Additionally, Spice enumerated other COG modules that contained other known flagellar-related COGs like COG1516, COG1345, and COG1815 and other known chemotaxis-related COGs such as COG0840, COG0643, and COG0835, supported by literature [ 8, 56, 57].
The new COG-centric matrix for this experiment can be found in Additional file 3. The set of enumerated COG modules with the statistically significant p-value of 0.05 is provided in Additional file 4. Spice was able to identify COG modules that are known to be associated with hydrogen production based on our literature review and prior knowledge.
To compute the significant of finding specific COGs modules, a p-value for each module was calculated based on the distribution of 10,000 random module sets of the same size (assuming a normal distribution) and our module predictions, therefore, representing the probability of seeing such modules at chance.
We also reveal various topologies of association networks among COGs (modules) from extracted multiple-to-one correlation rules relevant with the six phenotypes; including a well-connected network for motility, a star-shaped network for aerobic and intermediate topologies for the other phenotypes.
To compute the significant of finding specific COGs functional modules, we generated 10,000 random module sets of the same size, and counted the number of times we found each COGs module in each randomized network.
The other COGs showed either similar core module locations among all three species (I2) or similar locations between either of the monocot species and Arabidopsis (H1, S2).
Values associated with genes/proteins are mapped into Higher Order Variables (HOV) based on broad biological classifications including KEGG modules, COG letters, Enzyme Class numbers and MetaCyc pathways, allowing us to rapidly detect and evaluate system-wide changes in expression levels.
The association relationship between coexpression modules and COG categories became much clearer after clustering modules into groups (Figure 4).
The order, relative distance from each other and strand orientation of each putative TFBS that comprised a core module were remarkably conserved within each COG.
In the first module, two COGs (COG2710 and COG0120) were identified.
