Additional file 1 of Transcriptomic characterization of Trichoderma harzianum T34 primed tomato plants: assessment of biocontrol agent induced host specific gene expression and plant growth promotion
Creators: name: Aamir, Mohd
name: Shanmugam, V.
name: Dubey, Manish Kumar
name: Husain, Fohad Mabood
name: Adil, Mohd
name: Ansari, Waquar Akhter
name: Rai, Ashutosh
name: Sah, Pankaj
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Figure S1. Multidimensional scaling analysis of the gene expression data from both un-inoculated control (C) and treatment (T) to map the high dimensional data into two dimensions while keeping the relative distances between the observations constant. Figure S2. t-SNE plot displaying the points from a higher dimension to a lower dimension trying to preserve the neighborhood of that point. t-SNE plot t-SNE is also a un-supervised non-linear dimensionality reduction and data visualization. Figure S3. Pathway analysis of PCA rotation based on functional enrichement structured around biological process GO term. Figure S4. Pathway analysis of PCA rotation based on functional enrichement structured around molecular function GO term. Figure S5. Pathway analysis of PCA rotation based on functional enrichement based on Kyoto Encyclopedia of Genes and Genome(KEGG) pathway. The functional annotation and gene-specific pathway for the significant and associated hits were retrieved through ShinyGO based KEGG tool [91, 92]. Figure S6. Cytohubba constructed PPI network for upregulated genes showing the interactive associative network. Figure S7. Tree map based on Revi GO analysis showing the functional annotation of the enriched GO IDs associated with significant DEGs structured around gene ontological term biological process involved. Figure S8. Tree map based on Revi GO analysis showing the functional annotation of the enriched GO IDs associated with significant DEGs structured around gene ontological term molecular function. Table S1. Table showing the different values of multiple principle component analysis (PCAs), multidimensional scaling and t-SNE analysis for both un-incoculated control samples (C1, C2, and C3) and inoculated treatments(T1,T2, and T3). Table S2. Functional enrichment and annotation of the top 25 significant DEG (p cal-value &lt;0.05; pcal-value &lt;0.01, and p adj- value &lt;0.05) and upregulated (FC &gt;1) structured around the three ontological terms including biological process, molecular function, cellular component, and KEGG pathways. The PPI network was constructed based on high confidence interval with 10 additional nodes from database with significant enrichment value PPI enrichment (p-value &lt; 1.0e-16). Table S3. Functional enrichment and annotation of the top 25 significant DEG (pcal-value &lt;0.05; pcal-value &lt;0.01, and padj-value &lt;0.05) and down-regulated (FC &lt;1) structured around the three ontological terms including biological process, molecular function, cellular component, and KEGG pathways. The PPI network was constructed based on high confidence interval with 10 additional nodes from database with significant enrichment value PPI enrichment (p-value &lt; 1.0e-1).