heatmap generated in  (RStudio)

Journal: iScience

Article Title: Supinoxin blocks small cell lung cancer progression by inhibiting mitochondrial respiration through DDX5

doi: 10.1016/j.isci.2025.112219

Figure Lengend Snippet: RNA-seq analysis reveals downregulated mitochondrial function following Supinoxin treatment (A) A Venn diagram illustrating the total number of transcripts upregulated and downregulated following Supinoxin treatment and DDX5 knockdown. It was generated using the Venn diagram package in R Studio (version 2023.12.0). (B) A heatmap was generated to display the differential expression patterns of transcripts affected by Supinoxin treatment. Red indicates upregulation, while blue represents downregulation, based on Log 2 FC values. Z scores were applied to enhance gene clustering in response to Supinoxin treatment. Expression intensity values were calculated using RStudio to analyze gene expression levels. (C) Volcano plot depicting differentially expressed genes (DEGs) between H69AR cells with or without Supinoxin treatment. The plot was generated from the p values (∗<0.05, not significant) and Log 2 FC values (>1; <−1). The colored dots indicate genes with significant expression differences. Blue dots represent genes with significant differences based on p value alone, green dots on Log 2 FC alone, red dots represent genes with significant differences based on both p value and Log 2 FC, and gray dots are not significant in either term.

Article Snippet: The expression patterns of selected genes across treated and untreated samples were then illustrated in a heatmap generated in RStudio ( B).

Techniques: RNA Sequencing, Knockdown, Generated, Quantitative Proteomics, Expressing, Gene Expression

Journal: Frontiers in Plant Science

Article Title: In silico characterisation of the avocado WAK/WAKL gene family with a focus on genes involved in defence against Phytophthora cinnamomi

doi: 10.3389/fpls.2024.1474781

Figure Lengend Snippet: Expression profile heatmap of all PaWAK/WAKL genes during Phytophthora cinnamomi infection of a partially-resistant (Dusa ® ) and a susceptible (R0.12) avocado rootstock. More intense red blocks indicate a higher Log 2 FoldChange (Log 2 FC) and more intense blue blocks indicate a lower Log 2 FC compared to the controls. Values are shown for time points where the Log 2 FC change was significant, defined as P <0.05 and Log 2 FC > 1 or Log 2 FC < -1. All Log 2 FC values and P-values are provided in Supplementary Table S5 .

Article Snippet: The expression profiles for all PaWAK/WAKLs at these four time points were obtained and visualised through a heatmap generated with R-studio and TBtools v2.086 ( ; ).

Techniques: Expressing, Infection