Endosomal Vesicle Trafficking
Gene co-expression module in Macrophages
| Category | Vesicular traficking |
|---|---|
| Genes | 57 |
| Annotation certainty | 2 of 5 |
| Annotation consistency | 11 of 57 genes have a known function matching the annotation |
Why this annotation
Among the top hub genes, PICALM (clathrin assembly lymphoid myeloid protein, endocytosis), DNM2 (dynamin-2, membrane fission/endocytosis), ARFGEF1 (ARF guanine nucleotide exchange factor, vesicle budding), TRAPPC8 (TRAPP tethering complex, ER-to-Golgi trafficking), AP3B1 (AP-3 adaptor complex beta subunit, lysosomal/endosomal sorting), SCFD1 (Sec1/Munc18 family, vesicle docking/fusion) and DNAJC5 (cysteine string protein, vesicle exocytosis chaperone) collectively define a vesicular trafficking program. USP15 and USP4 (deubiquitinases), PIAS1 (SUMO E3 ligase), MARCHF6 (membrane-associated RING-CH E3 ligase), and ARID1B (SWI/SNF) add ubiquitin/SUMO regulatory components. GSK3B and CNOT4 (CCR4-NOT deadenylase) are additional regulators. The vesicular trafficking theme is the most coherent signal, consistent with macrophage endocytic/phagocytic function.
Genes
ADAM17, AP3B1, ARFGEF1, ARID1B, ARK2N, ASAP1, ATF6, ATP11A, CDC73, CNOT4, CPEB4, CPNE8, CTBP2, CUL3, DCAF1, DNAJC5, DNM2, EIF4G3, FAM222B, GALNT2, GLG1, GPBP1L1, GSK3B, HIPK3, KANSL1, KPNA1, LCOR, MAPKAP1, MARCHF6, NCOA6, NEK7, NT5C2, NUP98, OPA1, OXSR1, PDLIM5, PIAS1, PICALM, PLXDC2, PSEN1, PUM2, RASA2, RNF38, SMCHD1, TAOK3, TLK1, TRAPPC8, TRPC4AP, TRPM7, TUT7, UBE2H, UBE3C, UBR1, USP15, USP4, VPS13D, ZFC3H1
Most correlated modules
- Rho GTPase Signaling · correlation 0.97
- Ubiquitin-Proteasome Regulation · correlation 0.97
- Transcriptional Regulation · correlation 0.97
- Epigenetic Remodeling · correlation 0.97
- Rho GTPase Signaling · correlation 0.97
- MITF Lysosomal Program · correlation 0.97
- Innate Immune Dampening · correlation 0.97
- Chromatin Remodeling · correlation 0.95
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.