two researchers (JNH, KMW) read and coded the transcripts independently and after discussion reached consensus on identified categories and clustering of these categories into three themes.
The most abundant cluster of this category, LLAE0312C (containing 26 clones), is similar to heat shock protein 20.6 from Locusta migratoria (gb|ABC84493.1), with 66% of identity.
