Additional file 2 of Monocyte, neutrophil, and whole blood transcriptome dynamics following ischemic stroke
Bibliographic record
Abstract
Additional file 2: Supplemental Figure 1. Percentage of DEGs classified per biotype. For every time point and comparison between time points, the percentage of biotype categories for DEGs are shown in the bar plots and corresponding table for (A) monocytes, (B) neutrophils and (C) whole blood. Ig: immunoglobulin; TcR: T-cell receptor; TEC: To be Experimentally Confirmed. Supplemental Figure 2. Predicted upstream regulators for monocytes. (A) Venn diagram represents all upstream regulators predicted at 0-24 h, 24-48 h, and >48 h (Fisher’s p-value<0.05). (B) Top over-represented regulators common to all time points (Fisher’s p-value<0.05). (C) Top over-represented regulators that are specific for each time point (Fisher’s p-value<0.05). Up arrows indicate predicted significant activation (z ≥ 2) or down arrow - significant inhibition (z ≤ −2). White cells indicate no direction can be predicted. (*= Benjamini-Hochberg corrected p-value<0.05). R: receptor; N.R: nuclear receptor. Supplemental Figure 3. Predicted upstream regulators for neutrophils. (A) Venn diagram represents all upstream regulators predicted at 0-24 h, 24-48 h, and >48 h (Fisher’s p-value<0.05). (B) Top over-represented regulators shared at all time points (Fisher’s p-value<0.05). (C) Top over-represented regulators that are specific for each time point (Fisher’s p-value<0.05). Up arrows indicate predicted significant activation (z ≥ 2) or down arrow - significant inhibition (z ≤ −2). White cells indicate no direction can be predicted. (*= Benjamini-Hochberg corrected p-value<0.05). R: receptor; endo: endogenous; reg: regulator. Supplemental Figure 4. Predicted upstream regulators for whole blood. (A) Venn diagram represents all upstream regulators predicted at 0-24 h, 24-48 h, and >48 h (Fisher’s p-value<0.05). (B) Only 2 predicted regulators (Fisher’s p-value<0.05) are shared for the 3 time points. (C) Top over-represented regulators that are specific for each time point (Fisher’s p-value<0.05). Up arrows indicate predicted significant activation (z ≥ 2) or down arrow - significant inhibition (z ≤ −2). White cells indicate no direction can be predicted. R: receptor; reg: regulator; endo: endogenous. Supplemental Figure 5. tPA administration is not associated with differential expression. A) Characteristics of the five cases where tPA was administered. Principal Component Analyses (PCA) using the DEGs from the time points 0-24 and >24 h in LV and SV strokes in B) monocytes, C) neutrophils, and D) whole blood samples. Cases where tPA was administered are colored in orange. Supplemental Figure 6. Co-expression network construction. WGCNA Soft-thresholding power scale free topology fit (left panel) and mean connectivity (right panel) plots for all genes analyzed in (A) monocytes, (B) neutrophils and (C) whole blood. Reference lines are at 0.8 (red) and 0.9 (green) on the left panels and at 100 (red) and 200 (green) on the right panels. Supplemental Figure 7. Workflow of the study. Monocytes and neutrophils were isolated by flow cytometry (scatter plots adapted in part from Carmona-Mora et al. [18]. RNA-seq from the isolated cell samples and whole blood was used for two parallel approaches: differential expression and co-expression networks. For the first one, patients were split into time point groups and self-organizing maps were constructed with the differentially expressed genes. For the construction of co-expression networks, time was considered as a continuous variable.
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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 | 0.009 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.002 | 0.003 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.002 | 0.001 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.002 | 0.001 |
| Insufficient payload (model declined to judge) | 0.780 | 0.141 |
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".