Table 2. Top list of transcription factors that regulate differentially expressed genes in paired diagnosis and relapsed samples, ranked by incidence.
| Transcription Factor | Median P value (range) | Percentage of patients | Top target molecules in data set (portion of patients) |
|---|---|---|---|
| CEBPA | 2.6 x10-5 | 87 | MPO(12/20), S100A9(12/20), ID2 (11/20), SOD2 (11/20), ANXA1 (11/20), CXCR4 (10/20), BTG1 (10/20), H1FX (10/20) |
| (2.0E-03–1.5E-09) | |||
| GFI1 | 8.2E-03 | 69 | IL8 (14/16), ELANE(10/16), AZU1(9/16), RB1 (8/16), CDKN1A (6/16), SERPINA1(6/16) |
| (4.4E-02–1.1E-05) | |||
| SATB1 | 4.33E-03 | 69 | HBB (12/16), HSPAA90 (11/16), RGS1 (11/16), CLEC2B (8/16) |
| (2.7E-03–4.6E-05) | |||
| KLF2 | 7.1E-03 | 65 | IL8 (13/15), CCL23(12/15), CCL4(8/15),IL1B(7/15),PTGS2(7/15),SELL(7/15) |
| (2.3E-02–1.2E-05) | |||
| TBP | 3.1E-03 | 61 | TNFAIP3 (14/14), NFKBIA (10/14), IER3 (9/14), BCL2 (5/14), HLA-A (5/14) |
| (4.7E-02–5.9E-05) |
In particular, CEBPA, GFI1 and SATB1 that were affected in 20, 16 and 15 out of 23 patients, respectively. Either one of these transcription factors was predicted to be involved in the differential gene expression profiles of all 23 patients. Network visualization plots show which transcription factors were involved and their target molecules that were at least 2 fold differentially expressed for individual patients (S2 Fig). For example, in patient 3, differential gene expression of the target molecules was predicted to result primarily from CEBPA, GFI1, SATB1 and TBP1 activation/ inhibition (Fig 4). In addition, other transcription factors, such as CEBPD, BCRA1, MYC, SRF, and TAF4B were also significantly involved in this patient.