Table 3. Downregulated differentially expressed genes that are probably involved in embryo development.
| Gene ID | Gene length 1 | Full RPKM 2 | Empty RPKM 3 | log2 Ratio 4 | Up-Down 5 | P-value 6 | FDR 7 | Annotation |
|---|---|---|---|---|---|---|---|---|
| CL97.Contig2_D2 | 727 | 52 | 1 | -5.75 | Down | 2.60E-15 | 1.06E-13 | Late embryogenesis abundant protein |
| CL97.Contig1_D2 | 760 | 21 | 1 | -4.44 | Down | 4.05E-06 | 6.10E-05 | Late embryogenesis abundant protein [Catharanthus roseus] |
| Unigene22699_D2 | 933 | 298 | 38 | -3.02 | Down | 2.75E-53 | 4.28E-51 | Transformer-2 protein (TRA2) |
| CL2945.Contig1_D2 | 450 | 30 | 4 | -2.95 | Down | 2.21E-06 | 3.51E-05 | Transcription elongation factor SPT5 (SUPT5H) |
| CL3163.Contig3_D2 | 1041 | 161 | 28 | -2.57 | Down | 4.35E-25 | 3.02E-23 | Histone deacetylase 1/2 (HDAC1_2) |
| Unigene17483_D2 | 1258 | 69 | 24 | -1.57 | Down | 1.01E-06 | 1.70E-05 | Brassinosteroid insensitive 1-associated receptor kinase 1 (BAK1) |
| Unigene18327_D2 | 629 | 68 | 25 | -1.49 | Down | 3.01E-06 | 4.64E-05 | Amidophosphoribosyltransferase (purF) |
| Unigene19803_D2 | 1748 | 131 | 53 | -1.35 | Down | 1.53E-09 | 3.82E-08 | Protein-serine/threonine kinase transport inhibitor response 1 (TIR1) |
| Unigene18238_D2 | 953 | 1282 | 537 | -1.3 | Down | 1.18E-75 | 2.62E-73 | Superoxide dismutase, Fe-Mn family (SOD2) |
| CL3630.Contig1_D2 | 1710 | 237 | 111 | -1.14 | Down | 1.08E-12 | 3.60E-11 | polypeptide N-Acetylglucosaminyltransferase (OGT) |
| Unigene18285_D2 | 951 | 890 | 435 | -1.08 | Down | 7.83E-40 | 9.01E-38 | DNA polymerase epsilon subunit 3 (POLE3) |
1 Gene length: length of all exons in gene
2 Full RPKM: reads per kb per million reads of cDNA library generated from developing ovules
3 Empty RPKM: reads per kb per million reads of cDNA library generated from abortive ovules
4 log2 Ratio (empty RPKM / full RPKM), log2 (Fold Change)
5 Up-/down-regulation (empty/full): empty is up-/down-regulation in empty library relative to full library
6 P-value: p-value for hypothesis testing
7 FDR: false discovery rate.