Visualization of logic analysis of phylogenetic profiles (LAPP)

Recently Bowers et al analyzed triplet logic relationships among 4873 clusters of orthologous groups (COGS) from 67 fully sequenced organisms by calculating how well logic relationships between proteins a and b predicted the presence or absence of protein c (the uncertainty). The log of the normalized uncertainty distribution follows an approximately linear relationship for uncertainties in the interval [0.1, 0.9]. Using fitted parameters of this relationship as a characterization, we develop four types of visual analysis for LAPP data: distributions of uncertainty over logical relation type, distributions of uncertainty over functional categories, relationships of uncertainty of the overall population to known network relationships of a particular organism, and relationships of uncertainty distributions to groups obtained by standard clustering techniques. The purpose of this study is two-fold: to better understand the implications of uncertainty predictions for automatic protein network generation and to create new visualization tools for looking at this type of data.