Journal: NAR Genomics and Bioinformatics

Article Title: IsopretGO—analysing and visualizing the functional consequences of differential splicing

doi: 10.1093/nargab/lqae165

Figure Lengend Snippet: Gene visualization of the STE20-like kinase (SLK) gene. Panels (A)–(C) were exported from the isopretGO app from the gene visualization page that is opened by clicking on the ‘Visualize’ button for SLK as shown in Figure . ( A ) ENST00000369755.4 (isoform 1, the long isoform, 19 exons) and ENST00000335753.8 SLK-201 (isoform 2, the short isoform, 18 exons) are shown. ( B ) The protein (InterPro) domains relative to the exon structure of both isoforms are shown. ( C ) GO annotations predicted by isopretEM for both isoforms are shown. GO terms that are significantly overrepresented in the entire set of differentially spliced isoforms are highlighted.

Article Snippet: The isopretGO Java application is freely available under the GNU General Public License v3.0 at https://github.com/TheJacksonLaboratory/isopretGO .

Techniques:

Journal: iScience

Article Title: Pandemic-associated pernio harbors footprints of an abortive SARS-CoV-2 infection

doi: 10.1016/j.isci.2024.110525

Figure Lengend Snippet: Golden hamsters were intranasally treated with SARS-CoV-2 or PBS (mock) Lung and toe tissues from SARS-CoV-2- and mock-treated hamsters were longitudinally harvested at days 1, 3, 5, 7, 10, 14, and 30 post-infection ( n = 3 per condition per time point). (A and B) Lung tissues were then assessed for the presence of (A) SARS-CoV-2 sgN and (B) Isg15 transcripts via RT-qPCR. (C and D) Toe tissues were also assessed for (C) sgN and (D) Isg15 presence via RT-qPCR. Significance was evaluated via multiple unpaired t tests performed using a two-stage step-up method to control the false discovery rate (FDR). FDR q-values less than 0.05 are displayed. (E) Toes were harvested from 3dpi hamsters inoculated with SARS-CoV-2 via either intranasal (IN) or intravenous (IV) routes and assessed for the presence of infectious virus via plaque assay. 3 dpi lung samples from SARS-CoV-2-infected hamsters were included as a positive control ( n = 4 per condition). Significance was calculated using an ordinary one-way ANOVA with Tukey’s multiple comparisons test. ∗∗ p < 0.01. (F and G) Toe and lung tissues were harvested at 3 days post-infection (dpi) and 30 dpi and transcriptionally profiled using RNA sequencing. SARS-CoV-2- and mock-treated datasets were compared in differential expression analysis (n = 2–4 for respective time point and infection groups). Toe differential expression data of 3dpi harvested toes was in turn analyzed using gene set enrichment analysis (GSEA) for enrichment of ontology-related gene sets (MSigDB Gene Set C5). Top enrichments from these analyses are represented in (F) as a lollipop chart, with magnitude of the stalk representative of normalized enrichment score (NES) and dot size scaled to significance. (G) RNA sequencing data for SARS-CoV-2-infected toes and lungs at 3 and 30 dpi were compared to analogous mock-treated tissues using differential expression analysis. Log2(fold change) of type I interferon-stimulated genes are presented here as a heatmap. See also Figure S3 .

Article Snippet: Output from differential expression analysis was used to run Gene Set Enrichment Analysis (GSEA) (MacOS Java Application v4.1.0) (made available by the Broad Institute and the University of California) looking for enrichment of Molecular Signatures Database curated gene set C5 with a gene ranking factor of -log10( p -value)∗sign(log2FoldChange).

Techniques: Infection, Quantitative RT-PCR, Control, Virus, Plaque Assay, Positive Control, RNA Sequencing, Quantitative Proteomics

Journal: Biology of Sex Differences

Article Title: Integrative multi-omics characterization reveals sex differences in glioblastoma

doi: 10.1186/s13293-024-00601-7

Figure Lengend Snippet: Sex-specific transcriptome difference and pathway enrichment. A Analysis of differential gene expression in different sexes. The cutoff for log2fold change is 0.4, and the cutoff for p-value is 0.05. B Gene set enrichment analysis in different sexes. The gene set database used is the Human MSigDB, which includes Reactome, GO, and Wikipathways. C Single-sample gene set enrichment analysis (ssGSEA) of males and females. The significant gene sets are identified based on a p-value < 0.05. D The percentage of GBM transcriptional subtypes based on TCGA in patients (Wang et al.). Green represents MS (mesenchymal), purple represents PN (proneural), and cyan represents CL (classical). E The percentage of GBM pathway-based subtypes in patients (Garofano et al.). Red represents GPM (glycolytic/plurimetabolic), green represents MTC (mitochondrial), blue represents NEU (neuronal), and cyan represents PPR (proliferative/progenitor). F, G Immune cell type enrichment analysis of RNA expression data using the xCell tool. F Scores for three cell types. G Scores for immune cells that are important in GBM

Article Snippet: GSEAs were performed using the GSEA Java application, which was downloaded from the Broad Institute website ( https://www.gsea-msigdb.org/gsea/index.jsp ).

Techniques: Gene Expression, RNA Expression