Table 1.

Top-Ranking Fragments in PPR4 RIP-Chip Assays

Wild-Type Stromappr4 Mutant StromaComparison: Wild-Type versus ppr4 Stroma
Fragment NameFragment NumberaMedian Log2 Ratio (E)bnbMedian Log2 Ratio (E)bnbDifferential Enrichment (EWT − Eppr4)P Valuec
rps12int13′1942.5110−1.28103.794.93E-15
rps12int15′ex11312.059−1.69103.749.98E-09
rpl20/rps12int15′1300.369−1.86102.213.28E-08
rps18128−1.2010−3.09101.895.61E-06
rps12int2A190−1.989−3.68101.701.95E-06
rps18/rpl20129−0.7710−2.3291.558.66E-09
rps12ex1/clpP132−0.849−2.3181.477.62E-06
rps12ex2int13′193−0.9910−2.39101.404.06E-06
orf58/orf85196−1.2610−2.48101.221.08E-03
ndhAint2432.1510−3.37101.215.85E-02
psbH/petB5′139−1.919−2.91101.004.90E-02
infA156−1.5510−2.3290.764.20E-03
ndhAintex1244−2.0910−2.6670.563.57E-02
orf58195−1.4610−2.01100.556.04E-02
orf173-3′180−1.3610−1.8990.533.95E-02
rpl33127−1.6510−2.1490.491.72E-03
orf139176−1.729−2.12100.391.91E-01
trnL-CAA181−1.9210−2.2190.291.52E-01
rps2B54−1.628−1.5810−0.042.51E-01
trnV-UACex2int97−2.029−1.919−0.115.18E-01
petN3prime37−1.778−1.569−0.218.15E-01
ycf920−1.729−1.4010−0.322.26E-02
psaC/ndhE/ndhG236−2.058−1.657−0.411.89E-01
rrn16-3prime200−0.6860.926−1.601.25E-01
  • Elements ranking in the top 10% for median normalized enrichment ratio (E) from wild-type stroma are ordered according to the magnitude of their differential enrichment from wild-type versus ppr4 mutant stroma (EWT − Eppr4). Fragments that map within or adjacent to the two rps12 loci are in boldface.

  • a Fragments on the array are numbered according to chromosomal position. The nucleotide residues on each fragment are described in Array Express (accession number A-MEXP-164) and in Supplemental Table 1 from Schmitz-Linneweber et al. (2005).

  • b E = median (log2F635/F532) normalized across two replicate experiments with wild-type stroma and two with ppr4-1/ppr4-2 mutant stroma. Replicate experiments constitute a total of n replicate spots with signal above background.

  • c P values were calculated with a t test (two-tailed, unequal variance) and represent the probability that there is no difference in enrichment from wild-type and mutant extract.