Figure 2

Comparison of Target and Annotation Sources. Data sources as used by the corresponding annotation pipelines for linking probes to target genes (A) and for annotation retrieval (B): green checkmark = used, red cross = unused and orange checkmark/cross = partially used. *) IMAD ignores strand information and therefore might contain hits to intergenic space with Ensembl exons annotated on the opposite strand. **) sigReannot can report hits to intergenic space and introns using its UTR/intron extension feature. This requires a hit on a UniGene cluster located in a gene's intron or in a region of 1000 nucleotides up- or downstream of a gene. UTR/intron extension is only performed with sigReannot if there were no hits on Ensembl Genes. OligoRAP on the other hand takes all intergenic space into account irrespective of whether there are hits on Ensembl Genes or not. ***) To prevent redundancy OligoRAP takes only a subset of UniGene and RefSeq accessions into account: those that do not map with high confidence onto the reference assembly.