Table 2.
Selected list (first 20 genes) of the genes differentially expressed with a ≥2-fold difference in sea bass scales from treated versus control animals. The complete list with the expression and annotation details for the 332 genes with significant differential expression (FDR < 0.05 and FC ≥ 2) in each comparison can be consulted in Supplementary Table 1. Normalized expression levels in each experimental group are presented in fragments per kilobase of exon model per million reads mapped (fpkm) and significant differential expression for each comparison is presented in Log2 fold change (FC). The final annotation reached using the preference order strategy (Fig. 1 and Table 4) and revised by manual curation is presented, with the accession numbers from Swiss-Prot, Genbank or from the sea bass genome.
| Gene ID |
Relative expression levels (fpkm) |
Log2FC of E2 or Gen effects vs control at 1d |
Log2FC of E2 or Gen effects vs control at 5d |
Log2FC of C5d vs C1d |
Final gene annotation |
||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Cufflinks# | C1d | E1d | Gen1d | C5d | E5d | Gen5d | up in E2 | Down in E2 | Up in Gen | Down in Gen | E2 up | E2 down | Gen up | Gen down | C5d up | C5d down | Accession | Hit description | Symbol |
| XLOC_019555 | 5.4 | 14.8 | 37.7 | 33.7 | 5.3 | 34.0 | 1.4 | – | 2.8 | – | – | −2.7 | – | – | 2.6 | – | O75443 | Alpha-tectorin | TECTA |
| XLOC_019129 | 34.2 | 225.7 | 761.3 | 1735.6 | 22.0 | 1398.8 | 2.7 | – | 4.5 | – | – | −6.3 | – | – | 5.7 | – | DLAgn_00248120 | Mhc class ii antigen beta chain | HLADPB1 |
| XLOC_020058 | 0.5 | 3.8 | 4.0 | 3.1 | 6.2 | 6.0 | 2.9 | – | 2.9 | – | – | – | – | – | 2.6 | – | Q5W7F1 | Neutral ceramidase or N-acylsphingosine amidohydrolase 2 | ASAH2 |
| XLOC_019225 | 25.2 | 63.2 | 50.8 | 25.0 | 17.3 | 22.9 | 1.3 | – | 1.0 | – | – | – | – | – | – | – | Q02817 | Mucin-2 | MUC2 |
| XLOC_019447 | 10.8 | 22.6 | 22.4 | 12.0 | 13.6 | 11.7 | 1.1 | – | 1.0 | – | – | – | – | – | – | – | XP_019109670.1 | Integumentary mucin C.1-like | MUCC1 |
| XLOC_019084 | 20.6 | 47.4 | 38.1 | 15.9 | 14.5 | 40.0 | 1.2 | – | – | – | – | – | 1.3 | – | – | – | G8HTB6 | ZP domain-containing protein / CUB and zona pellucida like domains 1 | CUZD1 |
| XLOC_019425 | 437.4 | 1926.9 | 1162.0 | 1718.5 | 2043.4 | 2161.0 | 2.1 | – | – | – | – | – | – | – | – | – | P28064 | Proteasome subunit beta type-8 | PSMB8 |
| XLOC_021846 | 92.1 | 215.6 | 136.4 | 206.0 | 144.3 | 113.2 | 1.2 | – | – | – | – | – | – | – | 1.2 | – | – | No hit found | – |
| XLOC_020866 | 5.0 | 19.1 | 5.9 | 0.6 | 0.4 | 1.1 | 1.9 | – | – | – | – | – | – | – | – | – | DLAgn_00214300 | Protein fam111a-like | FAM111A |
| XLOC_009298 | 49.5 | 135.9 | 60.4 | 73.6 | 55.8 | 70.0 | 1.5 | – | – | – | – | – | – | – | – | – | DLAgn_00110020 | Uncharacterized protein loc101483146 | hyp_loc101483146 |
| XLOC_020865 | 260.9 | 1274.3 | 269.3 | 12.9 | 5.6 | 19.7 | 2.0 | – | – | – | – | – | – | – | – | – | DLAgn_00214300 | Protein fam111a-like | FAM111A |
| XLOC_018302 | 1.6 | 3.9 | 2.2 | 1.6 | 3.5 | 1.5 | 1.3 | – | – | – | – | – | – | – | – | – | XP_006805317.1 | Uncharacterized protein LOC102781223 | hyp_LOC102781223 |
| XLOC_001638 | 3.9 | 4.2 | 9.2 | 3.2 | 6.8 | 7.9 | – | – | 1.2 | – | 1.1 | – | 1.3 | – | – | – | P35448 | Thrombospondin-1 | THBS1 |
| XLOC_009985 | 1.1 | 0.6 | 2.8 | 0.6 | 1.9 | 2.9 | – | – | 1.4 | – | – | – | 2.2 | – | – | – | P43300 | Early growth response protein 3 | EGR3 |
| XLOC_009459 | 2.8 | 2.5 | 5.8 | 2.4 | 4.4 | 6.1 | – | – | 1.0 | – | – | – | 1.4 | – | – | – | Q9ET55 | Nocturnin | CCRN4L |
| XLOC_015202 | 6.1 | 6.1 | 19.3 | 3.5 | 5.0 | 8.4 | – | – | 1.7 | – | – | – | 1.3 | – | – | – | Q16690 | Dual specificity protein phosphatase 5 | DUSP5 |
| XLOC_009646 | 8.0 | 5.6 | 19.0 | 3.0 | 7.6 | 13.2 | – | – | 1.2 | – | – | – | 2.2 | – | – | −1.4 | Q20A00 | DNA damage-inducible transcript 4-like protein | DDIT4L |
| XLOC_018946 | 261.3 | 451.9 | 567.7 | 482.9 | 396.7 | 190.1 | – | – | 1.1 | – | – | – | – | −1.3 | – | – | DLAgn_00241010 | Complement c1q-like protein 4 precursor | C1QL4 |
| XLOC_011902 | 6.6 | 8.2 | 13.4 | 20.8 | 25.4 | 9.1 | – | – | 1.0 | – | – | – | – | −1.2 | 1.7 | – | XP_005946242.1 | RNA-directed DNA polymerase from mobile element jockey-like | pred_pol413 |
| XLOC_002574 | 0.8 | 1.4 | 2.0 | 0.8 | 0.9 | 1.0 | – | – | 1.3 | – | – | – | – | – | – | – | Q61391 | Neprilysin / membrane metallo-endopeptidase | MME |