Table 2.
Cadmium regulated microarray elements
| Up-regulated elements | |||||||
| Siga | Seqb | EST Cluster | M averagec | A averagec | Hit Description | P Valued | Putative GO annotations |
| 8 | 9 | Contig 262 | 1.02 ± 0.31 | 10.12 ± 1.88 | 2-domain hemoglobin protein subunit | < 0.001 | GO:0015671, GO:0005833, GO:0005344 |
| 2 | 16 | Contig 272 | 0.43 ± 0.21 | 9.06 ± 1.50 | CG30045-PA | < 0.001 | GO:0042302 |
| 1 | 1 | Singlet 433 | 0.71 | 12.08 | CG6305-PA | 0.062 | GO:0042302 |
| 1 | 1 | Singlet 498 | 1.02 | 9.15 | chitinase-1 | 0.028 | GO:0008061, GO:0006030, GO:0004568, GO:0005576 |
| 3 | 4 | Contig 213 | 0.82 ± 0.12 | 9.07 ± 0.53 | chitinase-2 | < 0.001 | GO:0008061, GO:0006030, GO:0004568, GO:0005576 |
| 1 | 3 | Contig 218 | 0.93 ± 0.19 | 9.64 ± 1.77 | chitotriosidase | 0.005 | GO:0008061, GO:0006030, GO:0016798, GO:0005576 |
| 1 | 3 | Contig 209 | 0.41 ± 0.17 | 12.21 ± 1.48 | CUO6 BLACRCuticle protein 6 (BcNCP14.9) | 0.06 | GO:0042302 |
| 4 | 6 | Contig 241 | 1.07 ± 0.31 | 10.76 ± 2.07 | cuticle protein-1 | 0.018 | GO:0042302 |
| 5 | 8 | Contig 257 | 1.03 ± 0.33 | 9.96 ± 1.54 | cuticle protein-2 | < 0.001 | GO:0042302 |
| 13 | 28 | Contig 273 | 0.91 ± 0.32 | 10.05 ± 1.65 | cuticle protein-3 | < 0.001 | GO:0042302 |
| 1 | 3 | Contig 149 | 0.72 ± 0.28 | 8.55 ± 0.92 | cuticle protein-4 | 0.011 | GO:0042302 |
| 5 | 8 | Contig 261 | 0.88 ± 0.30 | 9.87 ± 1.42 | cuticle protein-5 | < 0.001 | GO:0042302 |
| 1 | 1 | Singlet 15 | 1.23 | 14.06 | ERGA6350 | 0.009 | |
| 1 | 1 | Singlet 469 | 0.80 | 7.99 | helix-loop-helix transcription factor | 0.055 | GO:0006355, GO:0003677 |
| 1 | 1 | Contig 21 | 1.45 | 10.03 | hemoglobin-1 | 0.003 | GO:0015671, GO:0005833, GO:0005344 |
| 1 | 1 | Contig 16 | 1.08 | 9.81 | hemoglobin-2 | < 0.001 | GO:0015671, GO:0005833, GO:0005344 |
| 1 | 1 | Singlet 65 | 2.16 | 8.34 | Hypothetical protein CBG14247 | < 0.001 | |
| 4 | 4 | Contig 221 | 1.98 ± 0.47 | 8.88 ± 0.82 | Metallothionein | < 0.001 | GO:0046872, GO:0006875 |
| 1 | 5 | Contig 220 | 0.31 ± 0.49 | 8.95 ± 0.62 | myosin 2 light chain | 0.08 | GO:0005509 |
| 2 | 4 | Contig 227 | 0.70 ± 0.04 | 12.59 ± 2.37 | OPSC1 HEMSACompound eye opsin BCRH1 | 0.036 | GO:0007602, GO:0016021, GO:0001584, GO:0007186 |
| 1 | 1 | Singlet 251 | 1.18 | 10.90 | PREDICTED: similar to chitinase | 0.019 | GO:0008061, GO:0006030, GO:0016798, GO:0005576 |
| 1 | 1 | Singlet 459 | 1.15 | 7.42 | PREDICTED: similar to glutathione S-transferase | 0.021 | GO:0016740 |
| 1 | 1 | Singlet 1 | 1.94 | 8.99 | Unknown EST-1 | 0.009 | |
| 3 | 3 | Contig 232 | 1.14 ± 037 | 8.27 ± 0.99 | Unknown EST-2 | < 0.001 | |
| 7 | 8 | Contig 253 | 1.05 ± 0.44 | 9.99 ± 1.38 | Unknown EST-3 | < 0.001 | |
| 1 | 1 | Singlet 166 | 0.87 | 8.20 | Unknown EST-4 | 0.048 | |
| 1 | 1 | Singlet 64 | 0.75 | 9.95 | Unknown EST-5 | 0.059 | |
| 1 | 1 | Singlet 49 | 0.74 | 8.77 | Unknown EST-6 | 0.067 | |
| 1 | 5 | Contig 237 | 0.33 ± 0.21 | 10.11 ± 1.55 | Unknown EST-7 | 0.073 | |
| 1 | 1 | Singlet 172 | 0.68 | 8.23 | Unknown EST-8 | 0.071 | |
| 24 | Unsequenced | ||||||
| Down-regulated elements | |||||||
| Siga | Seqb | EST Cluster | M averagec | A averagec | Hit Description | P Valued | Putative GO annotations |
| 1 | 2 | Contig 135 | -0.36 ± 0.66 | 9.28 ± 0.08 | carboxypeptidase A1 | 0.068 | GO:0006508, GO:0004182 |
| 1 | 1 | Singlet 97 | -1.04 | 6.94 | endo-1,4-mannanase | 0.009 | GO:0016985, GO:0000272 |
| 1 | 3 | Contig 202 | -0.38 ± 0.36 | 8.39 ± 1.02 | PREDICTED: similar to CG31997-PA | 0.036 | |
| 2 | 2 | Contig 83 | -1.29 ± 0.06 | 8.00 ± 0.40 | PREDICTED: similar to monooxygenase | 0.001 | |
| 1 | 3 | Contig 162 | -0.37 ± 0.30 | 8.98 ± 1.04 | ribosomal protein S11-2 | 0.02 | GO:0006412, GO:0003735, GO:0005840 |
| 1 | 2 | Contig 191 | -0.61 ± 0.27 | 10.76 ± 3.35 | Unknown EST-1 | 0.019 | |
| 2 | 4 | Contig 212 | -0.72 ± 0.38 | 8.77 ± 0.97 | Unknown EST-2 | < 0.001 | |
| 4 | 5 | Contig 229 | -1.32 ± 0.11 | 9.96 ± 0.90 | Unknown EST-3 | < 0.001 | |
| 4 | 7 | Contig 249 | -1.08 ± 0.27 | 8.13 ± 0.98 | Unknown EST-4 | < 0.001 | |
| 1 | 2 | Contig 56 | -0.41 ± 0.36 | 9.25 ± 0.99 | Unknown EST-5 | 0.056 | |
| 1 | 1 | Contig 71 | -0.71 | 6.21 | Unknown EST-6 | 0.027 | |
| 1 | 1 | Singlet 79 | -1.08 | 8.90 | Unknown EST-7 | 0.014 | |
| 10 | Unsequenced | ||||||
aNumber of microarray elements determined to be significant on the array using the empirical Bayes method to shrink the gene-wise error estimate in cadmium treated vs. control Daphnia pulex (P < 0.05). control Daphnia pulex (P ≤ 0.05).
bNumber of microarray elements selected for sequencing based on cadmium response determined in the current study; Eads et al., in review; and Colbourne et al., in review.
cMean value (± SD) based on all sequenced microarray elements.
dPermutation tests were performed for clones sharing common putative annotations. These tests included 1000 simulations using the mean expression values to determine the Probability of obtaining the M average for an EST cluster.