Computational protocol: Genome-Wide Scleral Micro- and Messenger-RNA Regulation During Myopia Development in the Mouse

Similar protocols

Protocol publication

[…] Using WebGestalt software,, we determined the distribution of differentially regulated genes among cellular, molecular, and biological processes, querying the Gene Ontology database and comparing the relative distribution of genes that met specific significance criteria to the distribution of all detected genes. The hypergeometric method was used, and significance was set at an adjusted P value of <0.05 (Benjamini and Hochberg method), with a minimum requirement of 2 or more genes being involved, using detectable genes with valid gene symbols (Genome Reference Consortium Mouse Build 38). Predicted gene targets for mouse miRNAs were downloaded from TargetScan, EiMMo, and Microcosm. Three statistical tests of enrichment were used to determine whether the predicted targets of any miRNAs exhibited altered expression levels, which included miRNA Target Enrichment Analysis/miTEA,, permutation, and hypergeometric distribution tests. For miTEA, the list of differentially expressed genes ranked by fold-change was used as the input, and the tool searched for any miRNAs whose predicted targets (by any of the three prediction methods) were enriched at the top or bottom of the ranked list. For the hypergeometric test, the number of genes identified as being differentially expressed predicted target(s) of a given miRNA was compared to the expected number of such genes according to the hypergeometric distribution. A similar test was performed using a random selection of genes to build the distribution of expected gene numbers. […]

Pipeline specifications