Figure 1

The LDA model assumes a hidden generative process that can be inversed for statistical inference. In our approach, topics are assumed to represent the unknown biological modules that have shaped the contents of genomes. As a simplifying example, the influence of two modules on the contents of three genome annotations is considered. Panel A: Functional descriptors (FD terms) are associated with proteins in the modules, and each module is represented by a probability distribution over FD terms. Panel B: The hidden generative process: Genome annotations are assumed to be generated from weighted mixtures of the probability distributions. The two clouds show the FD term set with the highest probabilities for each module. Note that the second genome annotation is equally shaped by both modules, whereas the other two annotations are solely shaped by one module. Panel C: The input data as seen by our method. No a priori knowledge about the underlying modules is necessary. The potential functional modules are latent variables of the model that will be inferred from the collection. The identified modules are not necessarily specific to any given microbe, but potentially combine different realizations of a complex or pathway from different organisms.