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[…] ovided by miRBase v21. To reduce false-positive results, only common genes predicted by both softwares were chosen as target genes of deregulated miRNA for subsequent analysis., For the analyses of differentially expressed genes, the original data of the series GSE6740 were analyzed using the software Rv3.2.2 (https://www.r-project.org/). Initially, both index, including Relative Log Expression (RLE) and the Normalized Unscaled Standard Error (NUSE), were used to assess the quality of this microarray data []. Then, the method of Robust Multi-array Average (RMA) was applied to perform background adjustment, normalization and log transformation of the original microarray data []. Finally, the Linear Models for Microarray Data (LIMMA) package (http://bioconductor.org/biocLite.R) was used to identify differentially expressed genes (DEGs), which is a software package for constructing linear regression model []. The genes with FC > 1.5 and an adjusted p value <0.05 were regarded as DEGs., The dysregulated genes in different disease stages were extracted as DEGs, which needed further functional annotation. Only genes that exhibited significant expression differences (p value <0.05 and FC > 1.5) were functionally annotated. These DEGs were analyzed using Database for Annotation, Visualization, and Integrated Discovery v6.7 (DAVID v6.7) that is a useful bioinformatics enrichment tool for GO terms, KEGG pathway, and gene-disease association (http://david.abcc.ncifcrf.gov/) []. To functionally annotate DEGs identified by the aforementioned three comparison groups, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) were analyzed with DAVID v6.7 []. Cytoscape (http://www.cytoscape.org/) was used in miRNA-mRNA network analysis []., Through a comprehensive analysis of miRNA expression profiling in different disease stages following HIV-1 infection, a list of aberrantly expressed miRNAs was included (Table ). With at least twofold change and FDR-adjust p value of <0.01, we identified that 7 differentially expressed miRNAs (DEMs) in LTNPs, whose miR-342 was down-regulated and 6 miRNAs (miR-487b, miR-212, miR-494, miR-939, miR-1225 and miR-513a) were overexpressed in the LTNPs, compared with UCs, except of miR-768-5p because it overlaps an annotated snoRNA (HBII-239). Twenty DEMs were identified between CPs and UCs. Twelve miRNAs were higher and 7 DEMs were do […]

Pipeline specifications

Software tools TargetScan, Cytoscape, DAVID
Organisms Human immunodeficiency virus 1
Diseases Infection, Sexually Transmitted Diseases, Viral, Retroviridae Infections, HIV Infections