coregulated

Each dataset consists of ten coregulated genes from the reference species (proximity 0.80).

PLoS ONE Alerts: New Articles Valerie Storms et al. 2010

The tests consist of changing the distance (~ "proximity") for these four orthologs that were added to each coregulated reference gene.

PLoS ONE Alerts: New Articles Valerie Storms et al. 2010

This situation was mimicked by assuming that two of the reference genes were not truly coregulated with the other genes.

PLoS ONE Alerts: New Articles Valerie Storms et al. 2010

Here we simulated this situation by adding orthologs to a set of coregulated reference genes, but assuming that all added sequences derived from one species did not contain the motif site.

PLoS ONE Alerts: New Articles Valerie Storms et al. 2010

For each dataset, we started off with a real set of coregulated genes in the reference species

PLoS ONE Alerts: New Articles Valerie Storms et al. 2010

Panel (D) represents the results of a dataset containing for each coregulated reference gene six or five unaligned orthologs (the reference gene included).

PLoS ONE Alerts: New Articles Valerie Storms et al. 2010

Datasets consist of sets of coregulated genes from the reference species.

PLoS ONE Alerts: New Articles Valerie Storms et al. 2010

Datasets consist of coregulated genes in the reference species (coregulation space) complemented with their respective orthologs (orthologous space).

PLoS ONE Alerts: New Articles Valerie Storms et al. 2010

Table S5 (B) confirmed our expectation: compared to using orthologous sets containing only the four closely related orthologs, adding one distantly related ortholog to the orthologous set of each coregulated reference gene improved the RR of all algorithms.

PLoS ONE Alerts: New Articles Valerie Storms et al. 2010

To this end we used for each coregulated reference gene an orthologous set for which the relatedness was modeled by a

PLoS ONE Alerts: New Articles Valerie Storms et al. 2010