Table 1.
Top-Ranking Fragments in CRP1 RIP-Chip Assays
| Wild-Type Stroma
|
crp1 Mutant Stroma
|
Comparison: Wild-Type versus crp1 Stroma
|
||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Fragment Name | Fragment Numbera | Median Log2 Ratio (E)b | Median Percentile Rankc | nbc | Median Log2 Ratio (E)b | Median Percentile Rankc | nbc | Differential Enrichment (EWT – Ecrp1) | P (Enrichment Ratio)d | P (% Rank)d |
| psaC/ndhE | 235 | 1.82 | 1.00 | 15 | −3.61 | 0.16 | 9 | 5.43 | 5.3E-09 | 4.3E-10 |
| psaC-2 | 234 | 0.66 | 0.96 | 10 | −4.06 | 0.13 | 7 | 4.72 | 6.4E-05 | 4.2E-07 |
| ndhG-1 | 238 | 0.89 | 0.98 | 15 | −3.17 | 0.35 | 7 | 4.06 | 2.3E-04 | 1.6E-04 |
| cemA/petA | 114 | 0.68 | 0.99 | 15 | −3.22 | 0.38 | 8 | 3.9 | 2.4E-05 | 1.1E-06 |
| cemA | 113 | −0.25 | 0.94 | 15 | −3.39 | 0.15 | 10 | 3.14 | 4.6E-05 | 1.5E-09 |
| psaC-1 | 233 | −0.32 | 0.94 | 15 | −2.92 | 0.34 | 9 | 2.6 | 1.2E-04 | 1.3E-04 |
| petA-1 | 115 | −0.36 | 0.93 | 12 | −2.96 | 0.28 | 8 | 2.6 | 1.5E-05 | 1.0E-08 |
| atpB5′ | 104 | −1 | 0.86 | 15 | −3.54 | 0.24 | 9 | 2.54 | 1.8E-03 | 5.7E-07 |
| ndhE/ndhG | 237 | 0.2 | 0.95 | 15 | −1.86 | 0.74 | 8 | 2.06 | 5.9E-05 | 3.0E-04 |
| trnI/trnA | 205 | −0.16 | 0.95 | 15 | −1.9 | 0.54 | 10 | 1.74 | 1.4E-03 | 1.4E-04 |
| ndhA-3 | 244 | 0.07 | 0.94 | 15 | −1.17 | 0.88 | 9 | 1.24 | 1.4E-01 | 6.7E-02 |
| rps12-3 | 190 | 0.38 | 0.94 | 15 | −0.74 | 0.88 | 10 | 1.12 | 2.0E-01 | 3.1E-02 |
| rps18/rpl20 | 129 | −0.87 | 0.87 | 15 | −1.99 | 0.75 | 8 | 1.12 | 9.7E-02 | 9.3E-03 |
| Rpl2-1 | 167 | −0.23 | 0.93 | 15 | −1.03 | 0.85 | 10 | 0.8 | 1.5E-01 | 4.2E-03 |
| petA3′ | 116 | −0.39 | 0.92 | 11 | −1.17 | 0.80 | 5 | 0.78 | 2.8E-02 | 1.0E-01 |
| ndhA intron | 243 | 0.25 | 0.96 | 15 | −0.39 | 0.91 | 10 | 0.64 | 5.5E-02 | 5.1E-06 |
| Rrn16/trnI | 201 | −0.95 | 0.88 | 9 | −1.42 | 0.70 | 6 | 0.47 | 7.9E-02 | 1.3E-04 |
| psbH-2 | 140 | −0.18 | 0.91 | 15 | −0.62 | 0.93 | 10 | 0.44 | 8.6E-01 | 4.9E-01 |
| trnA intron | 207 | −0.59 | 0.90 | 15 | −0.97 | 0.85 | 10 | 0.38 | 3.0E-01 | 8.2E-02 |
| rps18 | 128 | −0.12 | 0.94 | 14 | −0.47 | 0.92 | 9 | 0.35 | 2.3E-01 | 1.6E-01 |
| petB-1 | 142 | 0.38 | 0.95 | 15 | 0.17 | 0.99 | 10 | 0.21 | 9.2E-01 | 7.5E-01 |
| Rpl2-2 | 169 | −0.01 | 0.95 | 15 | −0.12 | 0.98 | 9 | 0.11 | 3.7E-01 | 7.1E-04 |
| rps12 int1-1 | 131 | −0.02 | 0.94 | 15 | −0.11 | 0.92 | 10 | 0.09 | 5.1E-01 | 3.4E-01 |
| petB-2 | 139 | 0.36 | 0.97 | 15 | 0.51 | 0.98 | 10 | −0.15 | 6.8E-01 | 2.7E-01 |
| trnK intron | 6 | −0.41 | 0.92 | 15 | −0.05 | 0.96 | 10 | −0.36 | 5.0E-01 | 3.4E-01 |
| petB intron | 144 | −0.22 | 0.91 | 15 | 0.17 | 0.95 | 10 | −0.39 | 2.6E-01 | 8.4E-03 |
| ycf3-4 | 80 | −0.65 | 0.90 | 15 | 0.02 | 0.96 | 9 | −0.67 | 4.1E-02 | 1.3E-05 |
| rps125′ | 194 | 0.63 | 0.98 | 15 | 1.62 | 1.00 | 10 | −0.99 | 1.2E-02 | 5.1E-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.
Fragment numbers reflect chromosomal position (see Supplemental Table 1 online).
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.
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.
P values were calculated with a t test (two-tailed, unequal variance).