Figure 2.

Visualizations and detailed information about some genes identified in this study. For each region or for the strain distinction, up to 40 genes are shown (for space considerations), all of which have template-match p-values < 10-4. The genes are ranked by template-match p-value. Other rankings are possible on the basis of our data. The p-value cut-off (10-4) was chosen so that some genes would be listed for all categories; note that the 'best' genes in some categories are only comparable in specificity to the 'worst' genes in others. For two categories (cerebellum and midbrain), genes showing enrichment and depletion expression in the area of interest are separated. The results have been filtered to remove genes having primarily negative average difference values as described in Materials and methods. Besides the ANOVA and template-match p-values (p-values greater than 10-4 are not displayed), for each gene, the GenBank accession number of the sequence used to derive the probes is shown, along with the UniGene cluster number (if applicable), and annotations drawn primarily from UniGene and FANTOM databases [29]. UniGene cluster identity and annotations were based on the current information rather than the annotations originally provided by Affymetrix and may differ from those described in Sandberg et al. [1]. A bullet appears in the column Sb (Sandberg) if the gene was identified in Sandberg et al. [1] or Sandberg [12]. The need to limit the number of genes shown may give the misleading impression that relatively few new genes were identified, especially for the cerebellum-enriched genes. On the basis of accession number, UniGene ID, and annotation, some genes appear more than once on the same list. This duplication reflects multiple probe sets targeting the same sequence, or multiple probe sets targeting different sequences in the same UniGene cluster. The visualizations were prepared as described in Materials and methods, and we emphasize that the scale shown is normalized and thus arbitrary for each gene. Abbreviations are the same as for Figure 1. The complete lists of genes with annotations and p-values can be obtained from our website [32].

Pavlidis and Noble Genome Biology 2001 2:research0042.1-research0042.15   doi:10.1186/gb-2001-2-10-research0042