Table 3.
Selected list (first 20 genes) of the genes differentially expressed at FDR < 0.05 and at < 2-fold change difference, in sea bass scales from treated versus control animals. The complete list with the expression and annotation for the 417 genes with differential expression under these limits (FDR < 0.05 and FC < 2) can be consulted in Supplementary Table 2. 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) 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 | E2 up | E2 down | Gen up | Gen down | E2 up | E2 down | Gen up | Gen down | C5d up | C5d down | Hit description | Symbol |
| XLOC_017886 | 20.5 | 32.3 | 35.2 | 21.7 | 28.2 | 26.6 | 0.7 | – | 0.8 | – | – | – | – | – | – | – | sp|P51890|LUM_CHICK Lumican OS=Gallus gallus | LUM |
| XLOC_009066 | 20.1 | 32.2 | 23.6 | 14.9 | 18.8 | 16.6 | 0.7 | – | – | – | – | – | – | – | – | – | sp|Q6NVM0|H10_XENTR Histone H1.0 | H1F0 |
| XLOC_000057 | 39.9 | 63.9 | 54.8 | 51.8 | 66.1 | 52.3 | 0.7 | – | – | – | – | – | – | – | – | – | sp|Q04857|CO6A1_MOUSE Collagen alpha-1(VI) chain | COL6A1 |
| XLOC_014484 | 17.5 | 28.2 | 25.8 | 20.4 | 14.9 | 17.2 | 0.7 | – | – | – | – | – | – | – | – | – | sp|Q53RD9|FBLN7_HUMAN Fibulin-7 | FBLN7 |
| XLOC_019995 | 42.4 | 68.5 | 41.0 | 32.9 | 42.9 | 22.8 | 0.7 | – | – | – | – | – | – | – | – | – | sp|P55918|MFAP4_BOVIN Microfibril-associated glycoprotein 4 | MFAP4 |
| XLOC_006221 | 7.3 | 11.8 | 7.0 | 7.3 | 10.5 | 6.6 | 0.7 | – | – | – | – | – | – | – | – | – | sp|Q4R6P7|SESN1_MACFA Sestrin-1 | SESN1 |
| XLOC_002145 | 58.5 | 95.2 | 82.9 | 108.5 | 94.2 | 73.3 | 0.7 | – | – | – | – | – | – | – | 0.9 | – | sp|O95428|PPN_HUMAN Papilin | PAPLN |
| XLOC_022309 | 58.4 | 96.0 | 62.0 | 45.3 | 81.2 | 35.5 | 0.7 | – | – | – | 0.8 | – | – | – | – | – | sp|Q9U8W8|TL5A_TACTR Techylectin-5A | – |
| XLOC_003581 | 10.8 | 18.6 | 11.2 | 12.6 | 8.8 | 6.9 | 0.8 | – | – | – | – | – | – | −0.9 | – | – | sp|Q802Y8|ZB16A_DANRE Zinc finger and BTB domain-containing protein 16-A | ZBTB16 |
| XLOC_011142 | 1033.0 | 1793.0 | 979.6 | 1063.6 | 1387.2 | 709.6 | 0.8 | – | – | – | – | – | – | – | – | – | sp|Q66S03|LECG_THANI Galactose-specific lectin nattectin | LADD |
| XLOC_013333 | 40.4 | 70.4 | 59.7 | 50.9 | 50.7 | 48.9 | 0.8 | – | – | – | – | – | – | – | – | – | sp|Q90611|MMP2_CHICK 72 kDa type IV collagenase | MMP2 |
| XLOC_020568 | 323.2 | 571.3 | 392.8 | 275.6 | 447.7 | 280.9 | 0.8 | – | – | – | – | – | – | – | – | – | gap junction epsilon-1 | – |
| XLOC_016220 | 5.0 | 8.9 | 6.1 | 6.5 | 5.6 | 5.4 | 0.8 | – | – | – | – | – | – | – | – | – | sp|Q568Y7|NOE2_RAT Noelin-2 | OLFM2 |
| XLOC_006639 | 175.0 | 315.2 | 258.5 | 221.0 | 268.7 | 245.3 | 0.8 | – | – | – | – | – | – | – | – | – | sp|Q01584|LIPO_BUFMA Lipocalin | LCN1 |
| XLOC_015159 | 46.9 | 88.4 | 67.0 | 84.6 | 64.2 | 95.1 | 0.9 | – | – | – | – | – | – | – | 0.9 | – | sp|P27590|UROM_RAT Uromodulin | UMOD |
| XLOC_019689 | 26.0 | 49.4 | 26.6 | 17.3 | 18.0 | 17.4 | 0.9 | – | – | – | – | – | – | – | – | – | No hit found | – |
| XLOC_014167 | 3.2 | 6.1 | 5.1 | 3.4 | 2.6 | 2.7 | 1.0 | – | – | – | – | – | – | – | – | – | sp|Q5E9P5|PAMR1_BOVIN Inactive serine protease PAMR1 OS=Bos taur... 413 e-114 | PAMR1 |
| XLOC_022211 | 101.7 | 197.8 | 148.2 | 85.2 | 76.3 | 155.6 | 1.0 | – | – | – | – | – | – | – | – | – | No hit found | – |
| XLOC_008732 | 3.6 | 6.9 | 6.7 | 5.9 | 4.9 | 5.3 | 1.0 | – | 0.9 | – | – | – | – | – | – | – | sp|Q9BQB4|SOST_HUMAN Sclerostin | SOST |
| XLOC_018728 | 132.5 | 258.4 | 160.0 | 121.5 | 235.3 | 99.0 | 1.0 | – | – | – | 1.0 | – | – | – | – | – | No hit found | – |