Association network modeling from microarray data around fermentation stress response gene NSF1 (YPL230W) using significantly co-expressed gene set
Bibliographic record
Abstract
NSF1 is one of the newly discovered fermentation stress response proteins that play a crucial role in the adaptation of the yeast Saccharomyces cerevisiae to fermentation stress conditions. Using time course microarray gene expression profiles of Saccharomyces cerevisiae (DBY7286) grown in YPD media, we identified and mapped genes significantly correlated to the NSF1 expression, hence producing a framework of analysis conditioned on the NSF1 gene function. From the analysis, we developed a novel approach using clustering on the correlated variable that constructed a core set of co-expressed genes. The result is an inter-associated gene network conditioned on the expressed NSF1 gene. The complete-link clustering algorithm grouped the NSF1 associated genes into functional clusters with a high degree correspondence to known metabolic pathways. Co-expressed genes to formed distinct functional chromosomal neighborhoods.
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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 | 0.002 | 0.004 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| 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".