Table 3 Statistics on operon predictions.
From: Predicting protein linkages in bacteria: Which method is best depends on task
| Â | E. coli K12 | B. subtilis | |
|---|---|---|---|
Operon Database | RegulonDB Jun 2007 | RegulonDB Jan 2006 | DBTBS Sep 2007 |
Total # of known operons | 830 | 355 | 418 |
Completely predicted | 489 (59%) | 213 (60%) | 333 (80%) |
Completely missed | 152 (18%) | 52 (15%) | 24 (6%) |
Total # of GC predicted linkages | 1676 | 1676 | 2104 |
Both proteins in same operon (Fig 6 blue nodes) | 1282 (76%) | 661 (39%) | 843 (40%) |
Both operon proteins, not same operon (Fig 6 red nodes) | 46 (3%) | 12 (1%) | 20 (1%) |
Only 1 classified as an operon protein (Fig 6 yellow nodes) | 161 (10%) | 101 (6%) | 122 (6%) |
Both not classified as operon proteins (Fig 6 grey nodes) | 187 (11%) | 902 (54%) | 1119 (53%) |
Total # of GC predictions where both are operon proteins annotated with function | 1520 (EcoCyc Jun 2007) | 1392 (EcoCyc Jan 2006) | 1583 (DBTBS Sep07) |
Number of True Positives (same operon) | 1244 | 659 | 706 |
Mean (Median) intergenic distance in bases | 20.68 (10) | 22.04 (10) | 28.98 (17) |
Percentage with < 25 bases | 74 | 73 | 63 |
Percentage with > 25 and < 50 bases | 12 | 10 | 16 |
Percentage with > 50 bases | 14 | 17 | 21 |
Number of False Positives (diff operon) | 276 | 733 | 877 |
Mean (Median) intergenic distance in bases | 69.29 (74) | 38.79 (24) | 43.80 (29) |
Percentage with < 25 bases | 15 | 51 | 46 |
Percentage with > 25 and < 50 bases | 11 | 14 | 15 |
Percentage with > 50 bases | 74 | 35 | 39 |