Selection of GO terms enriched in the differentially regulated genes in rM versus naive and proinflammatory macrophages identified by VLAD analysis
| GO ID and GO term . | FDR0.001 and fold change > 2.0 (37 genes) . | FDR0.05 and fold change > 1.5 (342 genes) . | |||
|---|---|---|---|---|---|
| P . | k . | P . | k . | M . | |
| GO:0050896: response to stimulus | 1.90 × 10−6 | 19 | 5.23 × 10−11 | 110 | 5836 |
| GO:0007165: signal transduction | NA | NA | 1.35 × 10−4 | 64 | 3905 |
| GO:0010468: regulation of gene expression | NA | NA | 1.28 × 10−10 | 63 | 2570 |
| GO:0002376: immune system process | 4.19 × 10−7 | 9 | 1.19 × 10−16 | 43 | 908 |
| GO:0009966: regulation of signal transduction | 2.02 × 10−4 | 7 | 1.11 × 10−9 | 37 | 1142 |
| GO:0042981: regulation of apoptosis | 6.31 × 10−5 | 7 | 1.58 × 10−9 | 33 | 947 |
| GO:0002682: regulation of immune system process | 2.04 × 10−7 | 8 | 1.26 × 10−12 | 30 | 594 |
| GO:0010646: regulation of cell communication | 8.45 × 10−4 | 6 | 5.03 × 10−6 | 28 | 1042 |
| GO:0035556: intracellular signal transduction | NA | NA | 2.50 | 28 | 1004 |
| GO:0007049: cell cycle | NA | NA | 8.34 × 10−6 | 23 | 780 |
| GO:0030097: hemopoiesis | 1.79 × 10−5 | 5 | 4.57 × 10−10 | 19 | 300 |
| GO:0006952: defense response | 1.98 × 10−5 | 6 | 2.74 × 10−6 | 19 | 522 |
| GO:0031347: regulation of defense response | NA | NA | 5.80 × 10−9 | 17 | 276 |
| GO:0007155: cell adhesion | NA | NA | 7.09 × 10−4 | 16 | 610 |
| GO:0016477: cell migration | 7.10 × 10−4 | 4 | 9.65 × 10−6 | 15 | 373 |
| GO:0009611: response to wounding | 8.63 × 10−4 | 4 | 2.63 × 10−4 | 13 | 393 |
| GO:0050670: regulation of lymphocyte proliferation | 1.12 × 10−5 | 4 | 9.35 × 10−9 | 12 | 127 |
| GO:0034097: response to cytokine stimulus | 3.19 × 10−6 | 5 | 2.26 × 10−6 | 12 | 210 |
| GO:0030098: lymphocyte differentiation | 4.05 × 10−4 | 3 | 1.43 × 10−7 | 11 | 132 |
| GO:0001817: regulation of cytokine production | NA | NA | 1.05 × 10−4 | 11 | 263 |
| GO:0042110: T-cell activation | 5.22 × 10−4 | 3 | 2.81 × 10−6 | 10 | 144 |
| GO:0045087: innate immune response | 7.10 × 10−4 | 3 | 7.21 × 10−6 | 10 | 160 |
| GO:0002819: regulation of adaptive immune response | 5.31 × 10−8 | 5 | 4.25 × 10−8 | 10 | 92 |
| GO:0002697: regulation of immune effector process | NA | NA | 9.06 × 10−5 | 9 | 174 |
| GO:0030335: positive regulation of cell migration | 4.12 × 10−5 | 4 | 1.03 × 10−4 | 9 | 177 |
| GO:0019882: antigen processing and presentation | 3.19 × 10−9 | 5 | 7.23 × 10−8 | 8 | 53 |
| GO:0045088: regulation of innate immune response | NA | NA | 1.29 × 10−4 | 8 | 143 |
| GO:0001666: response to hypoxia | NA | NA | 1.07 × 10−5 | 8 | 101 |
| GO:0009615: response to virus | NA | NA | 1.75 × 10−5 | 8 | 108 |
| GO:0042113: B-cell activation | NA | NA | 2.60 × 10−4 | 6 | 85 |
| GO:0002690: positive regulation of leukocyte chemotaxis | 5.27 × 10−4 | 2 | 2.86 × 10−4 | 4 | 31 |
| GO ID and GO term . | FDR0.001 and fold change > 2.0 (37 genes) . | FDR0.05 and fold change > 1.5 (342 genes) . | |||
|---|---|---|---|---|---|
| P . | k . | P . | k . | M . | |
| GO:0050896: response to stimulus | 1.90 × 10−6 | 19 | 5.23 × 10−11 | 110 | 5836 |
| GO:0007165: signal transduction | NA | NA | 1.35 × 10−4 | 64 | 3905 |
| GO:0010468: regulation of gene expression | NA | NA | 1.28 × 10−10 | 63 | 2570 |
| GO:0002376: immune system process | 4.19 × 10−7 | 9 | 1.19 × 10−16 | 43 | 908 |
| GO:0009966: regulation of signal transduction | 2.02 × 10−4 | 7 | 1.11 × 10−9 | 37 | 1142 |
| GO:0042981: regulation of apoptosis | 6.31 × 10−5 | 7 | 1.58 × 10−9 | 33 | 947 |
| GO:0002682: regulation of immune system process | 2.04 × 10−7 | 8 | 1.26 × 10−12 | 30 | 594 |
| GO:0010646: regulation of cell communication | 8.45 × 10−4 | 6 | 5.03 × 10−6 | 28 | 1042 |
| GO:0035556: intracellular signal transduction | NA | NA | 2.50 | 28 | 1004 |
| GO:0007049: cell cycle | NA | NA | 8.34 × 10−6 | 23 | 780 |
| GO:0030097: hemopoiesis | 1.79 × 10−5 | 5 | 4.57 × 10−10 | 19 | 300 |
| GO:0006952: defense response | 1.98 × 10−5 | 6 | 2.74 × 10−6 | 19 | 522 |
| GO:0031347: regulation of defense response | NA | NA | 5.80 × 10−9 | 17 | 276 |
| GO:0007155: cell adhesion | NA | NA | 7.09 × 10−4 | 16 | 610 |
| GO:0016477: cell migration | 7.10 × 10−4 | 4 | 9.65 × 10−6 | 15 | 373 |
| GO:0009611: response to wounding | 8.63 × 10−4 | 4 | 2.63 × 10−4 | 13 | 393 |
| GO:0050670: regulation of lymphocyte proliferation | 1.12 × 10−5 | 4 | 9.35 × 10−9 | 12 | 127 |
| GO:0034097: response to cytokine stimulus | 3.19 × 10−6 | 5 | 2.26 × 10−6 | 12 | 210 |
| GO:0030098: lymphocyte differentiation | 4.05 × 10−4 | 3 | 1.43 × 10−7 | 11 | 132 |
| GO:0001817: regulation of cytokine production | NA | NA | 1.05 × 10−4 | 11 | 263 |
| GO:0042110: T-cell activation | 5.22 × 10−4 | 3 | 2.81 × 10−6 | 10 | 144 |
| GO:0045087: innate immune response | 7.10 × 10−4 | 3 | 7.21 × 10−6 | 10 | 160 |
| GO:0002819: regulation of adaptive immune response | 5.31 × 10−8 | 5 | 4.25 × 10−8 | 10 | 92 |
| GO:0002697: regulation of immune effector process | NA | NA | 9.06 × 10−5 | 9 | 174 |
| GO:0030335: positive regulation of cell migration | 4.12 × 10−5 | 4 | 1.03 × 10−4 | 9 | 177 |
| GO:0019882: antigen processing and presentation | 3.19 × 10−9 | 5 | 7.23 × 10−8 | 8 | 53 |
| GO:0045088: regulation of innate immune response | NA | NA | 1.29 × 10−4 | 8 | 143 |
| GO:0001666: response to hypoxia | NA | NA | 1.07 × 10−5 | 8 | 101 |
| GO:0009615: response to virus | NA | NA | 1.75 × 10−5 | 8 | 108 |
| GO:0042113: B-cell activation | NA | NA | 2.60 × 10−4 | 6 | 85 |
| GO:0002690: positive regulation of leukocyte chemotaxis | 5.27 × 10−4 | 2 | 2.86 × 10−4 | 4 | 31 |
k indicates the number of genes in the query set annotated to the GO term, or descendants of the GO term; M, number of genes in the background dataset annotated to the GO term, or descendants of the GO term; and NA, not applicable.
Supplemental Table 3 contains a full list of enriched GO terms and the list of the genes in the query set that are annotated to the GO terms. In this analysis, the regulation GO terms do not have a transitive relationship to the “parent” GO terms, so that there is not a complete overlap between the genes associated with GO:0030335: positive regulation of cell migration and those associated with GO:0016477: cell migration (supplemental Table 3).