Table 1

Comparison of numbers of genes identified as showing strain and/or regional variation in gene expression for different methods

The number of genes identified by each method, and by Sandberg et al. [1], for each condition or set of conditions is listed if appropriate. For ANOVA and template match, values for three different p-value thresholds are shown. For the various brain regions, the template-match counts include both matches (enriched genes) and anti-matches (genes expressed at lower levels in the region listed). None of the values given is corrected for genes dominated by negative average difference values. After filtering such genes (see Materials and methods) values would be about 5-10% lower. The values in the 'Sandberg' rows are the same in each column because Sandberg et al. did not generate confidence measures for the genes they selected. The totals for 'Sandberg' include genes listed both in Sandberg et al. [1] and Sandberg [12], and group together genes that were 'restricted', 'enriched', 'absent' and 'decreased'. Numbers in parentheses are the totals obtained if one includes genes mentioned in the text of [1] but not listed by name. *Genes specific to the cortex alone. Because Sandberg et al. do not appear to have specifically sought genes expressed only in the cortex (instead they compared cortex only to cerebellum and midbrain [12]), the number of genes in this category for Sandberg et al. are listed as zero. 'Forebrain' is the combination of cortex, hippocampus, entorhinal cortex and amygdala, which most closely matches the 'Cortex' group chosen in [1,12]. It is included here to allow a fair comparison to their methods. ^†This category does not include strain x region effects.

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