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

Janky, Rekin's; van Helden, Jacques

doi:10.1186/1471-2105-9-37

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	Acc_g	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

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ISSN: 1471-2105

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