Table 3.
Functional annotation of clusters derived from untreated and LPS treated F2 BMDM.
| Cluster Number (number of nodes) | Expression pattern | Representative genes | Enhanced terms (P value) |
|---|---|---|---|
| 001 (1396) | Unchanged by LPS | ACTA2, ADAMTSs, ASPH, COL1A1, COL1A2, FBN1, FN1, MFAPs, TGFB3, TGFBR2/3, THBS1, THBS2 | Protein processing in endoplasmic reticulum (5.5E-10); Poly(A) RNA binding (3.2E-8); Extracellular matrix (1.6E-6); Endoplasmic reticulum (8.7E-6); ER-Golgi transport (7.5E-5); Focal adhesion (1.5E-4) |
| 002 (485) | Unchanged by LPS | COL9A1, COL10A1, COL11A1, FGFRs, FOXO6, IRX5/6, MEF2A/B/C, PAX3, RUNX2, SIX2/3, SMAD1, SOX5/8/9 | Extracellular matrix (0.003); Secreted (0.007); Glycoprotein (0.012); Signal (0.038) |
| 003 (389) | Up with LPS | ATF3, BHLHE40, CD274, CEBPB, FOSL2, GGCL1, GVIN1, IFIT5, IFIH1, IRF1, IRF8, IRF9, OASL, SOCS1 | Zinc finger, RING/FYVE/PHD-type (0.02); Influenza A (0.01) |
| 004 (259) | Unchanged with LPS | CPSF2, DDX6, LEO1, PAPD5, PAPOLA, PARN, PRPF38B, PRPF39, PRPF40A, PRPF6, SMU1, TOP2B, TOP3B, TOPBP1 | Spliceosome (2.4E-9); Cytoplasmic mRNA processing body (0.0004) |
| 005 (168) | Down with LPS | C3AR1, CD14, FAAH, MAOA, PEX16, PSEN2, TNFAIP8L1, TUBB1 | Transmembrane helix (0.1); Aldolase-type TIM barrel (0.07) |
| 006 (167) | Unchanged by LPS | BUB1, BUB1B, BUB3, centromere protein genes, kinesin genes, kinetochore complex components | Cell cycle (4.9E-14); Mitosis (9.8E-13); Cell division (2.3E-11); Centromere (8.3E-11) |
| 007 (160) | Unchanged by LPS | RPL and RPS genes, translation initiation and elongation genes | Structural constituent of ribosome (3.6E-81); Ribosome (4.7E-79); Translation (1.2E-68); Protein biosynthesis (1.8E-7) |
| 008 (137) | Up with LPS | BACH1, IRF6, KLF8, MAFK, REL, TLR15 | No significant enrichment |
| 009 (100) | Down with LPS | IGF2, KLF3, KLF13, MAF1, TAF12 | No significant enhancement |
| 010 (76) | Unchanged by LPS | AAR2, CNOT10, EXOC1, GABPA, POLR1A | RNA recognition motif (0.002) |
| 011 (71) | Unchanged by LPS but one animal very high | ACTG2, CDH11, COL7A1, ENPP2/3, FGF7, NPY, PDGFRA, VAV2 | Calcium ion binding (0.2) |
| 012 (65) | No trend with LPS | All unannotated ENSGALG | |
| 013 (59) | Up with LPS | CCL4, BATF6, FLT1, IL13RA1, IL1B, NFKB1, NFKB2, NFKBIA, TRAF2, TRAF3, ZC3H12A | Toll-like receptor signaling pathway (0.0005); Cytosolic DNA sensing pathway (0.001); RIG-I-like receptor signaling pathway (0.001); Inflammatory response (0.01) |
| 014 (57) | Up with LPS | CCNE1, FMR1, SMCHD1, TRAF6, USP16 | Cell cycle (0.1) |
| 015 (57) | Down with LPS | Mostly unannotated ENSGALG and LOC genes | No significant enhancement |
| 016 (52) | Down with LPS | ATP6AP1, ATP6AP2, ATP6V0D1, CASP9 | No significant enrichment |
| 017 (52) | Unchanged with LPS | ACTR1A, COG5, E4F1, EIF2AK4, INSIG2 | No significant enrichment |
| 018 (52) | Variable response to LPS | All unannotated ENSGALG | |
| 019 (51) | Variable response to LPS | ACOD1 (IRG1), IRF2, MAP2K3, TAOK1, TBK1, USP15 | Protein ubiquitination involved in ubiquitin-dependent protein catabolic process (0.01) |
| 020 (45) | Unchanged with LPS | CCT genes, HSP genes | Positive regulation of protein localization to Cajal body (1.5E-10); Chaperonin TCP-1, conserved site (4.7E-10); Positive regulation of establishment of protein localization to telomere (2.7E-10); Chaperone (2.1E-9) |
| 021 (45) | Down with LPS in most | CSF1R, IL2RG, IL6R, TLR4 | No significant enrichment |
Benjamini Hochberg corrected P values are presented. First 21 clusters only as number of genes becomes too low for meaningful analysis in smaller clusters. This analysis used DAVID (https://david.ncifcrf.gov/home.jsp) to determine enrichment for annotation terms.