Table 4 

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

Experimental data 
RNAz hits 
intergenic transcripts 
pvalue 

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 pvalues (with a total of 6551 intergenic regions and 469 regions that are covered by at least one predicted RNA structure). The pvalues are calculated for the onesided hypergeometric test against the null hypothesis of oddsratio ≤ 1. 

Steigele et al. BMC Biology 2007 5:25 doi:10.1186/17417007525 