Gene sets regulated by idelalisib treatment in FL-FDC cocultures in sensitive patients
| Gene sets . | No. of enriched gene sets . | NES . | FDR, q . |
|---|---|---|---|
| Custom gene sets | |||
| Human angiogenesis | 1 | 2.63 | <.0001 |
| IRF4 pathway | 1 | 1.98 | .0045 |
| Cell cycle regulation | 2 | 1.98 | .0039 |
| Integrin pathway | 1 | 1.92 | .0067 |
| Serum response | 1 | 1.85 | .0131 |
| Canonical pathways (C2CP) | |||
| Focal adhesion-integrins | 12 | 2.80 | <.0001 |
| Extracellular matrix formation | 7 | 2.76 | <.0001 |
| Angiogenesis (VEGF/PDGF pathways) | 5 | 2.29 | <.0001 |
| Cell adherent junctions–ECadherin | 5 | 2.08 | .0009 |
| Cell cycle G1-M | 8 | 2.01 | .0027 |
| Transendothelial cell migration | 2 | 1.90 | .0115 |
| Motif gene sets (C3 TFT) | |||
| SRF | 6 | 2.31 | <.0001 |
| IRF | 2 | 1.85 | .0080 |
| NFAT | 1 | 1.73 | .021 |
| NF-κB | 1 | 1.64 | .041 |
| Hallmark gene sets (H) | |||
| Epithelial mesenchymal transition | 1 | 3.25 | <.0001 |
| Angiogenesis | 1 | 2.26 | <.0001 |
| mTOR | 1 | 1.95 | .0002 |
| Interferon α and γ responses | 2 | 1.6 | .015 |
| GO gene sets (C5) | |||
| Extracellullar matrix organization | 8 | 2.9 | <.0001 |
| Adhesion-integrins | 9 | 2.56 | <.0001 |
| Vasculature-angiogenesis-EC growth | 15 | 2.49 | <.0001 |
| Cell cycle G1-S and G2-M | 6 | 2.09 | .0007 |
| Gene sets . | No. of enriched gene sets . | NES . | FDR, q . |
|---|---|---|---|
| Custom gene sets | |||
| Human angiogenesis | 1 | 2.63 | <.0001 |
| IRF4 pathway | 1 | 1.98 | .0045 |
| Cell cycle regulation | 2 | 1.98 | .0039 |
| Integrin pathway | 1 | 1.92 | .0067 |
| Serum response | 1 | 1.85 | .0131 |
| Canonical pathways (C2CP) | |||
| Focal adhesion-integrins | 12 | 2.80 | <.0001 |
| Extracellular matrix formation | 7 | 2.76 | <.0001 |
| Angiogenesis (VEGF/PDGF pathways) | 5 | 2.29 | <.0001 |
| Cell adherent junctions–ECadherin | 5 | 2.08 | .0009 |
| Cell cycle G1-M | 8 | 2.01 | .0027 |
| Transendothelial cell migration | 2 | 1.90 | .0115 |
| Motif gene sets (C3 TFT) | |||
| SRF | 6 | 2.31 | <.0001 |
| IRF | 2 | 1.85 | .0080 |
| NFAT | 1 | 1.73 | .021 |
| NF-κB | 1 | 1.64 | .041 |
| Hallmark gene sets (H) | |||
| Epithelial mesenchymal transition | 1 | 3.25 | <.0001 |
| Angiogenesis | 1 | 2.26 | <.0001 |
| mTOR | 1 | 1.95 | .0002 |
| Interferon α and γ responses | 2 | 1.6 | .015 |
| GO gene sets (C5) | |||
| Extracellullar matrix organization | 8 | 2.9 | <.0001 |
| Adhesion-integrins | 9 | 2.56 | <.0001 |
| Vasculature-angiogenesis-EC growth | 15 | 2.49 | <.0001 |
| Cell cycle G1-S and G2-M | 6 | 2.09 | .0007 |
Gene sets regulated by idelalisib were identified by GSEA using custom gene sets experimentally derived (http://lymphochip.nih.gov/signaturedb/index.html), C2 canonical pathways, C3 motif gene sets, Hallmark, and C5-GO signatures obtained from the Molecular Signature Database (v2.5). Threshold: FDR < 0.05 and NES > 1.5. The number of enriched gene sets and the best FDR and NES scores are indicated for each biological process. A complete list of the enriched gene set is detailed in supplemental Table 3.
EC, endothelial cell; IRF, interferon response factor; IRF4, interferon regulatory factor 4; FDR, false discovery rate; mTOR, mammalian target of rapamycin; NES, normalized enriched score; NFAT, nuclear factor of activated T cells; NF-κB, nuclear factor κB; SRF, serum response factor.