Transcriptomic analysis of the program mediating enterocyte differentiation by HNF4, GATA4, or CDX2 in the rat ileal crypt cell line IEC‐6
Bibliographic record
Abstract
HNF4α (H), GATA4 (G), and CDX2 (X) are transcription factors (TF) proposed as central regulators of enterocyte differentiation. We studied the impact of these TF on enterocytes using stable IEC‐6 cell lines expressing H, G, or X. H increased microvilli density when grown on Matrigel and increased lipid/apolipoprotein synthesis. X‐cells had columnar morphology while G‐cells were larger and formed multiple layers at confluence. Array analysis on RNA from confluent cell lines (Affymetrix Rat 230 2.0 GeneChips, n=3/line) revealed many changes for each TF vs. control IEC‐6: at 1% false detection rate H, 3767 (52% up); G, 2409 (55%); X, 1977 (34%). Common transcript signatures may be due to cross‐regulation of the TF: H increased G (3.4x) and X (2.7x) mRNA; X increased H mRNA (2.1x) and protein; G increased X mRNA (3x) but suppressed H mRNA (70%). Cluster analysis revealed unique TF responses. Functional analysis showed that H increased lipid metabolism and tight junction transcripts, reduced cell cycle transcripts, and altered matrix protein transcripts. G reduced cell cycle and tight junction transcripts but increased those for apoptosis. X increased glycolysis and clathrin‐coated vesicle transcripts but reduced those for MAPK signaling and Golgi vesicle transport. Our data suggest that individual TF are critical drivers for specific enterocyte phenotypes. Supported by Showalter Trust (JCF), NSERC and CCFC (CA).
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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 | 0.000 | 0.000 |
| 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".