Identification of DEGs by the impact of miR-125b on breast cancer cells
To determine the mechanism of miRNA-125b on the transcriptome of human breast cancer cells, we analyzed the sorted cells with maximum and minimum miR-125b expression. A total of 48 genes were identified with the threshold of P< 0.05. The top ten of up-and-down-regulated genes by the impact of miR-125b on cancer cells are identified by the heatmap and volcano plot (Figure 1). The top DEGs were indicated in Table 1.
Enrichment analysis of DEGs by the impact of miR-125b on breast cancer cells
To further analyze the mechanism of miR-125b impacted cancer cells, we analyzed the KEGG and GO enrichment (Figure 2). The top ten KEGG items include “Pathways of neurodegeneration – multiple diseases”, “Oxidative phosphorylation”, “Protein processing in endoplasmic reticulum”, “Parkinson disease”, “Alzheimer disease”, “Non−alcoholic fatty liver disease”, “Diabetic cardiomyopathy”, “Chemical carcinogenesis−reactive oxygen species”, “Thermogenesis”, “Nucleocytoplasmic transport”. We then identified the top ten biological processes “Maintenance of location”, “Striated muscle tissue development”, “Maintenance of location in cell”, “Protein−containing complex localization”, “Ubiquitin−dependent ERAD pathway”, “Mitochondrial electron transport, ubiquinol to cytochrome c”, “Protein folding in endoplasmic reticulum”, “Lens morphogenesis in camera−type eye”, “Protein localization to endosome”, and “Regulation of protein sumoylation”. We also identified the top ten cellular components of GO including “Mitochondrial protein−containing complex”, “Inner mitochondrial membrane protein complex”, “Mitochondrial respirasome”, “Respiratory chain complex”, “Respirasome”, “Oxidoreductase complex”, “Mitochondrial respiratory chain complex III”, “Respiratory chain complex III”, “Endocytic vesicle lumen”, and “Endoplasmic reticulum quality control compartment”. We identified the top ten molecular functions of GO including “Transcription coregulator activity”, “Cadherin binding”, “Unfolded protein binding”, “Proton transmembrane transporter activity”, “Protein phosphatase binding”, “Transcription corepressor activity”, “Phosphatase binding”, “SMAD binding”, “Amyloid−beta binding”, and “Beta−catenin binding”.
PPI network construction
To further determine the relationship of the DEGs, we constructed the PPI network by String network and Cytoscape tool as described17-19. The combined score was set > 0.2 as a cutoff to construct the PPI network by using the 48 nodes and 32 edges. Table 2 showed the top ten molecules with the highest degree scores. The top two cluster modules were indicated in Figure 3. We further analyzed the DEGs and the PPI network by Reactome (Figure 4 and Supplemental Table S1). We also determined the top ten significant biological processes through Reactome map including “ATF6 (ATF6-alpha) activates chaperone genes”, “ATF6 (ATF6-alpha) activates chaperones”, “Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins”, “Formation of ATP by chemiosmotic coupling”, “Response of EIF2AK1 (HRI) to heme deficiency”, “Cristae formation”, “The citric acid (TCA) cycle and respiratory electron transport”, “Unfolded Protein Response (UPR)”, and “Cellular responses to stress”.