Table 4

Comparison of predicted RNA elements with yeast tiling array data or SAGE/EST data

Experimental data

RNAz hits

intergenic transcripts

p-value

RNAz hits

Intergenic regions

Transcripts

Intergenic regions


Davis et al [8]

41

36

196

196

1 × 10-7

David et al [9]

40

36

372

294

9.4 × 10-4

Samanta et al [7]

15

12

77

74

5.8 × 10-3

Combined

84

72

573

536

-

ESTs [66]

17

15

154

116

1.8 × 10-2

SAGE [28]

32

31

680

533

0.91

Total combined

124

109

1202

1035

-


A predicted RNA structure is reported as transcribed if its overlap with an experimentally verified transcript is larger than 50%. RNAz hits shows the total number of intergenic RNAz hits that overlap a transcript. Intergenic regions describes the number of intergenic regions, that are covered by at least one predicted RNA structure. Intergenic transcripts shows the total number of intergenic transcripts. Intergenic regions depicts the number of intergenic regions that are covered by at least one transcript. All transcripts that collapse to one genomic locus were counted once in the rows combined and total combined. The numbers given in the intergenic regions column were used to calculate p-values (with a total of 6551 intergenic regions and 469 regions that are covered by at least one predicted RNA structure). The p-values are calculated for the one-sided hypergeometric test against the null hypothesis of odds-ratio ≤ 1.

Steigele et al. BMC Biology 2007 5:25   doi:10.1186/1741-7007-5-25

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