Genome-wide estimation of firing efficiencies of origins of DNA replication from time-course copy number variation data

Table 2 Comparison of estimated locations of origins by SFTM and previous studies.

Organism	Method1 # of ORI	In common # of ORI	Method2 # of ORI	Average Distance (kbp)
	Cer-Raghuraman-SFTM 343	256	Cer-Raghuraman 332	3.318
*S. cerevisiae*	Cer-Alvino-SFTM 345	261	Cer-Alvino 275	1.877
	Pom-Heichinger-SFTM 589	375	Pom-Heichinger-HU 401	3.727
*S. pombe*	Pom-Heichinger-SFTM 589	269	Pom-Feng-cds1 321	3.444
	Pom-Eshaghi-SFTM 619	299	Pom-Heichinger-HU 401	3.838
	Pom-Eshaghi-SFTM 619	233	Pom-Feng-cds1 321	3.178

This table shows the extent of the match between locations of potential origins estimated by SFTM and previous studies. Each item in column 2 and 4 contains two parts: the representation of the method/paper used to detect the origins and the number of origins detected. Column 2 is the results from proposed SFTM method applied to the time-course microarray data as shown in Table 1. Column 4 is the results obtained from previous studies by Raghuraman et al ("Cer-Raghuraman") [21], Alvino et al ("Cer-Alvino") [22], Heichinger et al ("Pom-Heichinger-HU") [10] and Feng et al ("Pom-Feng-cds1") [28]. Column 3 displays the number of origins in common within 8 kbp distance estimated by the methods in column 2 and 4. The average distance of the origins in common are displayed in column 5.

ISSN: 1471-2105