Computational protocol: MicroRNA-Mediated Regulation of ITGB3 and CHL1 Is Implicated in SSRI Action

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Protocol publication

[…] The microRNAs miR-221, miR-222, and miR-151-a-3p, along with their binding sites, were explored in silico using miRBase (Griffiths-Jones et al., ), TargetScan, microRNAviewer (Kiezun et al., ), and the UCSC Genome Browser (Multiz Alignment of 100 Vertebrates) In compiling the data in Figure , we first compiled a list of 224 candidate biomarker SSRI response genes and miRNAs identified in our earlier studies using genome-wide searches (Morag et al., ; Oved et al., , ). We then created a list of the top 22 predicted miRNA-target gene pairs using TargetScan and additional software tools, based on miRNA-binding site conservation and a high level of agreement between different software (Oved et al., , ). Next, we screened for novel miRNA-target gene pairs for which, both miRNA and the target gene, were reportedly expressed in neuronal cells and were associated with brain plasticity (synaptogenesis/neurogenesis) or with psychiatric diseases; we identified five such pairs. […]

Pipeline specifications

Software tools TargetScan, miRviewer
Databases miRBase UCSC Genome Browser
Application Genome data visualization
Organisms Homo sapiens
Chemicals Serotonin, Paroxetine