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Significant differentially repressed genes could be divided into 4 main functional classes (Fig. 2D, Table S2).
Initially, loci were selected from two main functional classes: genes annotated as metabolic enzymes and genes annotated as regulators of gene expression.
The breakdown of significant differentially overexpressed genes in L-form colonies into 5 main functional classes using the COG functional classification system (Fig. 2C, Table S1) showed that the two classes containing the most genes were involved in unknown or poorly characterized functions (31.8%) and cellular processes (25.8%).
These genes were selected to represent the main functional classes affected by the treatments (Table 8).
Proteins were sorted into main functional classes based on the KOG database comparison.
Finally there are six main functional classes and eighty-five sub-subfamily classes (i.e., eight for oxidoreductases, seventeen for transferases, eighteen for hydrolases, eight for lyases, eight for isomerases, and six for ligases) in the benchmark dataset.
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15 main and 97 sub functional classes of S. mutans UA159 were compiled using the gene annotation information furnished in the Oralgen database (version 2011 and now re-named as The Bioinformatic Resource for Oral Pathogens).
The high proportion of genes detected in the main olfactory organ, the antennae, is consistent with the presence of multiple functional classes of sensilla recently described in Cx. quinquefasciatus [37].
Structuring this data in clusters provided a clear illustration of the main expression profiles of many novel genes, such as genes from the functional classes 'chemotaxis' and 'phage, transposon, or plasmid' which are found in clusters 1 and 5 respectively.
In the KOG database [ 21, 22] human genes were classified in 25 functional classes, denoted by capital letters in square brackets, and grouped in three main categories: i) information storage and processing, represented by five functional classes; ii) cellular processes and signaling, represented by ten functional classes; and iii) metabolism, represented by eight functional classes.
The significantly enriched functional classes varied quite a bit between Clusters 1 5 (Additional file 11), and they were consistent with the main biological processes for corresponding life cycle stages.
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