Table 1

Estimated coefficients of ribosome occupancy and ribosome density models
Parameter Variable to explain: Ribosome occupancy Variable to explain: Ribosome density
mRNA concentration 0.12 (p = 1.2 x 10-4) −0.15 (p = 4.0 x 10-6)
mRNA half-life −0.38 (p < 2.0 x 10-16) −0.36 (p < 2.0 x 10-16)
CDS length 0.24 (p = 2.3 x 10-14) −0.22 (p = 1.4 x 10-10)
Aromaticity / 0.09 (p = 8.7 x 10-3)
CAI 0.16 (p = 6.3 x 10-6) −0.11 (p = 7.6 x 10-3)
ΔGdown 0.12 (p = 4.0 x 10-5) 0.12 (p = 3.0 x 10-4)
ΔGup 0.15 (p = 4.0 x 10-7) 0.15 (p = 5.7 x 10-6)
Functional category AMI / −0.20 (p = 5.0 x 10-3)
Functional category COF / −0.35 (p = 4.4 x 10-2)
Functional category INT 0.68 (p = 1.6 x 10-3) /
Functional category REG 0.62 (p = 1.7 x 10-5) 0.45 (p = 3.9 x 10-3)
Functional category TRS −0.23 (p = 4.0 x 10-2) /
Adjusted R2 0.34 0.22

ΔGdown and ΔGup: free energy of the predicted minimum free energy structure for upstream mRNA sequences (from −100 to +24 bp relative to the start codon) and downstream sequences (from −24 to +100 bp relative to the stop codon), respectively. AMI: amino acid biosynthesis, COF: biosynthesis of cofactors, INT: central intermediary metabolism, REG: regulatory functions, TRS: transcription.

Picard et al.

Picard et al. BMC Genomics 2012 13:528   doi:10.1186/1471-2164-13-528

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