Progenitor Identity Program
Gene co-expression module in Goblet cells
| Category | Epithelial development |
|---|---|
| Genes | 12 |
| Annotation certainty | 4 of 5 |
| Annotation consistency | 8 of 12 genes have a known function matching the annotation |
Why this annotation
The top hub genes define a transcription factor network associated with intestinal stem/progenitor identity: SOX4 (progenitor TF), MEX3A (RNA-binding protein marking intestinal stem cells), TEAD2 (YAP/TAZ-TEAD Hippo pathway, active in progenitors), and NOTCH1 (essential for goblet cell specification and crypt progenitor maintenance). NREP is associated with regeneration. APEX1 supports DNA repair in proliferating/progenitor cells. MAP4K4 is a stress-activated kinase. The extremely strong downregulation in both UC and CD inflammation (delta ~-0.94) and robust restoration with CD treatment and UC remission is consistent with loss of progenitor/stem identity in inflamed goblet cells. Core coherence with all genes uniform supports a single tight program.
Genes
APEX1, FAM89B, MAP4K4, MEX3A, NOTCH1, NREP, RNF186, SOX4, TEAD2, TEX45, TMEM132A, TMEM35A
Most correlated modules
- Lipid Redox Homeostasis · correlation 0.91
- Chromatin Remodeling · correlation 0.84
- Chromatin RNA Regulation · correlation 0.84
- Colonocyte Metabolic Defense · correlation 0.83
- Epithelial Maintenance · correlation 0.80
- Chromatin Remodeling · correlation 0.78
- RNA Decay Processing · correlation 0.71
- mRNA Translation Initiation · correlation 0.69
Module annotations were drafted by a large language model from the module's genes, then reviewed and approved by a domain expert. See sources & licences.