An integrative approach to identify novel miRNA-mRNA interaction networks in LMNA-cardiomyopathy

Figures

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  Fig. 1. DEGs and DEMs in LMNAR249W tissue samples. (A) The volcano plots showing DEGs in LMNAR249W samples compared to wild type. (B) The volcano plots showing DEMs in LMNAR249W samples compared to wild type. The X axis represents the log2 FC and the Y axis corresponds to -log FDR. The dots are genes/miRNA which have been classified in colors: red dots represent transcripts with |log2FC| > 1 and FDR < = 0.05, blue dots are those with |log2FC| <= 1 and FDR < = 0.05, green is those with |log2FC| > 1 and FDR > 0.05 and grey the remaining. Dashed lines show the different FDR thresholds. RNA was obtained from myocardial tissue of 50-week-old Lmna+/R249W (n = 6) and age-matched wild-typed type mice (n = 6). Abbreviations: DEG differentially expressed genes; DEM: Differentially expressed micro-RNAs; FDR: false discovery rate; FC: fold change; log: logarithm; miRNA: micro RNA. https://drive.google.com/file/d/1-Ng6oPkTk6Zi48JRFrJP9Vaw3wX7RhcS/view?usp=drive_web.

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  Fig. 2. Enriched GO biological process and molecular function terms in differentially expressed genes. (A) Top 30 enriched GO Biological Process terms in DEGs. The color of the dots represents the FDR, and their size represents the number of DEGs annotated for each term. Two terms are linked when they shared annotated DEGs. The wider and shorter links correspond to more DEGs shared between terms. (B) Enriched GO Molecular Function terms in DEGs. Abbreviations: DEG differentially expressed genes; FDR: false discovery rate; GO: gene ontology. https://drive.google.com/file/d/1yt7qOhIeRaol9iQS_OloKMmhrpOvhbSu/view?usp=drive_web.

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  Fig. 3. Enriched pathways in differentially expressed genes. (A) Reactome pathways. (B) KEGG pathways. This plot shows as dots the top 30 enriched pathways in DEGs. The color of the dots represents the FDR, and their size represents the number of DEGs annotated for each pathway. Two pathways are linked when they share annotated DEGs. The wider and shorter links correspond to more DEGs shared between pathways. Abbreviations: DEG: differentially expressed genes; FDR: false discovery rate; KEGG: Kyoto Encyclopedia of Genes and Genomes96–98. https://drive.google.com/file/d/1D2_7SHOTomN1Kk5ARRE5uhiTQB6KRjkN/view?usp=drive_web.

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  Fig. 4. Integrative workflow for the identification of anticorrelated miRNA–mRNA pairs.

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  Fig. 5. Comparison of miRNA–mRNA integration strategies based on median odds ratio (OR) and target coverage. This plot shows the ranking of the different correlation strategies by their odds ratio (Y axis) and their coverage (X axis). The higher odds ratio stands for more representation of the correlated pairs in database. The coverage is the proportion of miRNA with correlated targets within strategy that showed significant overlap with databases according to Fisher test FDR < 0.05. Dots represent the diverse correlation strategies where color distinguish the different analytical approaches. The strategies used are: (i) Correlation between differentially expressed mRNAs and miRNAs, using either opposite expression patterns (DEGs_RNA_vs_miRNA_DEMs_opp) or similar patterns (DEGs_RNA_vs_miRNA_DEMs_sim); (ii) Module-level integration, correlating mRNA and miRNA eigengenes (Eigengene_RNA_vs_miRNA_Eigengene) or restricting to hub genes within modules (Eigengene_RNA_vs_miRNA_hub_1); (iii) Gene-level correlations using normalized expression, either for all genes in the dataset (Eigengene_RNA_vs_miRNA_normalized_counts and normalized_counts_RNA_vs_miRNA_normalized_counts) or focusing on hub…

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  Fig. 6. Enriched Gene Ontology Molecular Function terms in targets of the upregulated miRNA. This plot shows the significant enriched Gene Ontology Molecular Function terms (larger dots) in target genes (smaller dots). The color of the dots represents the miRNA that targets the gene and hence, the enriched term. The dots with two colors are targeted by two different miRNAs. The size of the term dot represents how many targets are annotated with it. Abbreviations: miRNA: micro-RNA. https://drive.google.com/file/d/1TnAszuM2gGV46APG6-o2kHAAI6SMIgcF/view?usp=drive_web.

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  Fig. 7. Enriched Gene Ontology Biological Process terms in targets of the upregulated miRNA. This plot shows the significantly enriched Gene Ontology Biological Process terms (larger dots) in target genes (smaller dots). The color of the dots represents the miRNA that targets the gene and hence, the enriched term. The dots with two colors are targeted by two different miRNAs. The size of the term dot represents how many targets are annotated with it. Abbreviations: miRNA: micro-RNA. https://drive.google.com/file/d/1tJhomdsp6oLoQ_paHhgYXd7WCXUSTN7y/view?usp=drive_web.

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  Fig. 8. Enriched Gene Ontology molecular function terms in targets of the downregulated miRNAs. This plot shows the significantly enriched Gene Ontology Molecular Function terms (larger dots) in target genes of each miRNA (smaller dots). The color of the dots represents the miRNA that targets the gene and hence, the enriched term. The dots with two colors are targeted by two different miRNAs. The size of the term dot represents how many miRNAs targeted genes annotated with each term. Abbreviations: miRNA: micro-RNA. https://drive.google.com/file/d/1jMLjuHDEjawPyAo7sIG8VD81wHWUVOQd/view?usp=drive_web.

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  Fig. 9. Enriched Gene Ontology Biological Process terms in targets of the downregulated miRNA. This plot shows the significant enriched Gene Ontology Biological Process terms (larger dots) in target genes of each miRNA (smaller dots). The color of the dots represents the miRNA that targets the gene and hence, the enriched term. The dots with two colors are targeted by two different miRNAs. The size of the term dot represents how many miRNAs targeted genes annotated with each term. Abbreviations: miRNA: micro-RNA. https://drive.google.com/file/d/1xPuPJgeH_a4wsRUF04I-FNWIDa6A7IQs/view?usp=drive_web.

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  Fig. 10. A qRT-PCR validation. Expression levels of miRNAs in LMNAR249W (n = 6) vs. wild-type (n = 6) analyzed by qRT-PCR. (A) Downregulated miRNAs. (B) Upregulated miRNAs. Statistical significance was determined using a two-tailed t test. * p < 0.05; ** p < 0.01. Abbreviations: miRNA: micro-RNA. https://drive.google.com/file/d/13IkSMdaSrOY7ykTe5zW4GkmAxAYw1MiK/view?usp=drive_web.