coregulation

Success rates observed in the coregulation space were treated as baseline levels.

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

We designed datasets (real and synthetic) covering different degrees of coregulation and orthologous information to test how well Phylogibbs and Phylogenetic sampler, as representatives of the motif detection algorithms with evolutionary model performed as compared to MEME, a more classical motif detection algorithm that treats orthologs independently.

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

We designed datasets (real and synthetic) covering different degrees of coregulation and orthologous information to test how well Phylogibbs and Phylogenetic sampler, as representatives of the motif detection algorithms with evolutionary model performed as compared to MEME, a more classical motif detection algorithm that treats orthologs independently.

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

It shows that coregulation information is sufficient to detect the correct motif provided that the motif has a high IC.

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

The growing number of sequenced genomes allows integrating orthology evidence with coregulation information when searching for motifs.

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

For the combined space, we extended the coregulation space by simulating the orthologous intergenic sequences for each of the ten coregulated reference genes according to a phylogenetic tree that describes the relatedness of the orthologous sequences to the ancestral sequence.

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

In this work, we tested the impact of using coregulation and/or orthologous information on the efficiency of regulatory motif discovery by two representative motif detection algorithms with an evolutionary model.

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

In this case we selected as reference target, a gene that contained exactly one copy of the motif site in its upstream region in order not to confound coregulation with orthologous information (as the presence of multiple copies confers coregulation information).

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

For the coregulation space we selected target genes in

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

We used a test setup similar as in the combined coregulation-orthology space, but instead of using a set of coregulated reference genes complemented with their orthologs, we used only one reference gene together with its orthologs (~one orthologous set).

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