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Out of the 74 and 332 annotated up- and downregulated ESTs, respectively, 50 and 156 D. melanogaster homologs were obtained.
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Of the 30 annotated up-regulated genes in Table 1, 23 genes (77%) are involved in immune response, inflammation and apoptosis.
To our knowledge, this is the first effort of an OS database containing manual reviewed and annotated up-to-date OS knowledge.
At 4 days post-infection, of the 10 annotated up-regulated genes, 70% genes are involved in inflammatory response and bacterial infection; only LGR1 is involved in connective tissue development.
Of the 10 annotated up-regulated genes in SL1344 infection at 8 hours, R ETNLB as a colon-specific gene has been reported to associate with bacteria infection, and RETNLB in situ hybridization occurs in proliferative mouse epithelial cells [ 50].
Such tools as the RAST server [26] can annotate up to 200 300 genomes per month.
However, four of the five top annotated up-regulated DE genes and all top five annotated down-regulated DE genes were the same in W15m vs. Wet and W15m vs. Dry comparisons.
Schenck et al. worked on a small set of articles curated in COSMIC that they annotated, recovering up to 30% of their annotated mutations.
The performance of PPB was evaluated by challenging its ability to recall the known targets of 670 compounds labelled as approved drug or drug in clinical trial and annotated with up to 20 targets in ChEMBL (4794 drug target interactions).
If a protein is annotated only up to an internal node, this means either that there is lack of evidence for a more specific annotation or an appropriate GO term for that protein has not yet been added to the ontology.
We annotated unigenes up to similar levels of related-species, especially in contigs (Table 2).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com