Gene sets up-regulated in CLL cells in LN compared with PB
| Gene sets . | Number of enriched gene sets . | NES . | FDR, q value . |
|---|---|---|---|
| Functional gene sets | |||
| B-cell receptor signaling | 1 | 2.06 | 0.0031 |
| T-cell receptor signaling | 2 | 2.01 | 0.0043 |
| P53 pathway | 5 | 2.00 | 0.0053 |
| NF-κB pathway* | 3 | 1.98 | < 0.0001 |
| Calcineurin-NFAT signaling | 1 | 1.92 | 0.0071 |
| MYC-regulated genes | 8 | 1.89 | 0.0088 |
| Proliferation/cell cycle | 7 | 1.88 | 0.0085 |
| Pyrimidine metabolism | 2 | 1.88 | 0.0085 |
| TNF pathway | 3 | 1.88 | 0.0085 |
| CLL BCR signature† | 1 | 1.81 | 0.006 |
| Toll receptor signaling | 2 | 1.80 | 0.0151 |
| E2F1-regulated genes | 1 | 1.80 | 0.0157 |
| Motif gene sets | |||
| E2F | 19 | 2.15 | < 0.0001 |
| ATF | 1 | 1.84 | 0.006 |
| NF-Y | 2 | 1.84 | 0.006 |
| CREB | 4 | 1.85 | 0.006 |
| Gene sets . | Number of enriched gene sets . | NES . | FDR, q value . |
|---|---|---|---|
| Functional gene sets | |||
| B-cell receptor signaling | 1 | 2.06 | 0.0031 |
| T-cell receptor signaling | 2 | 2.01 | 0.0043 |
| P53 pathway | 5 | 2.00 | 0.0053 |
| NF-κB pathway* | 3 | 1.98 | < 0.0001 |
| Calcineurin-NFAT signaling | 1 | 1.92 | 0.0071 |
| MYC-regulated genes | 8 | 1.89 | 0.0088 |
| Proliferation/cell cycle | 7 | 1.88 | 0.0085 |
| Pyrimidine metabolism | 2 | 1.88 | 0.0085 |
| TNF pathway | 3 | 1.88 | 0.0085 |
| CLL BCR signature† | 1 | 1.81 | 0.006 |
| Toll receptor signaling | 2 | 1.80 | 0.0151 |
| E2F1-regulated genes | 1 | 1.80 | 0.0157 |
| Motif gene sets | |||
| E2F | 19 | 2.15 | < 0.0001 |
| ATF | 1 | 1.84 | 0.006 |
| NF-Y | 2 | 1.84 | 0.006 |
| CREB | 4 | 1.85 | 0.006 |
Enriched gene sets were identified using GSEA, selected for FDR < 0.05 and NES ≥ 1.80. Where GSEA identified several gene sets with the same functional annotation, the total number of enriched gene sets is given and the NES and FDR of the most significantly enriched set is shown. Only gene sets in which at least 5 genes accounted for the enrichment score (leading edge genes) are included. Gene sets specific to nonlymphoid cell types are not shown.
NES indicates normalized enrichment score; and TNF, tumor necrosis factor.
Functional gene signatures of coordinately regulated genes derived from experimental validation: downloaded from the Staudt Lab Web site at http://lymphochip.nih.gov/signaturedb/index.html.
Functional gene signature of coordinately regulated genes derived from experimental validation: established as shown in Figure 3A.