Additional file 2 of Risk-focused differences in molecular processes implicated in SARS-CoV-2 infection: corollaries in DNA methylation and gene expression
Bibliographic record
Abstract
Additional file 2: Fig S1. Violin plots of sex-biased gene expression in NLRP2. Expression in blood was quantified as transcript counts (GTEx). Fig S2. Violin plots of sex-biased gene expression in XIST. (A)Expression in nasal epithelia was measured as log2 normalized values (GEO). (B)Expression in lung was quantified as transcript counts (GTEx). (C)Expression in blood was quantified as transcript counts (GTEx). Fig S3. Box plots of the three validated CpG sites (GPX1, ERC1 and TLE1) differentially methylated by sex in three tissues from the repeated exposure data set. Unadjusted DNA methylation values (β) were plotted on the y axis with CpG sites on the x axis. Genomic positions of the CpG sites are indicated below the respective plots. Fig S4. Box plots of the three validated CpG sites (GPX1, ERC1 and TLE1) differentially methylated by sex in blood. Unadjusted DNA methylation values (β) were plotted on the y axis against the CpG sites on the x axis, with genomic locations of the CpG sites plotted below the respective plots. Fig S5. Bar plots of age distributions in airway epithelia and nasal epithelia. Age group in years is indicated on the y axis while the x axis represents the number of males and females. Fig S6. Box plots of the three validated CpG sites (GPX1, ERC1 and TLE1) differentially methylated by sex across the age groups in airway epithelia and nasal epithelia. Unadjusted DNA methylation values (β) were plotted on the x axis with age groups in years on the y axis. Genomic positions of the CpG sites are represented below the respective plots. Fig S7. Box plots of the CpG sites that are differentially methylated by COVID-19 status in males (A) and in females (B). Unadjusted DNA methylation values (β) were plotted on the y axis and the box plots are colored by COVID-19 status.
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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 | 0.002 | 0.029 |
| 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 | 0.002 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.002 | 0.001 |
| Insufficient payload (model declined to judge) | 0.865 | 0.132 |
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".