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Table 2 Splicing variants that are differentially expressed (P-value < 0.01 and ±0.6 log2Fold-Change) in the gluteus medius muscle of HIGH (N = 26) vs LOW pigs (N = 26)a

From: Differential expression of mRNA isoforms in the skeletal muscle of pigs with distinct growth and fatness profiles

Feature ID

Feature transcript ID

Transcript ID

Length (bp)

Relative expression mean (%)

CLC Bio

STAR/RSEM/DESeq2

Log2(FC)

P-value

q-value

Log2(FC)

P-value

q-valueb

ENSSSCG00000000293

ENSSSCT00000000314

ITGA5–201

4445

99.00

0.85

2.64E-05

2.56E-02

0.85

2.54E-06

1.21E-03

ENSSSCG00000001252

ENSSSCT00000001367

UBD-201

1281

75.81

−0.72

1.37E-03

2.29E-01

−0.83

7.73E-04

NA

ENSSSCG00000003079

ENSSSCT00000003416

PVR-202

1167

48.41

0.77

7.76E-03

5.94E-01

0.66

9.27E-03

1.27E-01

ENSSSCG00000004578

ENSSSCT00000005057

ANXA2–202

1455

99.36

0.70

3.32E-06

6.56E-03

0.69

4.56E-06

1.58E-03

ENSSSCG00000012277

ENSSSCT00000013426

TIMP1–001

931

97.85

2.57

4.61E-07

1.68E-03

0.79

2.01E-04

1.32E-02

ENSSSCG00000012653

ENSSSCT00000013834

ZDHHC9–209

2967

17.79

0.77

3.29E-03

3.75E-01

0.77

2.56E-03

6.11E-02

ENSSSCG00000013579

ENSSSCT00000014831

CD209–001

1042

95.10

1.04

7.84E-05

4.18E-02

1.01

2.09E-05

NA

ENSSSCG00000006328

ENSSSCT00000033501

RXRG-202

544

17.68

−0.70

4.09E-04

1.18E-01

−0.76

9.31E-05

8.98E-03

ENSSSCG00000009584

ENSSSCT00000034286

SEMA4D-208

487

8.57

1.40

2.75E-06

6.53E-03

1.09

5.87E-05

6.59E-03

ENSSSCG00000024982

ENSSSCT00000036552

LITAF-201

2190

88.44

1.01

1.02E-04

4.38E-02

0.79

1.21E-04

1.04E-02

  1. 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
  2. bFor 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