2.5. Clusters of orthologous groups (COG) function categorization

The DEGs of each stage were categorized in to (COGs) and their correlations with the phenotypic changes in the biofilm cycle were sought. The DGEs of each stage were classified through homology with protein functions determined from clusters of orthologous groups (COG) database. The COG functional categories for the DEGs were obtained by annotating the protein sequences of the reference P. fragi 1793 genome using the Eggnog mapper v4.5.1 (http://eggnogdb.embl.de) and genes were placed into COG functional categories. The output of Eggnog provided GO terms, KEGG KO and seed orthologs of the genes. The gene locus tags, log₂-FC (fold change), FDR, COG categories and gene product description of the highest fifteen differentially expressed genes are provided in Table 1, Table 2, Table 3, Table 4.

Fifteen upregulated genes with the highest fold changes between biofilm initiation vs maturation.

Fifteen downregulated genes with the highest fold changes between biofilm initiation vs maturation.

Fifteen upregulated genes with the highest fold changes between biofilm initiation vs dispersal.

Fifteen downregulated genes with the highest fold changes between biofilm initiation vs dispersal.