Filtering of false positive microRNA candidates by a clustering-based approach

BMC Bioinformatics

Table 1 Effects on the distance of chromosomal separation of clustered miRNAs on the number of clustered miRNAs found in the human, mouse and rat genomes.

Genome	Effect	*Chromosomal distance at which two clustered miRNAs are separated*
		1500 nt	3000 nt	6000 nt	10000 nt	25000 nt	50000 nt
Human	# of clustered miRNAs	196	217	240	241	242	261
	# of clusters defined	71	68	60	60	60	65
	Average cluster size	2.76	3.19	4	4.02	4.03	4.02
Mouse	# of clustered miRNAs	204	215	237	243	253	260
	# of clusters defined	70	53	55	57	58	61
	Average cluster size	2.91	4.06	4.31	4.26	4.36	4.26
Rat	# of clustered miRNAs	119	129	145	154	154	160
	# of clusters defined	46	45	48	49	47	48
	Average cluster size	2.59	2.87	3.04	3.14	3.28	3.14

"Average cluster size" is equivalently to the average number of miRNAs found in a single cluster. It can be seen that there is an abrupt increase in the number of clustered miRNAs from the case of 3000 nt to the case of 6000 nt. There are little effects on the number of clustered miRNAs and the number of clusters defined when the separation is more than 10000 nt. To conclude, among the six distances that we have tested, 6000 nt is an optimal chromosomal distance bound within which two clustered miRNAs are separated.

ISSN: 1471-2105