Table 1.

Computational analysis and ranking of miRNA binding sites in candidate tumor suppressor genes implicated in T-ALL

miRNA/context scorea ,b	FBXW7	BIM	NF1	PTEN	IKZF1	PHF6	Sumc
miR-25/92d	−0.9	−0.6	−0.2	−0.4	−0.2	0.0	−3.2
miR-27	−0.8	−0.2	−0.2	0.0	−0.4	0.0	−3.0
miR-203	0.0	−0.2	−0.2	0.0	−0.7	−0.6	−2.9
miR-148/152d	0.0	−0.8	0.0	−0.7	−0.3	0.0	−2.4
miR-101	−0.2	−0.3	−0.4	0.0	−0.1	−0.2	−2.3
miR-26	0.0	0.0	0.0	−0.9	0.0	−0.4	−2.3
miR-103	−0.3	0.0	−0.9	−0.6	0.0	0.0	−2.2
miR-200	−0.6	−0.2	−0.4	−0.2	0.0	−0.4	−2.2
miR-144	0.0	−0.2	−0.9	−0.3	0.0	−0.2	−2.0
miR-128	−0.3	0.0	−0.3	0.0	−0.4	−0.5	−1.9
miR-19	0.0	−0.3	−0.3	−0.6	−0.1	0.0	−1.8
miR-223	−1.4	0.0	0.0	0.0	0.0	0.0	−1.8
miR-137	−0.3	−0.1	−0.4	0.0	−0.2	0.0	−1.7
miR-217	0.0	−0.2	−0.6	−0.1	−0.2	−0.5	−1.6
miR-20/93/106d	0.0	−0.2	0.0	−0.3	0.0	−0.2	−1.5

^aThe context score was calculated by correlating contextual features at a predicted site (local AU content, predicted binding at the 3′ end of the miRNA and position in the 3′ UTR) with extent of downregulation in miRNA transfection experiments and indicates the strength of the miRNA-mRNA interaction; larger negative values correspond to more effective sites; only values less than −0.1 are shown; scores are rounded to one decimal place.

^bWe tested the significance of this enrichment by randomly sampling 10,000 gene sets of the same size as the tumor suppressor gene set and computed how often the positive miRNAs showed the same enrichment. The enrichment of highly expressed miRNAs targeting tumor suppressor genes was significant (P < 0.043, empirical P value).

^cThe sum is calculated for all 12 genes included in the analysis; see Supplementary Table 9 for the full list of genes and miRNAs.

^dIndicates homologous miRNAs with identical seed sequences. See Supplementary Table 9 for the full analysis.