Table 2

Determination of directionality of mRNA decay for B. cereus strains ATCC 10987 and ATCC 14579, based on rank statistics (Spearman rho)

N (number

of ORFs analyzed)

5' to 3' direction of decay^a

3' to 5' direction of decay^a

Strain

N

rho^b 2.5 minutes

rho 5 minutes

rho 10 minutes

N

rho 2.5 minutes

rho 5 minutes

rho 10 minutes

B. cereus ATCC 10987

1,484

324 (22%)

0.2

0.23

0.52

327 (22%)

-0.19

-0.2

-0.54

B. cereus ATCC 14579

484

145 (30%)

0.23

0.35

0.51

86 (18%)

-0.15

-0.21

-0.57

^aThe log2 ratio of the coverage at each time-point to the coverage at t0 was calculated, and the rank correlation (Spearman rho) between this ratio (for each time-point separately) and the nucleotide number throughout each ORF (that is, distance to the 5' end) was determined. A positive rho signifies that coverage is dropping faster near the 5' end of the molecule, that is, the mRNA is predominantly degraded from the 5' end. For each ORF a rho higher than 0.3 or lower than -0.3, and a P-value < 0.0005 at t10, was interpreted as 5' to 3' direction of decay or 3' to 5' direction of decay, respectively. ^bThe average rho of the ORFs for which a direction of decay could be determined is given, showing that the directionality increases over time.

Kristoffersen et al. Genome Biology 2012 13:R30   doi:10.1186/gb-2012-13-4-r30