Ange| 0.five and p-value 0.05.Frontiers in Molecular Biosciences | www.frontiersin.orgJuly 2021 | Volume 8 | ArticleChen et al.A ceRNA Network in AsthmaHIV-2 site Robust Rank Aggregation AnalysisTo integrate the outcomes of multiple microarray datasets and minimize the bias and inconsistencies, the RRA method was adopted to determine the robust DEGs. The up- and downregulated DEGs have been firstly ranked by expression fold adjustments in every dataset and have been subsequently analyzed using the “Robust Rank Aggregation” R package (version 1.1) (Kolde et al., 2012). The score within the RRA outcome indicated the ranking degree of each gene within the final gene list. Genes with score 0.05 and |log2 fold alter| 0.five were viewed as because the significant robust DEGs.Hub Gene IdentificationCytoHubba is yet another plugin on the Cytoscape software for ranking nodes inside a network, which provides eleven topological evaluation solutions and six centralities to determine hub genes determined by shortest paths, including Maximal Clique Centrality (MCC), Density of Maximum Neighborhood Component (DMNC), Maximum Neighborhood Component (MNC), Degree, Edge Percolated Component (EPC), BottleNeck, EcCentricity, Closeness, Radiality, and Betweenness (Chin et al., 2014). Thinking about the potential heterogeneity in the biological network, the RRA strategy was adopted to integrate the results of unique evaluation techniques for catching crucial proteins.Visualization of Chromosome Places of Robust Differentially Expressed GenesThe “MAO-A medchemexpress RCircos” R package (1.two.1) was utilized to visualize the expression patterns and the chromosomal positions of all robust DEGs.GeneMANIA Database AnalysisGeneMANIA (http://www.genemania.org) database was made use of to construct the PPI network and discover the putative functions of up-loaded genes (Warde-Farley et al., 2010). To get a given query list, GeneMANIA analyzes target genes with functionally comparable genes collectively to receive regulatory networks.Functional and Pathway Enrichment AnalysesGene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses had been utilized to investigate the biological process (BP), the cellular component (CC), the molecular function (MF), and the involved pathways of selected molecules, which have been performed with the “clusterprofiler” R package (version 3.18.1) (Yu et al., 2012). The GO terms and KEGG pathways with p-value 0.05 had been considered statistically significant and further visualized via the “ggplot2” R package (version 3.3.three). The KEGG enrichment analysis of differentially expressed miRNAs was carried out employing the miRPathDB v2.0 (https://mpd.bioinf.uni-sb.de/) database (Kehl et al., 2020).CircRNA-miRNA-mRNA Network ConstructionThe Targetscan (http://www.targetscan.org/vert_72/) (Garcia et al., 2011), miRDB (http://mirdb.org/) (Chen and Wang, 2020), and miRWalk (http://mirwalk.umm.uni-heidelberg.de/) (Dweep et al., 2011) databases were used to predict the corresponding miRNAs of all 19 hub genes. The overlapping outcomes of three databases were then intersected using the differentially expressed miRNAs of GSE142237. The ENCORI (http://starbase.sysu.edu.cn/index.php) database (Li et al., 2014) was utilised to predict the upstream circRNAs from the selected miRNA-mRNA pairs. The final ceRNA network was further processed with the Cytoscape computer software (version three.eight.2).DisGeNET Database AnalysisDisGeNET (http://www.disgenet.org) database is amongst the largest out there platforms of human disease-associated genes and variants via manually i.