Table 4.
Comparison of subsets of CodY-binding regions with different strengths
| Enrichment (fold) | Number of: |
|||||
|---|---|---|---|---|---|---|
| CodY-binding regions | CodY-binding sites | upstream sites | overlapping CodY-binding motifs | ChIP-Seq regionsa | RNA-Seq regulated genesa | |
| Analysis I | ||||||
| >10 | 388 | 518 | 98 (19%) | 202 (39%) | 46 (12%) | 84 (22%) |
| >15 | 224 | 313 | 72 (23%) | 132 (42%) | 41 (18%) | 49 (22%) |
| >20 | 146 | 203 | 54 (27%) | 94 (46%) | 37 (25%) | 34 (23%) |
| >30 | 78 | 107 | 40 (37%) | 56 (52%) | 27 (35%) | 20 (25%) |
| >40 | 58 | 81 | 32 (40%) | 47 (58%) | 26 (45%) | 14 (24%) |
| >60 | 31 | 46 | 17 (37%) | 30 (65%) | 19 (61%) | 9 (29%) |
| >100 | 17 | 26 | 9 (35%) | 13 (50%) | 14 (82%) | 5 (29%) |
| Analysis II | ||||||
| 10–15 | 164 | 205 | 26 (13%) | 70 (34%) | 6 (3%) | 35 (21%) |
| 15–20 | 78 | 110 | 18 (16%) | 38 (35%) | 4 (5%) | 15 (19%) |
| 20–30 | 68 | 96 | 14 (15%) | 38 (40%) | 10 (15%) | 14 (21%) |
| 30–60 | 47 | 61 | 23 (38%) | 26 (43%) | 8 (17%) | 11 (23%) |
| >60 | 31 | 46 | 17 (37%) | 30 (65%) | 19 (61%) | 9 (29%) |
| ChIP-Seqb | 58 | 59 | 7 (12%) | 25 (42%) | 58 (100%) | 13 (22%) |
Various subsets of 388 CodY-binding regions and associated 518 CodY-binding sites identified by IDAP-Seq were analyzed and compared to the CodY-binding regions and sites identified by ChIP-Seq.
a
Data taken from our analysis of the previously obtained results (Lobel and Herskovits, 2016)
b
All regions with CodY-binding sites identified by ChIP-Seq in cells grown in BHI (Lobel and Herskovits, 2016)