Patent ID: 7941278

Claim:
A computer system for identifying a microRNA motif for a set of one or more target genes, comprising: one or more processors configured to execute program instructions; and a computer-readable medium containing executable instructions that, when executed by the one or more processors, cause the computer system to perform a method for identifying a microRNA motif for a set of one or more target genes, the method comprising: (a) providing a set of subject nucleic acid sequences that contain coding regions (CDRs), 5′ untranslated regions (5′ UTRs), and 3′ untranslated regions (3′ UTRs) of the set of one or more target genes; (b) selecting at least one test RNA motif from the subject nucleic acid sequences; (c) determining the DIFF CDRs or DIFF 5′UTRs value of the at least one test RNA motif in the subject nucleic acid sequences by a set of functions as follows: DIFF CDRs =ƒ(OBS 3′UTRs ,OBS CDRs ,EXP 3′UTRs ,EXP CDRs ) (I) DIFF 5′UTRs =g (OBS 3′UTRs ,OBS 5′UTRs ,EXP 3′UTRs ,EXP 5′UTRs ) (II) in which DIFF CDRs and DIFF 5′UTRs represent the degrees of the enrichment of the at least one test RNA motif in all of the 3′ untranslated regions in comparison with all of the coding regions and all of the 5′ untranslated regions, respectively; OBS 3′UTRs , OBS CDRs , and OBS 5′UTRs represent the observed counts of the at least one test RNA motif within all of the 3′ untranslated regions, all of the coding regions, and all of the 5′ untranslated regions, respectively, of the set of one or more target genes; EXP 3′UTRs , EXP CDRs , and EXP 5′UTRs represent the expected counts of the at least one test RNA motif within all of the 3′ untranslated regions, all of the coding regions, and all of the 5′ untranslated regions, respectively, of all gene transcripts; and wherein the set of functions take the form of Formula III and IV below: DIFF CDRs = OBS 3 ′ ⁢ UTRs - OBS CDRs MAX ⁡ ( EXP 3 ′ ⁢ UTRs , EXP CDRs ) ⁢ ⁢ and ( III ) DIFF 5 ′ ⁢ UTRs = OBS 3 ′ ⁢ UTRs - OBS 5 ′ ⁢ UTRs MAX ⁡ ( EXP 3 ′ ⁢ UTRs , EXP 5 ′ ⁢ UTRs ) ; ( IV ) and (d) selecting the at least one test RNA motif having both DIFF CDRs and DIFF 5′UTRs greater than 0 as a microRNA motif.