Bioinformatic Analyses for Nitrogen Responsive Transcriptome and De Novo Regulatory Motif Discovery in Potato «Solanum tuberosum»
Bibliographic record
Abstract
Nitrogen is an essential nutrient for plant growth and development, but high usage of nitrogen-based fertilizers can have adverse effects on crops, the environment, and the economy.To discover nitrogen responsive molecular mechanisms that could be used to develop nitrogen efficient potato varieties and optimal nitrogen fertilizer management strategies, differentially expressed genes were identified in the transcriptomes of tuber and leaf tissue from three commercial cultivars of potato S. tuberosum L. Solanaceae (Russet Burbank, Atlantic and Shepody).The upstream sequences of the differentially expressed genes were used with two de novo regulatory motif discovery algorithms (Seeder and Homer2), to pinpoint potential cis-regulatory element(s) most likely to be responsible for nitrogen response.The results confirm findings from an earlier study on the leaf as well as identifies novel tuberspecific genes and cis-regulatory motifs that are involved in response mechanisms, as well as nitrogen metabolism expressed in both tissue types.First of all, I would like to acknowledge my supervisor Dr.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.002 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.000 | 0.001 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.000 | 0.001 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.000 | 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 teacher head, 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".