Table 1.

Top-Ranking Fragments in CRP1 RIP-Chip Assays

Wild-Type Stromacrp1 Mutant StromaComparison: Wild-Type versus crp1 Stroma
Fragment NameFragment NumberaMedian Log2 Ratio (E)bMedian Percentile RankcnbcMedian Log2 Ratio (E)bMedian Percentile RankcnbcDifferential Enrichment (EWT – Ecrp1)P (Enrichment Ratio)dP (% Rank)d
psaC/ndhE2351.821.00153.610.1695.435.3E-094.3E-10
psaC-22340.660.96104.060.1374.726.4E-054.2E-07
ndhG-12380.890.98153.170.3574.062.3E-041.6E-04
cemA/petA1140.680.99153.220.3883.92.4E-051.1E-06
cemA1130.250.94153.390.15103.144.6E-051.5E-09
psaC-12330.320.94152.920.3492.61.2E-041.3E-04
petA-11150.360.93122.960.2882.61.5E-051.0E-08
atpB5′104−10.8615−3.540.2492.541.8E-035.7E-07
ndhE/ndhG2370.20.95151.860.7482.065.9E-053.0E-04
trnI/trnA205−0.160.9515−1.90.54101.741.4E-031.4E-04
ndhA-32440.070.9415−1.170.8891.241.4E-016.7E-02
rps12-31900.380.9415−0.740.88101.122.0E-013.1E-02
rps18/rpl20129−0.870.8715−1.990.7581.129.7E-029.3E-03
Rpl2-1167−0.230.9315−1.030.85100.81.5E-014.2E-03
petA3′116−0.390.9211−1.170.8050.782.8E-021.0E-01
ndhA intron2430.250.9615−0.390.91100.645.5E-025.1E-06
Rrn16/trnI201−0.950.889−1.420.7060.477.9E-021.3E-04
psbH-2140−0.180.9115−0.620.93100.448.6E-014.9E-01
trnA intron207−0.590.9015−0.970.85100.383.0E-018.2E-02
rps18128−0.120.9414−0.470.9290.352.3E-011.6E-01
petB-11420.380.95150.170.99100.219.2E-017.5E-01
Rpl2-2169−0.010.9515−0.120.9890.113.7E-017.1E-04
rps12 int1-1131−0.020.9415−0.110.92100.095.1E-013.4E-01
petB-21390.360.97150.510.9810−0.156.8E-012.7E-01
trnK intron6−0.410.9215−0.050.9610−0.365.0E-013.4E-01
petB intron144−0.220.91150.170.9510−0.392.6E-018.4E-03
ycf3-480−0.650.90150.020.969−0.674.1E-021.3E-05
rps125′1940.630.98151.621.0010−0.991.2E-025.1E-04
  • Fragments ranking in the top 15% for both median normalized enrichment ratio (E) and median percentile rank are listed and ordered according to the magnitude of their differential enrichment from wild-type versus crp1 stroma (EWT – Ecrp1). Fragments whose differential enrichment is highly significant (P < 3E-04) according to both methods are highlighted in boldface; this P-value cutoff would be anticipated to yield fewer than 0.1 false positives among the 248 array fragments.

  • a Fragment numbers reflect chromosomal position (see Supplemental Table 1 online).

  • b E = median (log2 F635:F532) normalized across three replicate experiments with wild-type stroma and two with crp1 mutant stroma. Replicate experiments constitute a total of n replicate spots with F532 above background.

  • c Median percentile ranks for three (wild type) or two (crp1) replicate experiments compared with other spots on the same array. Elements were ranked within a data set according to the nonnormalized F635:F532 value; median rank for n replicate spots in replicate experiments is shown.

  • d P values were calculated with a t test (two-tailed, unequal variance).