Skip to main content

Table 1 Comparison of numbers of genes identified as showing strain and/or regional variation in gene expression for different methods

From: Analysis of strain and regional variation in gene expression in mouse brain

   Number of genes selected at each p-value
Condition Method p < 0.001 p < 10-5 p < 10-6
Strain Sandberg 24 24 24
  ANOVA 213 65 36
  Template 150 56 34
Strain x region Sandberg 49 49 49
  ANOVA 17 1 0
All strain effects Sandberg 73 73 73
  ANOVA 230 66 36
  Template 150 56 34
Amygdala Sandberg 1(3) 1(3) 1(3)
  Template 74 2 0
Hippocampus Sandberg 2(10) 2(10) 2(10)
  Template 63 16 11
Cortex* Sandberg 0 0 0
  Template 35 0 0
Forebrain* Sandberg 58 58 58
  Template 771 191 112
Midbrain Sandberg 13 13 13
  Template 181 44 23
Cerebellum Sandberg 150 150 150
  Template 890 339 227
Entorhinal cortex Sandberg 2(10) 2(10) 2(10)
  Template 37 3 1
All tissue effects Sandberg 242 242 242
  ANOVA 874 289 168
  Template 2051 595 374
  1. 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.