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[…] tly, the adjusted P<0.05 and |log2FC|>0.52 were selected as the threshold values for screening., Since the inhibition of gene expression following transcription is realized by the combination of miRNA and mRNA, differentially expressed miRNAs in HCC samples were further analyzed to explore the significance of miRNA in liver cancer. In the present study, two experimental certificate databases including miRecords () and miRWalk () were used to explore suitable miRNA-target gene relations. The relations that existed in at least one kind of database aforementioned were selected, then the target genes of differentially expressed miRNAs identified by miRecords or miRWalk were obtained., The Database for Annotation, Visualization and Integrated Discovery (DAVID; David Bioinformatics Resource) () is a gene functional classification tool that provides a comprehensive set of functional annotation tools for investigators to understand the biological meaning behind large lists of genes. GO functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways (http://www.genome.jp/kegg/pathway.html) enrichment analysis () of DEGs were performed using DAVID. GO has 3 functional categories: Molecular function (MF); biological process (BP); and cellular component (CC). P<0.05 was considered to indicate a statistically significant difference., Each miRNA may have several target genes, but outstanding target genes are more likely to assemble transcription factors (). Thus, the analysis between transcription factors and miRNA is beneficial to understand this pathomechanism. iRegulon can be used to detect transcription factors, motifs and their optimal sets of direct targets from a set of genes (). In the present study, the iRegulon in Cytoscape software was used to explore the potential associations between miRNA and transcription factors. The minimum identity between orthologous genes was 0.05, while the maximum false discovery rate on motif similarity was 0.001. The normalized enrichment score (NES) of >4 was considered as the threshold value for the selection of potential associations., The Comparative Toxicogenomics Database (CTD) is a robust, publicly available database that is used to advance understanding regarding how environmental exposures affect human health (). In the present study, the investigation of HCC-associated miRNA was performed using the CTD database. The biomarkers of a disease are generally iden […]

Pipeline specifications

Software tools DAVID, iRegulon, Cytoscape
Databases CTD miRWalk