Modules of co-occurrence in the cyanobacterial pan-genome reveal functional associations between groups of ortholog genes
Fig 2
Network analysis of co-occurring CLOGs.
(A) Orthologous genes are identified using an all-against-all BLASTp comparison and are grouped into cluster of likely orthologous genes (CLOGs). CLOGs are classified into three sets: core CLOGs (present in all strains), shared CLOGs (present in several but not all strains) and unique CLOGs (present in a single strain). (B) The phylogenetic profile of each CLOG indicates the set of strains whose genome is annotated with genes corresponding to the CLOG. Pair-wise co-occurrence of CLOGs is identified using the similarity of phylogenetic profiles. CLOGs are grouped into modules of co-occurring CLOGs using a community-detection algorithm. (C) A network view on co-occurring CLOGs. We identify a total of 563 modules with 1930 CLOGs. Circular genome maps were constructed using the CiVi tool [60].