gene set enrichment analysis tool  (Partek)

Journal: bioRxiv

Article Title: Inhibition of the extracellular matrix protein fibulin-3 reduces immunosuppressive signaling in tumor stem cells and increases macrophage activation against glioblastoma

doi: 10.1101/2024.12.28.628031

Figure Lengend Snippet: A) Correlation of fibulin-3 mRNA expression with the expression of CSF-1, TGFβ, and the checkpoints CD47 and CD274 (PD-L1), extracted from the TCGA GBM dataset. B) Correlation of fibulin-3 co-expressed with the markers indicated in ( A ) in GBM tumors separated by their bulk transcriptional subtype. C) Heatmap showing top gene expression changes in two GSC lines (GBM34, GBM09) stably transfected with control or fibulin-3 shRNAs. D) Changes in gene expression observed in hallmark signatures for inflammatory response and signaling by interferon gamma and alpha (data analyzed using GSEA v.4.3.3), comparing fibulin-3-deficient GSCs ( fib-3 KD ) versus control cells.

Article Snippet: Gene ontology was analyzed using Gene Set Enrichment Analysis (GSEA) tools provided by Partek Flow.

Techniques: Expressing, Stable Transfection, Transfection, Control

Journal: eLife

Article Title: Nuclear receptor corepressor 1 controls regulatory T cell subset differentiation and effector function

doi: 10.7554/eLife.78738

Figure Lengend Snippet: ( a ) Contour plots show the gating strategy for the isolation of Treg cells for RNA-sequencing. Cells from spleen and lymph nodes of WT.DEREG and NCOR1-cKO.DEREG mice were isolated and EGFP + (i.e. FOXP3 + ) CD44 hi CD62L – and CD44 lo CD62L + cells were sorted and sequenced using the Illumina HiSeq 3000 platform. ( b ) Volcano plots depict a comparison of global gene expression profiles between naïve (CD44 lo CD62L + ) WT and NCOR1-cKO Treg cells (left plot) and effector (CD44 hi CD62L – ) WT and NCOR1-cKO Treg cells (right plot). On the x-axis log2-fold change is plotted, while the y-axis indicates adjusted p-values (-log10). 1027 genes were downregulated and 540 genes were upregulated in naïve NCOR1-cKO Treg cells. 275 and 299 genes were down- and upregulated, respectively, in effector NCOR1-cKO Treg cells. In addition to Ncor1 and Myc , the top five genes leading to enrichment of cholesterol homeostasis (*) and of Myc targets v2 hallmark gene signatures are shown. ( c ) Diagram showing the top hits of enriched hallmark gene signatures in WT (NES<0) and NCOR1-cKO (NES>0) naïve (top) and effector (bottom) Treg cells. The x axis indicates the Z score. ( d ) Gene set enrichment analysis (GSEA) plots of an ‘effector Treg gene set’ (containing a list of 100 genes) in naïve NCOR1-cKO Treg cells compared to naïve WT Treg cells. ( e ) Gene set enrichment analysis (GSEA) plots of a ‘naïve Treg gene set’ (containing a list of 100 genes) in effector NCOR1-cKO Treg cells compared to effector WT Treg cells. ( d,e ) Barcodes indicate the location of the members of the gene set in the ranked list of all genes. NES, normalized enrichment score. The lists of the ‘naïve Treg gene set’ and the ‘effector Treg gene set’ are provided in .

Article Snippet: Downstream pathway analysis was performed using the gene set enrichment analysis (GSEA) tools provided by the Broad Institute ( ) or ingenuity pathway analysis (IPA) (QIAGEN Inc) ( ) using default settings.

Techniques: Isolation, RNA Sequencing, Comparison, Gene Expression