Computational protocol: A direct regulatory link between microRNA-137 and SHANK2: implications for neuropsychiatric disorders

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Protocol publication

[…] Validated targets of miR-137 were collected from miRTarBase (, accessed January 2017) and PubMed (, accessed January 2017) database searches. miRTarBase targets were included if they were categorized as “strong evidence,” i.e., confirmed by experimental methods of validation including luciferase reporter assay, RT-qPCR, and/or Western blot analysis. Targets from the PubMed database search were considered as validated if a direct link was established by luciferase reporter assay, RT-qPCR, and/or Western blot analysis. Duplicates between databases were removed. A total of 71 validated targets were obtained; most of them have been investigated in cancer cells, whereas only 12 targets have been validated in neurons (details are shown in Additional file : Table S4). RNA sequencing data for the miR-137 target genes HCRT, SLC6A3, and SNAI1 was not available in the CommonMind dataset. The target gene network was analyzed through the use of QIAGEN’s Ingenuity®Pathway Analysis (IPA®, QIAGEN Redwood City, [...] Statistical analyses were performed using the SPSS software (IBM Corp.; IBM SPSS Statistics for Windows, Version 22.0.; Armonk, NY, USA). Two-way ANOVAs were performed considering the influence of the experiment and the respective condition. The data is shown as mean ± SEM. The validated miR-137 target genes (including SHANK2) were ranked according to their point-wise P values from the CommonMind analysis, and the Benjamini-Hochberg method was used to correct for multiple testing with a false discovery rate of 10% (Additional file : Table S5). A two-sided Χ2 test with Yates correction was used to compare the expression of validated target genes of miR-137 and five control microRNAs. The differentially expressed targets of the five control microRNAs were pooled together. Genes that were targets of more than one control microRNA were only counted once. Eight target genes that were not differentially expressed in SCZ and control individuals overlapped between miR137 and the five controls and were excluded from analysis. […]

Pipeline specifications

Software tools IPA, SPSS
Databases miRTarBase
Applications Miscellaneous, RNA-seq analysis
Organisms Homo sapiens, Mus musculus