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
Bibliographic record
Abstract
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 <0.05; pcal-value <0.01, and p adj- value <0.05) and upregulated (FC >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 < 1.0e-16). Table S3. Functional enrichment and annotation of the top 25 significant DEG (pcal-value <0.05; pcal-value <0.01, and padj-value <0.05) and down-regulated (FC <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 < 1.0e-1).
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.010 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.002 | 0.004 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.002 | 0.002 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.002 | 0.001 |
| Insufficient payload (model declined to judge) | 0.790 | 0.143 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".