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Table 3 Impact of the parametric choices on the correctness of the discovered motifs

From: Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution

Rank promoter bg filtering Taxon Accg Sn PPV
1 ortho taxfreq filtered Gammaproteobacteria 0.658 0.844 0.513
2 leader taxfreq filtered Gammaproteobacteria 0.657 0.844 0.512
3 ortho taxfreq filtered Proteobacteria 0.647 0.840 0.499
4 leader taxfreq filtered Proteobacteria 0.642 0.844 0.488
5 ortho taxfreq filtered Enterobacteriales 0.637 0.857 0.473
6 ortho taxfreq filtered Bacteria 0.634 0.799 0.503
7 leader taxfreq filtered Enterobacteriales 0.631 0.860 0.463
8 leader monad filtered Proteobacteria 0.622 0.798 0.484
9 leader taxfreq filtered Bacteria 0.621 0.796 0.485
10 leader monad filtered Gammaproteobacteria 0.607 0.757 0.487
11 ortho monad filtered Proteobacteria 0.605 0.76 0.482
12 ortho monad filtered Gammaproteobacteria 0.598 0.742 0.481
13 ortho monad filtered Bacteria 0.596 0.778 0.457
14 leader monad filtered Bacteria 0.593 0.810 0.433
15 leader monad filtered Enterobacteriales 0.548 0.714 0.420
16 ortho monad filtered Enterobacteriales 0.544 0.706 0.419
17 ortho taxfreq filtered Escherichia 0.533 0.626 0.453
18 leader taxfreq filtered Escherichia 0.528 0.626 0.445
19 ortho taxfreq no Escherichia 0.525 0.582 0.473
20 leader taxfreq no Escherichia 0.518 0.591 0.453
21 leader taxfreq no Gammaproteobacteria 0.500 0.694 0.360
22 leader taxfreq no Enterobacteriales 0.497 0.736 0.335
23 ortho taxfreq no Enterobacteriales 0.495 0.735 0.333
24 ortho taxfreq no Gammaproteobacteria 0.488 0.706 0.338
25 leader monad no Enterobacteriales 0.480 0.574 0.402
26 ortho monad no Enterobacteriales 0.480 0.573 0.402
27 ortho taxfreq no Proteobacteria 0.463 0.738 0.291
28 leader taxfreq no Proteobacteria 0.461 0.719 0.295
29 ortho monad no Gammaproteobacteria 0.453 0.545 0.376
30 leader monad no Gammaproteobacteria 0.451 0.551 0.370
31 ortho taxfreq no Bacteria 0.435 0.644 0.294
32 leader monad no Proteobacteria 0.428 0.605 0.303
33 ortho monad no Proteobacteria 0.428 0.564 0.324
34 leader taxfreq no Bacteria 0.418 0.634 0.276
35 ortho monad filtered Escherichia 0.397 0.391 0.403
36 leader monad filtered Escherichia 0.396 0.402 0.390
37 ortho monad no Escherichia 0.384 0.366 0.403
38 leader monad no Escherichia 0.383 0.373 0.395
39 ortho monad no Bacteria 0.367 0.607 0.222
40 leader monad no Bacteria 0.341 0.631 0.184