Infer Probabilities of MiRNA-mRNA Interaction Signature (ProMISe) using paired expression data from a single sample. Roleswitch operates in two phases by inferring the probabilities of mRNA (miRNA) being the targets ("targets") of miRNA (mRNA), taking into account the expression of all of the mRNAs (miRNAs) due to their potential competition for the same miRNA (mRNA). Due to mRNA transcription and miRNA repression events simultaneously happening in the cell, Roleswitch assumes that the total transcribed mRNA levels are higher than the observed (equilibrium) mRNA levels and iteratively updates the total transcription of each mRNA targets based on the above inference. NB: in the paper, we used ProMISe as both the model name and inferred score name.
Create diagnostic plot for understanding the roleswitch outputs. Create a 2 by 4 panels of plots. From left to right, the top panel displays the observed N mRNA and M miRNA expression (x.o and z.o), the N by M seed-match matrix (c), and the inferred total mRNA expression; the bottom panel displays the inferred probability of the M miRNAs targeting the N mRNA (miRNA-mRNA; p.x), the probability of the N mRNA "targeting" the M miRNAs (mRNA-miRNA; p.z), the dot product of the above two matrices (Joint) and the convergence rate (delta.p.all).
Given N mRNA and M miRNA IDs or simply the species common names (e.g., human), obtain the N by M seed match matrix as a the number of target sites each mRNA has for each miRNA.
Infer Probabilities of MiRNA-mRNA Interaction Signature (ProMISe) using paired expression data from a single sample. Roleswitch operates in two phases by inferring the probabilities of mRNA (miRNA) being the targets ("targets") of miRNA (mRNA), taking into account the expression of all of the mRNAs (miRNAs) due to their potential competition for the same miRNA (mRNA). Due to mRNA transcription and miRNA repression events simultaneously happening in the cell, Roleswitch assumes that the total transcribed mRNA levels are higher than the observed (equilibrium) mRNA levels and iteratively updates the total transcription of each mRNA targets based on the above inference. NB: in the paper, we used ProMISe as both the model name and inferred score name.
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