Table 1

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

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


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-research0042.15   doi:10.1186/gb-2001-2-10-research0042

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