Additional file 1 of The application of epiphenotyping approaches to DNA methylation array studies of the human placenta
Notice bibliographique
Résumé
Additional file 1: Fig. S1. Sample map for EPIC array processing. Depiction of sample distribution across Illumina Infinium MethylationEPIC array chips, colored by randomization variables (sex, SSRI exposure status, COSMOSS stress score, replicate status, trimester, cell type). Chips are grouped by batch. Fig. S2. Heatmap of the strength of association between pairs of covariates. R2 values of linear models run on Covariate ~ Covariate demographic variables. “Ethn” denotes ethnicity, “P(African/Asian/European)” refer to the continuous PlaNET ancestry probabilities, “SD” refers to standard deviation, “wt” refers to weight, “GA” refers to gestational age at birth, “Cyto” refers to cytotrophoblast, and “nRBC” refers to nucleated red blood cells. Fig. S3. Relationship between processing time and cell type proportions. (A) Placental processing time in hours after delivery (Proc time) is plotted along the Y axis, with cohort plotted along the X axis. (b) Estimates of cell type proportions (Y axis) were plotted against placenta processing time (hours) from all cohorts. Significant Pearson correlations (Estimate ~ Cell Type) are indicated with p < 0.05 in the figure legend. (C) Samples from the V-SSRI cohort were excluded, to evaluate the impact of processing time on cell type proportions independent of the few samples in V-SSRI with unusually long processing times. Significant Pearson correlations are indicated with p < 0.05 if the figure legend. Fig. S4. Relationship between cell type proportions and sex, self-reported maternal ethnicity, and PlaNET ancestry. (A, C, E) All Cohorts, (B,D,F) Vancouver-collected cohorts only, QF2011 cohort excluded. Significance of comparisons are indicated when p < 0.05. Fig. S5. Relationship between cell type proportions and placental to fetal weight ratio and residual. (A) Fetal to placental weight ratio association with cell type proportions. Significant correlations are indicated with p < 0.05 in the legend. (B) Residual of fetal weight regressed on placental weight showed no significant association with any cell type proportion. Fig. S6. Distribution of all nominal p values for linear models run with adjustment for epiphenotype variables. “Base” refers to the base linear model of DNAme ~ Cohort + Sentrix Position + Sex + ε. Additional models refer to the base model plus the specified additive covariate. For example, GA (gestational age) refers to DNAme ~ Cohort + Sentrix Position + Sex + GA + ε. P values investigated are those associated with the term “Cohort”. RRPC indicates robust refined placental clock, Ancestry refers to adjustment for PlaNET ancestry continuous values, Cells refers to adjustment for continuous PlaNET cell composition estimates. Listing > 1 variable indicates additive adjustment for all indicated variables (such as adjustment for both ancestry and cell composition as indicated by the notation Ancestry_Cells). A horizontal dashed line indicates p = 0.05. The p values shown in this plot arise from linear models run on V-SSRI and V-NORM (n = 99) at all filtered autosomal CpGs. Table S1. Lambda values from linear models for differential DNAme by Cohort. Lambda was calculated in each case from all nominal p values associated with the Cohort term in each model. GA refers to gestational age, RRPC refers to the robust refined placental clock gestational age, Ancestry and Cell Types refer to the PlaNET epiphenotype variables for ancestry and cell composition, included as continuous additive covariates.
Récupéré en direct depuis OpenAlex et désinversé. Les résumés ne sont pas conservés dans cette base de données : les index inversés représentent 8,6 Go des 9,3 Go de texte de la base, et le serveur dispose de 13 Go libres.
Comment cette classification a été obtenuedéplier
Prédiction machine sur la base complète
Imitation des enseignantsNi prévalence calibrée, ni vérité terrain. Validation humaine à venir. Le volet Gemma est une étiquette directe du modèle pour chaque travail de la base, lue sur la notice réduite au titre. Le volet Codex est un classifieur appris des 10 348 étiquettes directes de Codex et calibré sur les taux pondérés de l'échantillon; les champs sans appui suffisant ne portent aucun appel Codex. Le mode candidate est l'union des deux volets; le consensus est leur intersection. Ces sorties portent le statut machine_predicted_unvalidated et ne sont pas des étiquettes humaines.
Scores du classifieur distillé par catégorie (deux têtes)
| Catégorie | Codex | Gemma |
|---|---|---|
| Métarecherche | 0,003 | 0,029 |
| Méta-épidémiologie (sens strict) | 0,002 | 0,001 |
| Méta-épidémiologie (sens large) | 0,002 | 0,001 |
| Bibliométrie | 0,003 | 0,004 |
| Études des sciences et des technologies | 0,001 | 0,000 |
| Communication savante | 0,002 | 0,001 |
| Science ouverte | 0,003 | 0,001 |
| Intégrité de la recherche | 0,001 | 0,001 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,883 | 0,197 |
Scores machine (provisoires)
Les deux têtes enseignantes du modèle étudiant, lues sur ce travail. Un score ordonne la base pour la relecture; il n'affirme jamais une catégorie, et le statut de validation accompagne chaque rangée tel quel.
Scores de référence d'un modèle non mature (critères de maturité non atteints, 7 itérations). Un score ordonne; il n'affirme jamais une catégorie.
score_only:v0-immature-baseline · tel quel depuis la passe de notation : score_only signifie que le nombre peut ordonner les travaux, et qu'aucune étiquette de catégorie n'en découleClassification
machine, non validéePrédiction automatique; un appel candidat d’une seule source (Gemma direct ou Codex distillé), pas un consensus.
Le détail, modèle par modèle et score par score, se trouve en fin de page sous « Comment cette classification a été obtenue ».