Additional file 1 of Systematic characterization of Brassica napus UBC13 genes involved in DNA-damage response and K63-linked polyubiquitination
Bibliographic record
Abstract
Additional file 1: Table S1. The characteristics of identified Brassica napus UBC13 genes and gene products. Table S2. Saccharomyces cerevisiae strains. Table S3. Primers used to amplify BnUBC13 genes. Fig. S1. A flowchart outlining experimental designs of this study. Fig. S2. Synteny analysis of UBC13 family genes among Arabidopsis thaliana, Brassica napus, B. rapa and B. oleracea. Identified gene pairs were displayed by circos plots ( http://circos.ca/ ). All chromosomes from four species are indicated by blocks scaled by chromosome length with chromosome names. The UBC13 family genes and chromosomes from different species are indicated by different colors: red, A. thaliana; yellow, B. napus; purple, B. rapa and green, B. oleracea. Synteny gene pairs are linked by lines: pink, genes with a close relationship to AtUBC13A; brown, genes with a close relationship to AtUBC13B. For gene ID from B. rapa, the species name “_BraROA” is omitted to reduce the length for plotting. Fig. S3. Original images of (A) Fig. 6A and (B) Fig. 6B. Fig. S4. Original images of (A) Fig. 8A and (B) Fig. 8B.
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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 | 0.009 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.003 | 0.004 |
| Science and technology studies | 0.002 | 0.000 |
| Scholarly communication | 0.002 | 0.002 |
| Open science | 0.003 | 0.001 |
| Research integrity | 0.001 | 0.002 |
| Insufficient payload (model declined to judge) | 0.838 | 0.207 |
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".