Genome-Wide Detection of Gene Coexpression Domains Showing Linkage to Regions Enriched with Polymorphic Retrotransposons in Recombinant Inbred Mouse Strains
Bibliographic record
Abstract
Although gene coexpression domains have been reported in most eukaryotic organisms, data available to date suggest that coexpression rarely concerns more than doublets or triplets of adjacent genes in mammals. Using expression data from hearts of mice from the panel of AxB/BxA recombinant inbred mice, we detected (according to window sizes) 42-53 loci linked to the expression levels of clusters of three or more neighboring genes. These loci thus formed "cis-expression quantitative trait loci (eQTL) clusters" because their position matched that of the genes whose expression was linked to the loci. Compared with matching control regions, genes contained within cis-eQTL clusters showed much greater levels of coexpression. Corresponding regions showed: (1) a greater abundance of polymorphic elements (mostly short interspersed element retrotransposons), and (2) significant enrichment for the motifs of binding sites for various transcription factors, with binding sites for the chromatin-organizing CCCTC-binding factor showing the greatest levels of enrichment in polymorphic short interspersed elements. Similar cis-eQTL clusters also were detected when we used data obtained with several tissues from BxD recombinant inbred mice. In addition to strengthening the evidence for gene expression domains in mammalian genomes, our data suggest a possible mechanism whereby noncoding polymorphisms could affect the coordinate expression of several neighboring 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 | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.002 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
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".