differential expression analysis using deseq2  (RStudio)

Journal: bioRxiv

Article Title: Regionalization of gene expression and cell types in the silk gland of the pantry moth Plodia interpunctella

doi: 10.1101/2025.07.11.664249

Figure Lengend Snippet: A. Heatmap of the top 229 DEGs between MSG and PSG (adjusted p < 0.01, |log 2 FoldChange| > 3, DESeq2 normalized counts > 300). Gene expression profiles across tissues are shown with a Z-score transformation and sorted by hierarchical clustering (SalG: salivary glands ; Heads: larval heads). B. Scatter plot highlighting expression level difference of individual genes between the PSG and MSG (x-axis, log2FC), and their relative transcript abundance within their tissue of enrichment (y-axis, log 2 TPM). Coloring highlights genes with DESeq2 adjusted p < 0.05 and log 2 TPM > 0.01. Non-significant, lowly-expressed genes (log 2 TPM < -2) are not shown. Asterisks: the genes prospero ( pros ), rtoA , and DNAH2 are respectively adjacent to DEGs FibH, MG4 , and SerP150 , which may drive their enrichment in the corresponding tissues. C. Transcript representation within the PSG and MSG tissues (TPM as %). Ribosomal protein genes were pooled. D. Amino-acid composition of three major secreted proteins detected in the MSG, each showing extensive serine-rich stretches and repeats characteristic of sericin proteins. Accession numbers: XP_053622673 (Pi_Ser3b), XP_053622719 (Pi_MG4), XP_053613126 (Pi_SerP150).

Article Snippet: The count data generated by FeatureCounts was used to perform differential expression analysis using DESeq2 in RStudio .

Techniques: Gene Expression, Transformation Assay, Expressing

Journal: Genome Research

Article Title: Developmental transcriptomics in Pristionchus reveals the environmental responsiveness of a plasticity gene-regulatory network

doi: 10.1101/gr.279783.124

Figure Lengend Snippet: A subset of the mouth-form GRN is environmentally responsive. ( A – E ) Volcano plots of genes differentially expressed between worms grown on agar and in liquid culture at five developmental time points. Significant genes are colored by the condition in which they were upregulated: blue for liquid culture and red for agar. Significant mouth-form genes are labeled on the plot in gold. A dashed line represents the significance cutoff (adjusted P -value < 0.05). ( F – O ) Mean expression of normalized counts from DESeq2 with SEM for mouth-form genes. (*) Time points with significant differences in expression (adjusted P -value < 0.05).

Article Snippet: We imported the quantified reads to RStudio (version 2022.2.3.492) ( ) using tximport and performed differential gene-expression analysis using DESeq2 ( ) and R (version 4.2.0) ( ).

Techniques: Labeling, Expressing

Journal: Genome Research

Article Title: Developmental transcriptomics in Pristionchus reveals the environmental responsiveness of a plasticity gene-regulatory network

doi: 10.1101/gr.279783.124

Figure Lengend Snippet: Transcriptional effects of mutations in the mouth-form GRN are temporally restricted. ( A – K ) Mean expression from DESeq2 normalized counts of mouth-form genes in wild-type PS312 and the indicated mutant line. (*) Time point with significant differences in expression (adjusted P -value < 0.05). ( L ) Mouth-form GRN with St-promoting genes colored in blue and Eu-promoting genes colored in red. Genes in black may regulate the development of both morphs. Solid lines represent gene ordering resulting from epistatic analysis, whereas dashed lines represent untested gene interactions. Gold lines represent new regulatory links inferred from the results of this study.

Article Snippet: We imported the quantified reads to RStudio (version 2022.2.3.492) ( ) using tximport and performed differential gene-expression analysis using DESeq2 ( ) and R (version 4.2.0) ( ).

Techniques: Expressing, Mutagenesis

Journal: Genome Research

Article Title: Developmental transcriptomics in Pristionchus reveals the environmental responsiveness of a plasticity gene-regulatory network

doi: 10.1101/gr.279783.124

Figure Lengend Snippet: Natural variation in mouth-form transcriptomics. ( A – D ) Volcano plots of differentially expressed genes between pooled St- and Eu-biased strains of P. pacificus at four developmental time points. Significant genes (adjusted P -values < 0.05) upregulated in St are colored blue, and those upregulated in Eu are colored red. Gold points represent components of the mouth-form GRN, and significant mouth-form genes are labeled in gold on the plot. ( E – N ) Mean expression of normalized counts from DESeq2 for mouth-form genes in pooled St- and Eu-biased strains. (*) Time points with significant expression differences (adjusted P -value < 0.05).

Article Snippet: We imported the quantified reads to RStudio (version 2022.2.3.492) ( ) using tximport and performed differential gene-expression analysis using DESeq2 ( ) and R (version 4.2.0) ( ).

Techniques: Labeling, Expressing