Integrated miRNA-mRNA analysis revealing the potential roles of miRNAs in chordomas
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ABSTRACT:
ORGANISM(S): synthetic construct Homo sapiens
PROVIDER: GSE56183 | GEO | 2014/03/29
SECONDARY ACCESSION(S): PRJNA242940
REPOSITORIES: GEO
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Project description:Emerging evidence suggests that microRNAs (miRNAs) are crucially involved in tumorigenesis and that paired expression profiles of miRNAs and mRNAs can be used to identify functional miRNA-target relationships with high precision.However, no studies have applied integrated analysis to miRNA and mRNA profiles in chordomas. The purpose of this study was to provide insights into the pathogenesis of chordomas by using this integrated analysis method Differentially expressed miRNAs and mRNAs of chordomas (n = 3) and notochord tissues (n = 3) were analyzed by using microarrays with hierarchical clustering analysis. Subsequently, the target genes of the differentially expressed miRNAs were predicted and overlapped with the differentially expressed mRNAs. Then, GO and pathway analyses were performed for the intersecting genes
2014-03-29 | E-GEOD-56183 | biostudies-arrayexpress
Project description:Emerging evidence suggests that microRNAs (miRNAs) are crucially involved in pathogenesis of NAFLD. The integrated analysis of expression profiles of miRNAs and mRNAs can be used to identify functional miRNA-target relationships with high precision. The purpose of this study was to provide insights into the immunopathogenesis of NAFLD using this integrated analysis method.Differentially expressed miRNAs and mRNAs of CD4+ T lymphocytes from liver and mesenteric lymph nodes(MLN) of NAFLD and normal mice were analyzed by microarrays and RNA sequencing respectively. Subsequently, the target genes of the differentially expressed miRNAs were predicted and overlapped with the differentially expressed mRNAs. Then, GO and pathway analyses were performed for the intersecting key genes. The microarray analysis indicated that 170 miRNAs and 2,791 mRNAs were significantly dysregulated in CD4+ T lymphocytes from liver between the two groups. Among the 2,791 mRNAs, 911 overlapped with putative miRNA target genes. A pathway analysis showed that the MAPK pathway was consistently enriched in the liver of NAFLD mice. miR-149-3p, miR-663a, miR-1908, miR-2861 and miR-3185 likely play important roles in the regulation of MAPK pathways. Furthermore, the Notch signaling pathway This study provides an integrated dataset of the miRNA and mRNA profiles in NAFLD, and the results demonstrate that not only the MAPK pathway and its related miRNAs but also the Notch pathway may be involved in NAFLD immunological development.
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Project description:Integrated miRNA-mRNA analysis revealing the potential roles of miRNAs in chordomas
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Project description:Microarray?based techniques are being used to obtain miRNA and gene expression signatures associated with different samples. In order to deepen our understanding of BRCA1-associated tumorigenesis, we integrated data from microarray experiments to obtain significant miRNA-mRNA relationships associated with the presence of the BRCA1 gene. We obtained significant miRNA-gene-pathway relationships underlying the array signatures. Furthermore, we have demonstrated that miR-146a, miR-99b and miR-205, induced in HCC1937 BRCA1-expressing cells, commonly regulate the TRAF2 gene, a key regulator of NF-?B and MAPK pathways. In addition, re-expression of miR-146a, miR-99b or miR-205 in HCC1937 BRCA1-null cells was sufficient to modulate NF-?B activity. Thus, integration between miRNA-mRNA expression data allowed us to define genes and pathways controlled by miRNAs induced in the context of BRCA1 expression. Comparison of miRNA expression profiles between two isogenic cell lines differing in BRCA1 gene expression status. Single-color experiments in a pairwise comparison design with three technical replicates per cell line.
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