Autophagy Vesicle Trafficking
Gene co-expression module in Macrophages
| Category | Lysosomal & pahgocytosis |
|---|---|
| Genes | 35 |
| Annotation certainty | 2 of 5 |
| Annotation consistency | 11 of 35 genes have a known function matching the annotation |
Why this annotation
Hub genes: CHD1 (chromodomain helicase DNA binding protein 1, chromatin remodeling), MALT1 (mucosa-associated lymphoid tissue lymphoma translocation gene 1 — paracaspase, NF-κB activation in immune cells including macrophages), WDR45B (WIPI3, autophagy PI3P effector), ATG2A (autophagy-related 2A, autophagosome formation), NFIL3 (E4BP4 — circadian clock TF and macrophage differentiation/survival factor), STX11 (syntaxin-11, SNARE protein for vesicle fusion, critical in macrophage/NK cell cytotoxic degranulation), RAB20 (Rab GTPase, endosomal/phagosomal trafficking), ARFGAP3 (ARF1 GAP, Golgi vesicle trafficking), LPCAT1 (lysophosphatidylcholine acyltransferase, membrane phospholipid remodeling), ERCC6 (CSB, DNA repair helicase), RANBP2 (nuclear pore/SUMOylation). The module combines autophagy (WDR45B, ATG2A), vesicle/phagosomal trafficking (STX11, RAB20, ARFGAP3), and transcriptional regulation (CHD1, NFIL3, MALT1). The autophagy-vesicle trafficking theme is the most coherent signal in the macrophage context, with NFIL3 adding macrophage differentiation context.
Genes
ADNP2, AGO2, AP1G1, ARFGAP3, ATG2A, BANP, CHD1, CHD2, ERCC6, FAM107B, GPBP1, LPCAT1, MALT1, NFIL3, PDE4A, PLEKHG2, PNPLA8, PPP4R3A, RAB11FIP1, RAB20, RANBP2, RILPL2, SAMD8, SCML1, SLC8B1, STK17B, STX11, SYAP1, TENT4B, TPRA1, WDR45B, YPEL5, YTHDC1, ZNF394, ZRANB1
Most correlated modules
- Transcriptional Repression · correlation 0.95
- NF-κB AP-1 Signaling · correlation 0.95
- Epigenetic Remodeling · correlation 0.95
- Ubiquitin-Proteasome Regulation · correlation 0.93
- NF-κB Inflammatory Activation · correlation 0.93
- Transcriptional Regulation · correlation 0.92
- ER-Golgi Trafficking · correlation 0.91
- mRNA Splicing Processing · correlation 0.90
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.