Table 1

Contrasting features of housekeeping and hypervariable genes.

Gene feature

Housekeeping

Hypervariable

Genome


CDS length (bp)a

2624 (s.e. = 89)

1178 (s.e. = 73)

1931 (s.e. = 8)

Gene length (bp)a

3117 (s.e. = 87)

1493 (s.e. = 78)

2229 (s.e. = 8)

Total exon length (bp)a

1941 (s.e. = 52)

1169 (s.e. = 50)

1568 (s.e. 6)

Total intron length (bp)a

1173 (s.e. = 52)

323 (s.e. = 44)

660 (s.e. = 4)

Number of exons (pb)a

8 (s.e. = 0.31)

3 (s.e. = 0.24)

5 (s.e = 0.03)

Genes without introns

6% (p = 5E-16)

33% (p = 0.0007)

28%


Average number of transcription factor binding sitesb

27 ± 1.2 (p < 0.01)

46 ± 1.8 (p < 0.0001)

30 ± 0.1


TATA-containing genesc

5% (p = 1.3E-6)

45% (p = 6.1E-15)

15%


Genes coding for unstable transcriptsd

0% (n.a.)

8% (p = 9E-11)

1%


Shared among eukaryotese

18% (p = 0.002)

7%

14%

Plant-specifice

11%

34% (p = 2E-10)

14%


Body methylationf

63% (p = 1.5E-35)

8% (p = 2E-10)

34%

Promoter methylationf

3%

3%

5%

Body methylationg

36% (p = 9.1E-21)

2% (p = 3.8E-8)

20%


The first column lists various features analyzed for housekeeping genes (second column), hypervariable genes (third column) and the whole genome (fourth column). Rows report average and standard error or percentage values. P values for significant (p < 0.01) enrichment or depletion as compared to the genome occurrence are shown in parenthesis. a, differences between all groups are significant (p < 0.01) as determined by ANOVA.b, average number of cis-acting regulatory elements as defined in the AGRIS database [47]. p-value was determined by a t-test. C, presence of TATA-box as determined by the MotifSearch algorithm [26]. Similar results were obtained with an alternative TATA-box definition [27]. d, unstable transcripts as defined in [19]. e, phylogenetic profiles as defined previously [18]. Only significantly enriched profiles are listed. f, methylation patterns as determined in [24]. g, methylation patterns as determined in [25]. n.a., not applicable.

Aceituno et al. BMC Genomics 2008 9:438   doi:10.1186/1471-2164-9-438

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