Journal: Breast Cancer Research : BCR

Article Title: Key regulators of lipid metabolism drive endocrine resistance in invasive lobular breast cancer

doi: 10.1186/s13058-018-1041-8

Figure Lengend Snippet: Cholesterol synthesis is predicted to be upregulated in long-term estrogen deprivation (LTED) cells. (a, b) Gene set enrichment analysis (GSEA) of ( a ) E2F activation signature and ( b ) cholesterol biosynthesis signature (Reactome Cholesterol Synthesis) in LTED variants. Differential expression (DE) genes used in GSEA were ranked by log2(fold change). c Growth of parental and LTED cells with treatment of 25-hydroxycholesterol (25-HC) and 27-hydroxycholesterol (27-HC). Parental cells were hormone-deprived before being seeded in hormone-deprived media (charcoal-stripped fetal bovine serum, or CSS). Cells were collected after 5-day treatment. Fold growth was compared with control group (data not shown), which was treated with vehicle (ethanol). Plots are representative of at least two independent experiments. Data are mean ± standard deviation (SD) of six replicates. One-way analysis of variance (ANOVA) followed by Dunnett’s post hoc test for multiple comparisons was used to test the significance between 25-HC/27-HC–treated groups to the control groups (data not shown), * P <0.05, ** P <0.01, *** P <0.001. d The activation z-score of sterol regulatory element-binding proteins (SREBPs) in LTED cells. The upstream regulator analysis was performed in individual LTED cell variants separately with Ingenuity Pathway Analysis (IPA) software. DE genes (absolute log2(fold change) > log2(1.5) and adjusted P value of less than 0.001) and their log2(fold change) were used as input. Upstream regulators with z-score of more than 2 were defined as “activated” (labeled in red). Abbreviation: ES enrichment score.

Article Snippet: GseaPreranked function in Gene Set Enrichment Analysis (GSEA) (version 2.2.2, Broad Institute, Cambridge, MA, USA) was performed using the Reactome cholesterol synthesis signature (Additional file : Table S4), downloaded from the Molecular Signature Database (MsigDB, version 6.0, Broad Institute).

Techniques: Activation Assay, Quantitative Proteomics, Control, Standard Deviation, Binding Assay, Software, Labeling

Journal: Genome Biology

Article Title: Quantifying the phase separation property of chromatin-associated proteins under physiological conditions using an anti-1,6-hexanediol index

doi: 10.1186/s13059-021-02456-2

Figure Lengend Snippet: Comparison between AICAP and proteins in biomolecular condensates. A Distribution of AICAP values of proteins in different condensates. B GSEA enrichment of “Nuclear puncta” using AICAP ranked proteins. C Distribution of AICAP values of proteins annotated to be of different material states. D Distribution of AICAP values of self-assembling (Self) and partner-dependent (Partner) proteins

Article Snippet: Using Gene Set Enrichment Analysis (GSEA) analysis, we observed that nuclear puncta proteins annotated by OpenCell were significantly enriched at the low AICAP end (Fig. B, Additional file ).

Techniques: Comparison

Journal: Frontiers in Cellular and Infection Microbiology

Article Title: Evaluation of Beauvericin’s activity and mode of action against all life stages of L. tropica for cutaneous Leishmaniasis therapy

doi: 10.3389/fcimb.2025.1599766

Figure Lengend Snippet: Over-representation analysis (ORA) reveals conserved and stage-specific functional enrichments following BEA treatment in L. tropica . Bar plots depict the top significantly enriched Gene Ontology (GO) terms among differentially expressed genes (DEGs) in promastigotes and intracellular amastigotes. Notable enrichments include transmembrane transport, protein phosphorylation, oxidative stress response, and calcium-binding functions, which were subsequently used to define biologically coherent gene sets for GSEA analysis.

Article Snippet: Gene Set Enrichment Analysis (GSEA) was conducted using RStudio (version 4.3.0) to classify genes according to their expression levels and identify enriched gene sets within the transcriptome following BEA exposure ( ).

Techniques: Functional Assay, Phospho-proteomics, Binding Assay