Methods of Predicting The Probability of Modulation of Transcript Levels By RNAI Compounds

1 - 114 . (canceled)

115 . A method of selecting one or more siRNAs from among a plurality of siRNAs based on silencing specificity, comprising:

(a) determining the seed-sequence-dependent signature of each siRNA in said plurality of siRNAs by a method comprising:

(i) calculating, on a suitably programmed computer, a score representing a probability that said siRNA modulates a transcript of a gene in a set of genes of interest according to a linear model of:

Score= A*#pm+B*#m 1-7 +C*#m 2-8 +D*#m 2-7 +E *length(3 ′UTR )+optionally F+optionally G*X

wherein

said #pm is the number of pm seed match types between a 3′UTR sequence of said transcript and a seed sequence, or a variant thereof, of said siRNA;

said seed sequence consists of the first 8 nucleotides, numbered 1-8, respectively, at a 5′ end of said siRNA;

said #m 1-7 is the number of m 1-7 seed match types between said 3′UTR sequence and said seed sequence or said variant thereof;

said #m 2-8 is the number of m 2-8 seed match types between said 3′UTR sequence and said seed sequence or said variant thereof;

said #m 2-7 is the number of m 2-7 seed match types between said 3′UTR sequence and said seed sequence or said variant thereof; and

said length(3′UTR) is the length in number of nucleotides of said 3′UTR sequence; wherein said variant is said seed sequence except that a nucleotide U replaces the nucleotide at position 1 of said seed sequence;

wherein

said pm seed match type=perfect match of all nucleotides 1-8 in said seed sequence or said variant thereof;

said m 1-7 seed match type=perfect match of nucleotides 1-7 and mismatch of nucleotide 8 in said seed sequence or said variant thereof;

said m 2-8 seed match type=perfect match of nucleotides 2-8 and mismatch of nucleotide 1 in said seed sequence or said variant thereof; and

said m 2-7 seed match type=perfect match of nucleotides 2-7 and mismatches of nucleotides 1 and 8 in said seed sequence or said variant thereof;

wherein a perfect match means a complementary nucleotide is present, and a mismatch means absence of a complementary nucleotide; wherein coefficients A, B, C, D, E, F and G are constants; and wherein X is the value of one or more additional features characterizing the influence of said siRNA on said gene; and

(ii) repeating step (i) for each gene in said set of genes, thereby determining a set of scores indicating the probability that said siRNA modulates said respective transcript; and

(iii) calculating, on a suitably programmed computer, the seed-sequence-dependent signature size of said siRNA, wherein said seed-sequence-dependent signature size is, or an indication of, the number of genes that have a transcript which said score predicts is modulated by said siRNA;

(b) ranking, on a suitably programmed computer, said siRNAs by seed-sequence-dependent signature sizes; and

(c) selecting one or more siRNAs whose seed-sequence-dependent signature size is below a preselected threshold, or selecting N siRNAs with the 1 st to N th smallest seed-sequence-dependent signature size, wherein N is a positive integer.

116 . The method of claim 115 , wherein said score of part (a) is selected from the group consisting of: (i) a log-odds that the null hypothesis that said transcript is not modulated or is not down-regulated by said siRNA is true, (ii) a p-value that is the probability that the null hypothesis that said transcript is not modulated or is not down-regulated by said siRNA is true, and (iii) a measure of the relative expression of said transcript by a cell containing said siRNA and expression of said transcript by an analogous cell not containing said siRNA; and

wherein said seed-sequence-dependent signature size is calculated as follows:

(1) when said score is said log-odds, calculating said seed-sequence-dependent signature size comprises: (A) calculating the standard deviation of said set of scores, or (B) calculating the mean of the absolute values of said set of scores, or (C) counting the number of log-odds in said set of scores that have a value below a first preselected threshold; and

(2) when said score is said p-value, calculating said seed-sequence-dependent signature size comprises counting the number of p-values in said set of scores that have a value below a second preselected threshold; and

(3) when said score is said measure, calculating said seed-sequence-dependent signature size comprises counting the number of measures in said set of scores that have a value above a third preselected threshold and/or below a fourth preselected threshold.

117 . The method of claim 116 wherein said score is the log-odds of the null hypothesis that said transcript is not down-regulated by said siRNA is true.

118 . The method of claim 116 , wherein said score is said measure, wherein said measure is the relative expression of said transcript by a cell not containing said siRNA and expression of said transcript by an analogous cell containing said siRNA, and said seed-sequence-dependent signature size is the number of measures in said set of scores that have a value above a fifth preselected threshold and/or below a sixth preselected threshold.

119 . The method of claim 118 , wherein said measure of the relative expression is the mean log ratio, wherein said mean log ratio is a mean of the log ratios of signal intensities from a pair of microarray experiments where fluorescent dye labeling of nucleic acids contacted with a microarray is reversed in one microarray experiment relative to the other.

120 . The method of claim 115 , wherein said seed-sequence-dependent signature size is a standard deviation of log-odds, wherein said step (c) comprises selecting one or more siRNAs whose seed-sequence-dependent signature size is below a preselected threshold, and wherein said preselected threshold is 0.250, or 0.289.

121 . The method of claim 115 , wherein the seed-sequence-dependent signature size is a mean of the absolute value of log-odds, wherein said step (c) comprises selecting one or more siRNAs whose seed-sequence-dependent signature size is below a preselected threshold, and wherein said preselected threshold is 10 th , or 25 th percentile of all siRNAs.

122 . The method of claim 115 , wherein the seed-sequence-dependent signature size is expression log 2 ratio, wherein step (c) comprises selecting one or more siRNAs whose seed-sequence-dependent signature size is below a preselected threshold, and wherein said preselected threshold is 1.2 fold, 1.5 fold, or 2 fold reduction of expression level.