Table 2.
Gene ontology and pathway classifications of genes regulated by PU.1 in pro-T cells.
| (A) Genes upregulated by PU.1 in CD25+ cells with gain of function, downregulated with sgRNA, relative to all genes expressed in cells | ||
|---|---|---|
| GO biological process complete (top 21) | Fold enrichment | Adjusted P-value |
| Peptidyl-tyrosine phosphorylation (GO:0018108) | 7.18 | 2.40E-02 |
| Myeloid leukocyte activation (GO:0002274) | 7.05 | 9.14E-03 |
| Reactive oxygen species metabolic process (GO:0072593) | 6.97 | 3.05E-02 |
| Regulated exocytosis (GO:0045055) | 6.87 | 3.43E-02 |
| Peptidyl-tyrosine modification (GO:0018212) | 6.87 | 3.43E-02 |
| Exocytosis (GO:0006887) | 5.11 | 1.14E-02 |
| Immune response-activating signal transduction (GO:0002757) | 4.99 | 1.46E-02 |
| Inflammatory response (GO:0006954) | 4.76 | 7.00E-06 |
| Immune response-regulating signaling pathway (GO:0002764) | 4.74 | 2.53E-02 |
| Activation of immune response (GO:0002253) | 4.63 | 6.83E-03 |
| Myeloid cell differentiation (GO:0030099) | 4.55 | 3.80E-03 |
| Positive regulation of protein secretion (GO:0050714) | 4.21 | 2.11E-02 |
| Regulation of body fluid levels (GO:0050878) | 4.21 | 4.39E-02 |
| Positive regulation of peptide secretion (GO:0002793) | 4.15 | 1.23E-02 |
| Adaptive immune response (GO:0002250) | 4.1 | 2.92E-02 |
| Positive regulation of defense response (GO:0031349) | 4.07 | 1.59E-02 |
| Regulation of MAP kinase activity (GO:0043405) | 3.95 | 2.32E-02 |
| Defense response to other organism (GO:0098542) | 3.93 | 3.28E-03 |
| Regulation of inflammatory response (GO:0050727) | 3.87 | 2.96E-02 |
| Immune effector process (GO:0002252) | 3.74 | 5.31E-04 |
| Innate immune response (GO:0045087) | 3.73 | 3.02E-04 |
| (B) Genes downregulated by PU.1 in CD25+ cells with gain of function, upregulated with sgRNA, relative to all genes expressed in cells | ||
| GO biological process complete | Fold enrichment | Adjusted P-value |
| Defense response to protozoan (GO:0042832) | 27.62 | 1.72E-02 |
| Response to protozoan (GO:0001562) | 25.11 | 2.57E-02 |
| Cell activation (GO:0001775) | 4.44 | 2.43E-03 |
| Immune response (GO:0006955) | 3.55 | 6.41E-03 |
| Immune system process (GO:0002376) | 2.86 | 2.26E-04 |
| Cellular response to stimulus (GO:0051716) | 1.75 | 4.20E-02 |
| (C) Genes upregulated by PU.1 in CD44+ CD25- cells with gain of function, downregulated with sgRNA, relative to all genes expressed in cells | ||
| GO biological process complete (top 21) | Fold enrichment | Adjusted P-value |
| Regulation of coagulation (GO:0050818) | 8.85 | 5.55E-03 |
| Regulation of blood coagulation (GO:0030193) | 8.58 | 2.49E-02 |
| Regulation of hemostasis (GO:1900046) | 8.36 | 2.98E-02 |
| Positive regulation of inflammatory response (GO:0050729) | 7.17 | 3.76E-05 |
| Myeloid leukocyte activation (GO:0002274) | 6.03 | 1.61E-02 |
| Regulated exocytosis (GO:0045055) | 5.93 | 4.94E-02 |
| Defense response to bacterium (GO:0042742) | 5.16 | 5.18E-03 |
| Positive regulation of stress-activated protein kinase signaling cascade (GO:0070304) | 5.04 | 2.95E-03 |
| Inflammatory response (GO:0006954) | 4.98 | 5.37E-09 |
| Positive regulation of stress-activated MAPK cascade (GO:0032874) | 4.77 | 1.29E-02 |
| Regulation of body fluid levels (GO:0050878) | 4.62 | 1.78E-04 |
| Leukocyte activation involved in immune response (GO:0002366) | 4.53 | 4.90E-02 |
| Positive regulation of defense response (GO:0031349) | 4.51 | 2.71E-05 |
| Positive regulation of MAP kinase activity (GO:0043406) | 4.42 | 6.86E-03 |
| Exocytosis (GO:0006887) | 4.29 | 4.18E-02 |
| Regulation of inflammatory response (GO:0050727) | 4.29 | 6.51E-05 |
| Positive regulation of response to external stimulus (GO:0032103) | 4.09 | 2.38E-03 |
| Regulation of MAP kinase activity (GO:0043405) | 4.01 | 8.19E-04 |
| Activation of immune response (GO:0002253) | 3.85 | 3.77E-02 |
| Positive regulation of protein serine/threonine kinase activity (GO:0071902) | 3.8 | 1.28E-02 |
| Defense response to other organism (GO:0098542) | 3.7 | 8.48E-04 |
| (D) Genes downregulated by PU.1 in CD44+ CD25- cells with gain of function, upregulated with sgRNA, relative to all genes expressed in cells | ||
| GO biological process complete | Fold enrichment | Adjusted P-value |
| T cell activation (GO:0042110) | 4.77 | 3.82E-04 |
| Lymphocyte activation (GO:0046649) | 4.51 | 7.36E-07 |
| Cell-cell adhesion (GO:0098609) | 4.22 | 9.44E-03 |
| Cell activation (GO:0001775) | 4.19 | 1.78E-08 |
| Lymphocyte differentiation (GO:0030098) | 4.18 | 1.07E-02 |
| Leukocyte activation (GO:0045321) | 4.12 | 1.14E-06 |
| Regulation of cell-cell adhesion (GO:0022407) | 3.98 | 6.49E-04 |
| Leukocyte differentiation (GO:0002521) | 3.52 | 2.88E-02 |
| Positive regulation of cell adhesion (GO:0045785) | 3.45 | 2.10E-02 |
| Regulation of defense response (GO:0031347) | 3.11 | 1.15E-02 |
| Regulation of cell adhesion (GO:0030155) | 3.09 | 1.01E-03 |
| Biological adhesion (GO:0022610) | 2.9 | 2.29E-02 |
| Positive regulation of transcription by RNA polymerase II (GO:0045944) | 2.46 | 2.21E-03 |
| Regulation of immune system process (GO:0002682) | 2.35 | 3.85E-03 |
| Immune system process (GO:0002376) | 2.3 | 3.44E-05 |
| Regulation of multicellular organismal process (GO:0051239) | 1.74 | 3.15E-02 |
| Positive regulation of biological process (GO:0048518) | 1.48 | 6.54E-03 |
The table shows PANTHER Overrepresentation Analysis (www.geneontology.org) of categories of genes upregulated or downregulated by PU.1. In each case, responding genes were defined by reciprocal changes in expression in PU.1 gain of function and PU.1 loss of function experiments in the DN2a-DN2b interval as in Table 1. Whereas Table 1 shows the three-way intersection of genes affected in loss of function, in gain of function for cells remaining CD25+, and in gain of function for cells becoming CD25− CD44+, here the effects of the gain of function perturbations were separated to allow comparison of results from cells remaining in the T-cell pathway (CD25+) with results from cells likely deviating toward another fate (CD44+). Database for comparison was all genes expressed in control DN2 cells. Statistical results shown are for a Fisher Test with Bonferroni correction for multiple sample testing. The PANTHER Overrepresentation Test version was released 2018-10-10 using the GO Ontology database released 2018-10-08. For PU.1 activated genes, only the top 21 enriched categories are shown.