Identification of key miRNA-gene pairs in chronic lymphocytic leukemia through integrated analysis of mRNA and miRNA microarray.

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The miRNA expression dataset GSE62137 and mRNA expression dataset GSE22529 were downloaded from National Center of Biotechnology Information Gene Expression Omnibus database. In CLL samples compared with normal B cell samples, differentially expressed miRNAs (DEMs) were identified via the GEO2R instrument of GEO and differentially expressed genes (DEGs) were obtained via the limma package of R. Functional enrichment analysis of the DEGs was performed via the Database for Annotation, Visualization and Integrated Discovery. The targets of the DEMs were identified based on the miRNAWalk platform. The overlaps between the DEGs and the targets of the DEMs were selected, and the miRNA-Gene regulatory network was constructed based on the overlaps and the corresponding DEMs. A total of 63 DEMs and 504 DEGs were identified in CLL samples compared with normal B cell samples. Eleven enriched functional clusters of the DEGs were obtained. 405 miRNA-Gene regulatory pairs were identified. The miRNA-Gene regulatory pairs contained 351 target genes of the DEMs, including 9 overlaps with the DEGs. A miRNA-Gene regulatory network was constructed. Bioinformatics methods could help us develop a better understanding of the molecular mechanism of CLL. MiRNAs may play a critical role in regulating the process of CLL. They may affect CLL by regulating the processes of immunoreactivity and protein degradation. Genes such as Neurogenic Locus Notch Homolog Protein 2, PR/SET domain 4 and A-kinase anchoring protein 12 may be their regulating targets in CLL.", "claims": [{"id": "claim-method", "statement": "DEGs in CLL samples compared with normal B cell samples were identified via the limma package (24) of R.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29285196", "locator": "sections[5] \"Identification of differently expressed miRNAs and genes\" paragraph 2", "quote": "DEGs in CLL samples compared with normal B cell samples were identified via the limma package (24) of R."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The miRNA expression dataset GSE62137 (21) and mRNA expression dataset GSE22529 (22) were downloaded from National Center of Biotechnology Information (NCBI) Gene Expression Omnibus (GEO; http://www.ncbi.nlm.nih.gov/geo/) database. 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The miRNA dataset GSE62137 contained 44 samples, including 38 CLL cell samples and 6 normal B cell samples."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using GEO2R for miRNAs and limma for mRNAs on GSE62137 and GSE22529 downloaded from NCBI GEO, the study identified 63 differentially expressed miRNAs and 504 differentially expressed genes in CLL samples compared with normal B cell samples.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:29285196", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The miRNA expression dataset GSE62137 and mRNA expression dataset GSE22529 were downloaded from National Center of Biotechnology Information Gene Expression Omnibus database."}, {"asset": "source:pmid:29285196", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "A total of 63 DEMs and 504 DEGs were identified in CLL samples compared with normal B cell samples."}, {"asset": "source:pmid:29285196", "locator": "sections[5] \"Identification of differently expressed miRNAs and genes\" paragraph 2", "quote": "For the miRNA dataset, DEMs in CLL samples compared with normal B cell samples were identified via the GEO2R application of GEO."}, {"asset": "source:pmid:29285196", "locator": "sections[5] \"Identification of differently expressed miRNAs and genes\" paragraph 2", "quote": "For the mRNA dataset, the raw data with CEL files were background corrected, normalized and log2 transformed using the affy package in R. 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