using a curated database on signaling networks and systems biology package (Metacore®, Genego, www.genego.com).
Next, we examined possible network overlaps by analyzing separately for the GKO and KKO differential gene lists, the possible network connectivity using a curated database of functional interactions, as previously described (Ingenuity pathways, http://www.ingenuity.com, methods).
In order to develop hypotheses about the biological processes regulated by estrogen in this system we undertook further analysis using the gene ontology tool Onto-Express [20] and Ingenuity Pathways Analysis, which uses a curated database of known functional interactions to identify networks of mammalian genes.
Functional analysis was done using a curated and constantly updated literature database (Ingenuity Pathways Analysis) to populate known pathways with significantly differentially expressed genes.
The resistance gene profiles and content (resistome) of each isolate were characterised using a manually curated database, based on the ResFinder database (Zankari et al, 2012).
Next, using a large curated database (Ingenuity® Systems [ 34]), the Th cell differentiation pathway was identified as the most enriched in the GWAS genes measured by the P-values from a FET (n = 38, FE = 5.3, Bonferroni-corrected P < 10-15; Table S3 in Additional file 1 shows all genes and pathways).
Thirdly, the annotation process was exhaustive, using similarity approaches with a curated database and other small databases that contained characterized genes involved in pathogenesis, improving the efficiency of the whole annotation.
We then corroborated a subset of GAP's novel predictions using an expert curated database of genes associated to the autism spectrum disorders, under the assumption that genes participating in the same phenotype are expected to be functionally related.
We also provided extra supporting evidence for subset of the predicted functionally-associated pairs using an expert curated database of genes associated to autism spectrum disorders.
In OncoFinder, we use a manually curated database of molecular signaling pathways that includes the functional roles present in a pathway [ 27, 28].
We used an online tool based on a curated database, the Ingenuity Pathways Knowledge Base (IPKB), to annotate genes and to determine potential regulatory networks and pathways.
