Table 1 The software packages used for each omics analysis in this study.
From: Effects of moderate intensity exercise on liver metabolism in mice based on multi-omics analysis
Methods | Technical details | Platform/software packages | |
|---|---|---|---|
Transcriptomics analysis | Principal component analysis | “princomp” function | R package “stats” (version 4.3.1) |
Differential expression analysis | p < 0.05 & (FC > 1.2 or FC < 0.83) | R package limma (version 3.46.0) | |
Functional enrichment analysis | p < 0.05 | David (version 2024q1, https://david.ncifcrf.gov/) | |
Protein-protein interaction network | interaction score > 0.4 | STRING (version 12.0, https://cn.string-db.org/), Cytoscape (version 3.8.2) | |
Proteomics and lactylation modification analyses | Differential expression analysis | p < 0.05 & (FC > 1.2 or FC < 0.83) | Student’s t-test |
Metabolomics analysis | Differential expression analysis | p < 0.05 & (FC > 1.2 or FC < 0.83) | Student’s t-test |
Functional enrichment analysis | p < 0.05 | MBROLE 2.0 (http://csbg.cnb.csic.es/mbrole2/index.php) |
