Additional file 2 of Increased biological relevance of transcriptome analyses in human skeletal muscle using a model-specific pipeline

Additional file 2: Functional annotation using gene ontology terms. Significance tests for functional annotation using rank-based and over-representation based analysis. ID: Gene ontology (GO) id; go_category: GO category, bp, Biological process; cc, cellular component; mf, molecular function; name: Descriptive GO name; normalization_model: Indicate normalization model used to test enrichment: lib_size_normalized, gene counts are modeled with study conditions as fixed effects and participant id as random effects and with the addition of library size as a fixed effect, tissue_offset_lib_size_normalized, same as lib_size_normalized but with the addition of tissue weight used in library prep as an offset. The non-normalized model is not included; coefficient: Names of coefficients used to test enrichment (fixed effects, time and volume conditions). timew2pre and timew12 indicates differences from timew0 (intercept) in rested state models. timew2post indicates differences from timew2pre (intercept) in acute exercise models. setsmultiple indicates interaction effects, the difference between setssingle (reference level) and setsmultiple; cerno_statistic: Test statistic from the rank-based cerno-test; cerno_auc: Area under the curve from the Cerno test (see tmod documentation for details, https://CRAN.R-project.org/package=tmod ); cerno_pval: Un-adjusted P-values from cerno test, cerno_padj: Adjusted P-values (default settings in tmodCERNOtest, see tmod documentation); fgsea_pval: Un-adjusted P-values from gene set enrichment tests performed with the fgsea package; fgsea_padj: Adjusted fgsea P-values; NES: Normalized enrichment scores from gene set enrichment tests; set_size: Size of gene sets using genes expressed in the present data set; ora_geneRatio: Gene ratio in over-representation analysis of genes identified as differentially expressed; ora_padj: Adjusted p-values from over-representation analysis.