Table 3.
Relative expression of the set of isoforms of four loci (TIMP1, ITGA5, ANXA2 and LITAF) in HIGH (N = 26) vs LOW (N = 26) pigsa
| Feature ID | Feature transcript ID | Transcript ID | Length (bp) | Typeb | Relative expression mean (%) | CLC Bio | STAR/RSEM/DESeq2 | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Log2 (FC) |
P-value | q-value | Log2 (FC) |
P-value | q-valuec | ||||||
| ENSSSCG00000004578 | ENSSSCT00000034155 | ANXA2–201 | 1609 | Protein coding | 0.64 | 0.21 | 6.77E-01 | 1.00E + 00 | 0.07 | 9.20E-01 | NA |
| ENSSSCG00000004578 | ENSSSCT00000005057 | ANXA2–202 | 1455 | Protein coding | 99.36 | 0.70 | 3.32E-06 | 7.23E-03 | 0.69 | 4.56E-06 | 1.58E-03 |
| ENSSSCG00000000293 | ENSSSCT00000000314 | ITGA5–201 | 4445 | Protein coding | 99.00 | 0.85 | 2.64E-05 | 2.82E-02 | 0.85 | 2.54E-06 | 1.21E-03 |
| ENSSSCG00000000293 | ENSSSCT00000035821 | ITGA5–203 | 1255 | NMD | 0.34 | −0.03 | 9.18E-01 | 1.00E + 00 | – | – | – |
| ENSSSCG00000000293 | ENSSSCT00000034427 | ITGA5–204 | 1013 | NMD | 0.71 | −0.08 | 1.00E + 00 | 1.00E + 00 | – | – | – |
| ENSSSCG00000000293 | ENSSSCT00000033141 | ITGA5–205 | 766 | NMD | 0.48 | −0.29 | 1.00E + 00 | 1.00E + 00 | −0.01 | 9.97E-01 | NA |
| ENSSSCG00000012277 | ENSSSCT00000013426 | TIMP1–001 | 931 | Protein coding | 97.86 | 2.57 | 4.61E-07 | 1.85E-03 | 0.79 | 2.01E-04 | 1.32E-02 |
| ENSSSCG00000012277 | ENSSSCT00000033796 | TIMP1–002 | 598 | Protein coding | 0.38 | 1.12 | 5.56E-01 | 1.00E + 00 | 0.38 | 8.98E-01 | NA |
| ENSSSCG00000012277 | ENSSSCT00000034602 | TIMP1–003 | 641 | Protein coding | 1.57 | 1.19 | 8.47E-01 | 1.00E + 00 | −0.19 | 7.39E − 01 | NA |
| ENSSSCG00000012277 | ENSSSCT00000036308 | TIMP1–004 | 173 | Protein coding | 0.19 | 3.05 | 4.21E-01 | 1.00E + 00 | 0.18 | 9.52E-01 | NA |
| ENSSSCG00000024982 | ENSSSCT00000036552 | LITAF-201 | 2190 | Protein coding | 88.45 | 1.01 | 1.02E-04 | 4.82E-02 | 0.79 | 1.21E-04 | 1.04E-02 |
| ENSSSCG00000024982 | ENSSSCT00000025103 | LITAF-202 | 2370 | Protein coding | 11.55 | -0.04 | 1.00E + 00 | 1.00E + 00 | 0.49 | 7.52E-01 | NA |
aDifferentially expressed mRNA isoforms that remained significant after correction for multiple testing (q-value < 0.05 and ±0.6 log2Fold-Change) are shown in bold. A positive log2FC means that the gene is upregulated in HIGH pigs
bNMD Nonsense-mediated mRNA decay
cFor multiple testing correction, DESeq2 carries out a filtering step based on the average expression strength of each gene across all samples with the aim of discarding genes which are likely to loose significance after correcting for multiple testing. The purpose of this filtering step is to increase statistical power by reducing the list of candidate genes to be tested. The q-values of the genes which do not pass the filtering step are set to NA