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Related Concept Videos

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MicroRNA (miRNA) are short, regulatory RNA transcribed from introns (non-coding regions of a gene) or intergenic regions (stretches of DNA present between genes). Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself, forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA...
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MicroRNA (miRNA) are short, regulatory RNA transcribed from introns—non-coding regions of a gene—or intergenic regions—stretches of DNA present between genes. Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After...
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Dissecting the biological relationship between TCGA miRNA and mRNA sequencing data using MMiRNA-Viewer.

Yongsheng Bai1,2, Lizhong Ding3, Steve Baker4

  • 1Department of Biology, Indiana State University, Terre Haute, IN, 47809, USA. Yongsheng.Bai@indstate.edu.

BMC Bioinformatics
|October 22, 2016
PubMed
Summary
This summary is machine-generated.

This study introduces MMiRNA-Viewer, a tool for visualizing miRNA-mRNA relationships in cancer. It helps identify key gene pairs and biological pathways involved in cancer development.

Keywords:
CancerCorrelationExpressionMMiRNA-ViewerRegulationTCGAVisualizationmRNAmiRNA

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Area of Science:

  • Genomics
  • Bioinformatics
  • Cancer Research

Background:

  • MicroRNAs (miRNAs) regulate gene expression by interacting with messenger RNAs (mRNAs).
  • The Cancer Genome Atlas (TCGA) provides extensive cancer genomic data, but lacks tools for visualizing miRNA-mRNA interactions in both normal and tumor samples.
  • Existing analyses have not fully explored multi-cancer miRNA-mRNA relationships using integrated web-based approaches.

Purpose of the Study:

  • To develop an interactive visualization tool, MMiRNA-Viewer, for concurrent display of miRNA-mRNA co-expression and targeting relationships.
  • To enable comparison of these relationships between tumor and normal samples across multiple cancer types.
  • To facilitate the investigation of biological functions and pathways associated with miRNA-mRNA interactions in cancer.

Main Methods:

  • Developed MMiRNA-Viewer for interactive visualization of miRNA-mRNA expression, correlation, and predicted targets.
  • Utilized TCGA datasets from eight cancer types, applying filtering steps to identify relevant miRNA-mRNA pairs.
  • Performed Gene Ontology (GO) analysis and calculated centrality measurements for key genes and miRNAs within connected networks.

Main Results:

  • MMiRNA-Viewer successfully visualizes co-relationships between miRNA-mRNA pairs in tumor and normal samples.
  • Analysis of eight TCGA cancer datasets revealed significant biological functions and pathways involving identified genes.
  • Top-ranked genes and miRNAs with high centrality measurements were identified in cancer-specific networks.

Conclusions:

  • MMiRNA-Viewer provides an intuitive platform for exploring miRNA-mRNA co-relationships in cancer.
  • Suggests that inversely correlated miRNA-mRNA pairs with opposing expression changes in tumor vs. normal samples are crucial for understanding mRNA targeting disruptions.
  • Highlights the potential of MMiRNA-Viewer for elucidating cancer-specific molecular mechanisms.