gene sets including kegg, go biological process reactome, and hallmark  (Broad Institute Inc)

Journal: Skeletal Muscle

Article Title: The transcriptomic signature of age and sex is not conserved in human primary myotubes

doi: 10.1186/s13395-026-00416-7

Figure Lengend Snippet: Comparisons between the transcriptomic signature of muscle tissue samples. A Differences in gene expression in young male (control, N = 10) and young female (case, N = 10) muscle tissue. Genes differentially expressed at FDR < 0.05 and |Log 2 fold change| > 1 are depicted in red. B Reactome pathways downregulated in young male ( N = 10) versus young female ( N = 10) muscle tissue. C Differences in gene expression in young male (control, N = 10) and older male (case, N = 10) muscle tissue. Genes differentially expressed at FDR < 0.05 and |Log 2 fold change| > 1 are depicted in red. D Reactome pathways upregulated (left panel) or downregulated (right panel) in young male ( N = 10) versus older male ( N = 10) muscle tissue

Article Snippet: Reactome gene sets from Homo sapiens were based on the msigdbr package (v7.5.1) and curated for skeletal muscle tissue activation using PubChem and The Human Protein Atlas, with all non-filtered gene sets presented in Supplementary Tables.

Techniques: Gene Expression, Control

Journal: Skeletal Muscle

Article Title: The transcriptomic signature of age and sex is not conserved in human primary myotubes

doi: 10.1186/s13395-026-00416-7

Figure Lengend Snippet: Comparisons between the transcriptomic signature of muscle tissue and differentiated HPMCs. A Principal component analysis of the transcriptome of N = 30 human muscle tissue samples (control, N = 10 young females, N = 10 young males, N = 10 older males) and the corresponding N = 30 differentiated HPMC lines grown from the same donors (case). B Differences in gene expression in human muscle tissue ( N = 30) compared to differentiated primary muscle cell lines grown from the same donors ( N = 30). Genes differentially expressed at FDR < 0.05 and |Log 2 fold change| > 1 are depicted in red. C Reactome pathways upregulated (left panel) or downregulated (right panel) in muscle tissue ( N = 30) versus differentiated HPMCs ( N = 30). D Average sum of normalised counts of the 13 mitochondrial protein-coding genes in cell (blue) and tissue (red) samples

Article Snippet: Reactome gene sets from Homo sapiens were based on the msigdbr package (v7.5.1) and curated for skeletal muscle tissue activation using PubChem and The Human Protein Atlas, with all non-filtered gene sets presented in Supplementary Tables.

Techniques: Control, Gene Expression

Journal: Skeletal Muscle

Article Title: The transcriptomic signature of age and sex is not conserved in human primary myotubes

doi: 10.1186/s13395-026-00416-7

Figure Lengend Snippet: Maintenance of the age phenotype between muscle tissue and differentiated HPMCs. A Scatter plot depicting the log 2 fold-change of each individual gene expressed in young ( N = 10) and older ( N = 10) muscle tissue and in the corresponding young ( N = 10) and older ( N = 10) differentiated muscle cell lines. Genes differentially expressed at FDR < 0.05 and down regulated in both young cell and muscle tissue are depicted in black. Genes differentially expressed at FDR < 0.05 and down regulated in young cells only are depicted in blue. Genes differentially expressed at FDR < 0.05 and up regulated in young cells only are depicted in green. Genes differentially expressed at FDR < 0.05 and down regulated in young muscle tissue only are depicted in orange. Genes differentially expressed at FDR < 0.05 and up regulated in young muscle tissue only are depicted in dark red. B Differential expression rank–rank density contour plot with cell and tissue contrasts on the x- and y-axes, respectively. Each point represents a gene ranked by its differential expression in both contrasts, and the filled contours indicate gene density across the rank space. The four quadrants correspond to directional patterns of regulation: genes upregulated in both contrasts (top right), downregulated in both (bottom left), or oppositely regulated (top left and bottom right). The relatively even spread of density across all quadrants reflects the absence of a consistent transcriptional signature shared between aged muscle tissue and cultured cells. C Heatmap depicting the differentially regulated Reactome pathways in young ( N = 10) and older ( N = 10) muscle tissue (control) and in the corresponding young ( N = 10) and older ( N = 10) differentiated HPMC lines (case)

Article Snippet: Reactome gene sets from Homo sapiens were based on the msigdbr package (v7.5.1) and curated for skeletal muscle tissue activation using PubChem and The Human Protein Atlas, with all non-filtered gene sets presented in Supplementary Tables.

Techniques: Quantitative Proteomics, Cell Culture, Control

Journal: iScience

Article Title: Distinct transcriptomic signatures in pulmonary tissue resident and vascular resident-like T cells in nonhuman primates

doi: 10.1016/j.isci.2025.112745

Figure Lengend Snippet: Pathway enrichment analysis (PEA) suggests ivs+ CD8 + T cells have an enhanced ability to interact with endothelial cells (A) Tree plot illustrating significantly enriched pathways in lung ivs+ CD8 + T cells. Hierarchical clustering of enriched terms based on Jaccard’s similarity index (JC). (B and C) Gene-concept network plots depicting genes (blue dots) involved in enriched terms (red dots) associated with signaling events (B) and vascular interactions (C). (D) Reactome “cell surface interactions at the vascular cell wall” pathway associated genes upregulated or downregulated in lung ivs+ CD8 + T cells. For PEA an adj p value (FDR) ≤ 0.05 was used to determine significance. See also and .

Article Snippet: We performed PEA using the Reactome gene collection from The Broad Institute Molecular Signature Database (MSigDB), , which was filtered to contain only genes present in our dataset in order to avoid bias.

Techniques: