4.2.1. Orthologous/Homologous Gene is Absent From Gene Group

The CORG database takes a gene-centered view of phylogeny. CORG employs single linkage clustering on the graph of EnsEMBL orthologous gene pairs to define the CORG gene groups. This approach is error prone in the sense that the grouping of genes is occasionally ambiguous, and homology relationships are not clearly resolved.

4.2.2. Gene Structure Looks Bizarre

First exon prediction is a difficult business. Therefore, it happens that the 5' end of a gene does not look like what one would expect. If the sequence region is still contained in the CORG upstream region, one may circumvent this problem by directly targeting this region.

4.2.3. Unexpected Degree of Similarity in Upstream Region

This could be either too little or too much conservation. For the latter case, consider using a more distantly related species to attain more discriminatory power for the footprinting approach (e.g., for mouse-rat comparisons, try man-mouse instead). In case of too little conservation, make sure that a true ortholog was considered. Alternatively, select a more closely related species. Since evolutionary parameters vary from locus to locus, the possibility cannot be excluded that some comparisons are uninformative.

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