Gene-by-gene inspection of the bicluster's 20 most differentially-expressed genes (according to GSEA) at P60 indicated that while a fraction of the genes have previously assigned roles in neuronal and synaptic development, notably Mef2a, Dlgh2 (PSD93) and Stxbp1, many have not previously been implicated in neural processes (Fig. 6A).
Since pathway categorization is a difficult problem, as partition of the global interaction network in "parts" inevitably introduces artefacts, we also proceeded to a detailed, gene-by-gene inspection of the most discriminative genes based on inspection of literature data.
Based upon meta-analysis fold changes, we identified the top 100 PP-increased and top 100 PP-decreased genes; inspection of PP/PN fold changes for these genes in our current dataset yielded the expected trends for all 14 patients (Additional file 2h).
The diagonal band represents QTL that are located coincident with the gene under inspection.
If the top hit was not the corresponding gene, manual inspection of these candidate genes was performed to resolve potential chimeric assembly problems and the candidate genes were confirmed again with BLASTX.
Despite starting with the same initial set of gene set, inspection of both prognostic and predictive algorithms revealed an overlap of only one gene; splA/ryanodine receptor domain and SOCS box containing 3 (SPSB3).
For most of them, we did not find homologies to predicted gene models: Inspection of the 30 longest ESTs showed that 67% shared sequence similarity with O. sativa but not to predicted genes, 23% with genes of predicted functions, and 10% with genes encoding hypothetical proteins.
Although computational methods can be used to prioritize candidate genes (Köhler et al., 2008), sequencing large numbers of candidate genes remains a time consuming and expensive task, and it is often not possible to identify the correct disease gene by inspection of the list of genes within the interval.
That is, when synteny is conserved, the same intergenic regions from each species will be examined regardless of the gene chosen; inspection of the output and, ultimately, experimental validation become necessary in order to evaluate whether a predicted site is associated with the chosen gene, with the divergently transcribed gene, or with both.
If all of the enzymes proposed by the other annotation sources are contained within the list of enzymes found to relate to the gene through inspection of iCyt773, the annotation is not listed as conflicting and the enzymes from the model are used.
