Additional file 1 of Gene coexpression networks reveal molecular interactions underlying cichlid jaw modularity
Bibliographic record
Abstract
Additional file 1: Figure S1. Schematic depiction of the dissection strategy utilised in this study. Red dotted lines mark the cuts made. RNA from oral jaws (upper + lower) and the lower pharyngeal jaw were separately extracted. The dissection included the following tissues: bone, cartilage, teeth, muscle, tendons, fat, and blood vessels. Figure S2. Conditional coexpression analysis: fitting scale free topology to establish softpower for constructing the separate OJA and LPJA adjacency matrices. Softpower of 18 was chosen for both. Figure S3. Global coexpression analysis: fitting scale free topology to establish softpower for constructing jaw adjacency matrices with OJA and PJA data together. Softpower of 6 was chosen. Figure S4. Conditional coexpression analysis: Preservation of modules in the GCNs underlying oral (OJA) and lower pharyngeal jaws (LPJA). a Preservation of genes found in LPJA modules in the OJA coexpression network calculated by a Zsummary statistic based on a permutation test that takes into account the connectivity and density of genes in a module. Zsummary < 2 represents lack of preservation (dotted blue line). Zsummary between 2 and 10 implies moderate preservation. Zsummary > 10 supports strong preservation of module. b Visual representation of module preservation. Top: LPJA modules in the LPJA GCN. Bottom: LPJA modules in the OJA GCN. Figure S5. Global coexpression analysis: Gene co-expression network of the oral and pharyngeal jaws. Dendrograms produced by average linkage hierarchical clustering of 16,669 genes based on topological overlap matrix (TOM). Modules within the network were assigned colours based on the horizontal bar underneath the dendrogram. Figure S6. Global coexpression analysis: Barplot of mean trait-based gene significance across modules in the oral and pharyngeal jaw co-expression network. Figure S7. Global coexpression analysis: Per module gene significance and connectivity in the oral and pharyngeal jaw co-expression network and connectivity in the oral and pharyngeal jaw coexpression network. Figure S8. Global coexpression analysis: enriched pathways in Black and Purple species-specific gene expression modules.
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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 | 0.014 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.003 | 0.004 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.002 | 0.002 |
| Open science | 0.003 | 0.001 |
| Research integrity | 0.002 | 0.002 |
| Insufficient payload (model declined to judge) | 0.839 | 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".