Additional file 3 of Sex-based disparities in DNA methylation and gene expression in late-gestation mouse placentas
Bibliographic record
Abstract
Additional file 3: Figure S1. Expression of Y chromosome genes in male placentas A) Differential expression analysis of Y chromosome genes in male and female E18.5 placentas (n = 121). Colored dots represent statistically significant DEGs (p < 0.05; n = 7) B) Expression levels (z-scores) of the Y chromosome DEGs. Figure S2. DEG abundance in male and female placentas A–B) MA plot of the differential expression (log2 fold change) values of normalized read counts and their average expression levels in A) male and B) female E18.5 placentas. The plots include all analyzed genes (left; n = 29,480); genes with read counts > 10,000 (middle; n = 29,165 and 29,160 in male and female placentas, respectively), and genes with read counts > 100 (right; n = 18,160 and 18,173 in male and female placentas, respectively). Colored dots represent significant DEGs on autosomes (pink) and X chromosomes (blue). The dotted black rectangle indicates the subset of the graph shown on the right. C) Differential expression values of each analyzed gene) in male and female placentas relative to their promoter’s GC content (%). Significant DEGs on autosomes and X chromosomes are shown in pink and blue, respectively. Figure S3. DMRs occur throughout the E18.5 placenta genome but are concentrated on the X chromosomes A) DNA methylation levels of a random subset of tiles in the individual male and female placenta samples. B) Mean DNA methylation levels within ± 15 kb of a transcriptional start site (TSS) or transcriptional end site (TES) in all analyzed tiles from male and female placentas. C) Distributions of the DNA methylation levels of various chromosomes in male and female placentas. Median DNA methylation values are indicated with diamonds. D) DNA methylation levels in tiles associated with autosomes (top) and X chromosomes (bottom) in male and female placentas. ****p < 0.0001, ***p < 0.001 by two-proportion z-test. E) Average DNA methylation levels in tiles associated with various genomic features on the autosomal (top) and X (bottom) chromosomes of male and female placentas. Figure S4. DNA methylation sex differences in various genomic elements A) DNA methylation levels of top changed genes on the autosomes (left) and X chromosomes (right) of male and female placentas. B) Distributions of autosomal (pink) and X chromosome (blue) DMRs located in various genomic elements in male and female placentas. C) Average DNA methylation levels of DMRs in autosomes (left) and X chromosomes (right) based on their location’s genomic annotation. Figure S5. DNA methylation and expression patterns of genes essential for placental development A) DNA methylation levels of autosomal (left) and X chromosomal (right) tiles associated with key placental developmental genes in male and female E18.5 placentas. B) DNA methylation levels of autosomal and X chromosomal DMRs associated with placental development genes in male and female placentas. C) Distributions of all analyzed tiles and DMRs located in essential placental development genes on the autosomes and X chromosomes. D) Distributions of individual placenta developmental genes on the autosomes and X chromosomes in the analyzed tiles and DMRs. E) DNA methylation levels of selected placenta developmental gene-related DMRs in male and female placentas. F) The top five pathways enriched for the placental development-associated DMRs in B). G) Expression levels (z-scores) of differentially expressed essential placental development genes.
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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 | 0.016 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.002 |
| Bibliometrics | 0.002 | 0.004 |
| Science and technology studies | 0.002 | 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) | 0.838 | 0.144 |
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".