Table 5.
GSEA-enriched pathways for cluster 1
| Pathway | Description | Curator | Size, no. genes | Enrichment score | FDR |
|---|---|---|---|---|---|
| CSK pathway | Csk inhibits T-cell activation by phosphorylating Lck; Csk is regulated by cAMP-dependent kinases and is opposed by the T-cell activator CD45. | BioCarta | 24 | 0.8398 | < .001 |
| T helper pathway | Helper T cells coordinate the actions of B cells, macrophages, and other immune cells via surface molecules such as T-cell receptor/CD3 and their characteristic marker CD4. | BioCarta | 23 | < .001.8698 | < .001 |
| T cytotoxic pathway | Cytotoxic T cells release perforin and granzyme to lyse foreign cell targets and express Fas ligand to promote Fas-induced apoptosis. | BioCarta | 23 | < .001.8513 | .003 |
| GATA1 mutant megakaryoblasts | Genes up-regulated in megakaryoblasts of GATA1-mutant mice. GATA1 (a hematopoietic transcription factor) has been implicated in leukemogenesis in patients with Down syndrome. | Li et al46 | 22 | < .001.6708 | .017 |
| T-cell receptor pathway | T-cell receptors bind to foreign peptides presented by MHC molecules and induce T-cell activation. | BioCarta | 24 | < .001.7998 | .020 |
| IL-17 pathway | Activated T cells secrete IL-17, which stimulates fibroblasts and other cells to secrete inflammatory and hematopoietic cytokines. | BioCarta | 16 | < .001.7848 | .020 |
| T-cell receptor activation pathway | The kinases Lck and Fyn phosphorylate and activate the T-cell receptor, which recognizes antigen-bound MHC II and leads to T-cell activation. | BioCarta | 17 | < .001.9049 | .020 |
| T-cell signal transduction | On activation of the T-cell receptor, phospholipase C is activated to produce second messengers DAG and PIP3, both required for T-cell activation. | STKE | 29 | < .001.7062 | .034 |
In addition to the pathway name and description, curator (source of the pathway), size (number of genes in the pathway), ES (calculated by the GSEA algorithm, giving a statistical measure of the enrichment of the sample class by pathway genes), P value, and FDR, which corrects the P value for multiple-testing correction, are also provided. All P values were 0.