TABLE 2.
Reactome pathway enrichment analysis. Statistically significant pathways are summarized for primary B cell DN community C2 and C4. In the full analysis, we omitted small communities with fewer than 8 genes Reimand et al. (2019); Gene Set Enrichment Analysis (2022), and 14 communities (C0 to C13) qualified for the pathway analysis.
| Pathway Name | Entities FDR | Submitted entities found |
|---|---|---|
| B cell DN: C2 | ||
| Peptide chain elongation | 1.3E-06 | EEF1A1, RPL4, RPL7A, RPL27A, RPS6, RPL36, RPL14, RPS20, RPL15, FAU, UBA52, RPL28 |
| Response of EIF2AK4 (GCN2) to amino acid deficiency | 1.3E-06 | RPL4, RPL7A, RPL27A, RPS6, RPL36, RPL14, RPS20, FAU, RPL15, UBA52, RPL28, ATF3 |
| Eukaryotic Translation Elongation | 1.6E-06 | EEF1A1, RPL4, RPL7A, RPL27A, RPS6, RPL36, RPL14, RPS20, RPL15, FAU, UBA52, RPL28 |
| GTP hydrolysis and joining of the 60S ribosomal subunit | 5.9E-06 | RPL4, EIF4A1, RPL7A, RPL27A, RPS6, RPL36, RPL14, RPS20, RPL15, FAU, UBA52, RPL28 |
| L13a-mediated translational silencing of Ceruloplasmin expression | 5.9E-06 | RPL4, EIF4A1, RPL7A, RPL27A, RPS6, RPL36, RPL14, RPS20, RPL15, FAU, UBA52, RPL28 |
| Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) | 5.9E-06 | RPL4, RPL7A, RPL27A, RPS6, RPL36, RPL14, RPS20, RPL15, FAU, UBA52, RPL28 |
| Formation of a pool of free 40S subunits | 7.7E-06 | RPL4, RPL7A, RPL27A, RPS6, RPL36, RPL14, RPS20, RPL15, FAU, UBA52, RPL28 |
| Eukaryotic Translation Termination | 7.7E-06 | RPL4, RPL7A, RPL27A, RPS6, RPL36, RPL14, RPS20, RPL15, FAU, UBA52, RPL28 |
| Cap-dependent Translation Initiation | 9.2E-06 | RPL4, EIF4A1, RPL7A, RPL27A, RPS6, RPL36, RPL14, RPS20, RPL15, FAU, UBA52, RPL28 |
| Eukaryotic Translation Initiation | 9.2E-06 | RPL4, EIF4A1, RPL7A, RPL27A, RPS6, RPL36, RPL14, RPS20, RPL15, FAU, UBA52, RPL28 |
| B cell DN: C4 | ||
| Metabolism of RNA | 1.4E-02 | SF3B4, MT-ND6, NUP205, UTP3, POP1, DDX23, CSTF2, PHAX, PLRG1, DIEXF, ZFP36L1, FTSJ3, CHERP, PSMD8, EFTUD2, PSMD9, PSMC4, PSME3, NUP35, SKIV2L2 |
| Mitotic Anaphase | 1.4E-02 | PSMD8, PSMD9, NUP205, CCNB1, SPAST, PSMC4, PSME3, NUP35, SMC1A, EMD, KPNB1 |
| Mitotic Metaphase and Anaphase | 1.4E-02 | PSMD8, PSMD9, NUP205, CCNB1, SPAST, PSMC4, PSME3, NUP35, SMC1A, EMD, KPNB1 |
| FCERI mediated NF-kB activation | 1.4E-02 | IGLV2-11, PSMD8, PSMD9, IGKV2-29, IGKV1-16, PSMC4, PSME3, IGKV4-1 |
| Signaling by the B Cell Receptor (BCR) | 1.4E -02 | IGLV2-11, PSMD8, PSMD9, IGKV2-29, IGKV1-16, PSMC4, PSME3, IGKV4-1, PIK3AP1 |
| Fc epsilon receptor (FCERI) signaling | 1.4E-02 | IGLV2-11, PSMD8, PSMD9, IGKV2-29, IGKV1-16, PSMC4, PSME3, IGKV4-1 |
| Host Interactions of HIV factors | 1.4E-02 | PSMD8, PSMD9, NUP205, PSMC4, PSME3, NUP35, KPNB1 |
| G1/S Transition | 1.4E-02 | PSMD8, PSMD9, CCNB1, MCM7, PSMC4, PSME3, KPNB1 |
| ABC-family proteins mediated transport | 1.4E-02 | PSMD8, PSMD9, PSMC4, PSME3, CSTF2, EIF2S1 |
| Assembly of the pre-replicative complex | 1.4E-02 | PSMD8, PSMD9, MCM7, PSMC4, PSME3 |