PHDcleav: a SVM based method for predicting human Dicer cleavage sites using sequence and secondary structure of miRNA precursors

Table 5 Analysis of functional consequences of SNPs on Dicer processing sites using PHDcleav.

miRBase 19 ID	Reference		Genetic variant
	Cleavage Position	PHDcleav Score	Variation	dbSNP ID	SNP location on hairpin	Cleavage Position	PHDcleav Score	Effect on Dicer cleavage site
hsa-mir-196a-2	47	2.326	g.78C>T	rs11614913	Mature	47	2.326	remain same
	46	2.055				46	2.055
	48	1.614				48	1.614
hsa-mir-335	39	2.855	g.39T>C	MIR335_00001*	Mature	37	1.653	loss of site
	38	1.367				36	1.337
	37	1.338				35	1.027
hsa-mir-570	46	2.025	g.34T>C	rs9860655	Stem	46	2.025	remain same
	45	1.126				45	1.126
	39	0.908				40	0.994
hsa-mir-650	35	1.366	g.71C>G	rs59996397	Stem	35	1.366	remain same
	36	1.349				36	1.349
	38	1.271				38	1.271
hsa-mir-941-3	57	2.095	g.69C>G	rs12625445	Mature	57	2.398	altered
	55	1.011				56	*1.034*
	56	0.750				55	1.023

Top three scores of PHDcleav with their corresponding cleavage sites are given in the table, higher score indicates most probable Dicer cleave site. miRBase annotated canonical cleavage site is shown in bold, while altered cleavage site is shown in bold and italics.
*miRvar DB-ID [43].

ISSN: 1471-2105