Previous work by Chang and coworkers, using a compendium of about 200 publicly available transcriptomic profiles of mouse lungs, showed differences in pathogenicity among respiratory viruses were explained in part by the changes in magnitude of gene expression [ 37].
Using a compendium of cell-state-specific gene expression data, we identified genes that uniquely define cell states, including those thought to represent various developmental stages.
Using a compendium of microarray gene expression data obtained from Escherichia coli, we constructed a series of Bayesian network models for the reactive oxygen species (ROS) pathway as defined by EcoCyc.
Using a compendium of microarray gene expression data from the M3D database [30], networks were constructed for the 27 genes contained in the ROS pathway as defined by the EcoCyc database [1] (Figure 2).
Each activity was then assigned an energy expenditure value using a compendium of physical activity energy costs.
We translated the LAPAQ-reported PA into MET-values using a compendium 20, 21 (see Table 1).
We calculated the metabolic equivalents (METs) for each activity, using a compendium of physical activity values [ 10].
Thus, by using a larger expression compendium, S-MAP was able to expand the number of individual genes implicated in stemness beyond the one gene, Itga6, identified by the original founder studies.
For all our motif enrichment analyses we used a compendium of 884 motifs ("JASPAR+Jolma compendium") that we created by combining all vertebrate motifs from JASPAR [ 23] with all the SELEX-based motifs from [ 3].
