Table 4.
Numbers of genes and proteins associated with transcription, pre-mRNA processing, and ribosomal assembly that were higher (H) or lower (L) in breast muscle of high feed efficiency (FE) compared to low FE pedigree broiler male for the terms provided obtained from global expression microarray, proteomics, and RNAseq datasets and for numbers of all three global expression datasets combined.
| Microarraya — | Proteomicsb — | RNAseqc — | |||||||
|---|---|---|---|---|---|---|---|---|---|
| Terms | H | L | P* | H | L | P* | H | L | P* |
| RNA Polymerase | 14 | 13 | 1 | 2 | 28 | 8 | 0.0004 | ||
| Transcription | 16 | 22 | 0.0812 | 3 | 1 | 94 | 69 | 0.0092 | |
| TATA Box, T-box | 6 | 4 | 0 | 0 | 19 | 8 | 0.0165 | ||
| Small nuclear (sn) ribonucleoproteins (RNP) and heterogeneous (hn) RNP | 10 | 1 | 0.0054 | 4 | 1 | 12 | 1 | 0.0016 | |
| Spliceosome, helicase, | 6 | 1 | 0.0547 | 4 | 0 | 0.0625 | 27 | 11 | 0.0044 |
| pre mRNA processing | |||||||||
| RNA Binding Motif | 11 | 8 | 0 | 0 | 39 | 13 | 0.0001 | ||
| Ribosome-Ribosomal | 8 | 1 | 0.0017 | 41 | 4 | 4 × 10−9 | 57 | 49 | 0.0573 |
| Transfer RNA (tRNA) | 8 | 8 | 6 | 0 | 0.0156 | 64 | 11 | 1.0 × 10−10 | |
| Translation (Eukaryotic initiation-elongation) | 12 | 11 | 12 | 7 | 0.0961 | 43 | 13 | 3.0 × 10−5 | |
| Karyopherins (Nuclear transport proteins) | 5 | 6 | 0.0537 | 1 | 0 | 24 | 15 | 0.0457 | |
| (Nucleoporins, Karyopherins, Importins, Exportins) | |||||||||
| Small ubiquitin-like modifier (SUMO) | 1 | 1 | 1 | 1 | 9 | 2 | 0.0269 | ||
| (peptidase, isopeptidase, ligase) | |||||||||
cDNA microarray—Kong et al. (2011).
Shotgun proteomics—Kong B. et al. (2016).
RNAseq—Bottje et al. (2017).
Binomial (exact) P values for H vs. L (higher vs. lower) in each dataset.
P values not underlined indicate a significant bionomial skew in high FE numbers.
P values that are underlined indicate a significant skew in low FE numbers.
P values that are blank are indicative of values > 0.10.