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Binary fission is the primary mode of asexual reproduction in prokaryotes, such as bacteria. It results in the production of two genetically identical daughter cells. This highly efficient process ensures the rapid propagation of bacterial populations under favorable conditions and involves coordinated cellular and molecular events.DNA Replication and SeparationThe process begins with the replication of the bacterial chromosome. The circular DNA molecule unwinds at a specific origin of...
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In eukaryotes, transcription and translation are compartmentalized; an mRNA is first synthesized in the nucleus and then selectively transported to the cytoplasm for protein synthesis. Before transport, a pre-mRNA undergoes several steps of post-transcriptional modifications including splicing, 5' capping, and the addition of a poly-adenine tail. Various proteins bind to the pre-mRNA during these modifications. The mRNA transport takes place with the help of multiple proteins playing...
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Before mRNAs are exported to the cytoplasm, it is crucial to check each mRNA for structural and functional integrity. Eukaryotic cells use several different mechanisms, collectively known as mRNA surveillance, to look for irregularities in mRNAs. Irregular or aberrant mRNA are rapidly degraded by various enzymes. If a defective mRNA escapes the surveillance, it would be translated into a protein which would either be non-functional or not function properly. One of the primary irregularities in...
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In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or pre-mRNA to distinguish it from mature mRNA.
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HisCoM-mimi: Software for Hierarchical Structural Component Analysis for miRNA-mRNA Integration Model for Binary

Yongkang Kim1, Taesung Park1,2

  • 1Department of Statistics, Seoul National University, Seoul 08826, Korea.

Genomics & Informatics
|April 2, 2019
PubMed
Summary

We introduce HisCoM-mimi, a new software tool to identify microRNA-messenger RNA (miRNA-mRNA) interactions linked to binary phenotypes. It integrates multiple databases and advanced algorithms for broader biological data analysis.

Keywords:
integration analysismRNAmiRNAmiRNA database

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • MicroRNA-messenger RNA (miRNA-mRNA) interactions play crucial roles in gene regulation.
  • Identifying these interactions is vital for understanding binary phenotypes.
  • Existing methods often rely on single databases or limited algorithms.

Purpose of the Study:

  • To develop an advanced software application for miRNA-mRNA integration (HisCoM-mimi) tailored for binary phenotypes.
  • To enhance the identification of miRNA-mRNA interaction pairs by incorporating multiple data sources and improved algorithms.

Main Methods:

  • The HisCoM-mimi model utilizes a hierarchical structural component approach.
  • It integrates data from TargetScan and miRTarBase, a manually-verified database.
  • Updated algorithms include lasso and elastic-net penalties for model selection.

Main Results:

  • The enhanced HisCoM-mimi supports integration of data from both TargetScan and miRTarBase.
  • It enables analysis of a broader range of miRNA-mRNA target information from the literature.
  • The inclusion of penalized regression methods allows for fitting models with fewer selected miRNAs and mRNAs.

Conclusions:

  • The advanced HisCoM-mimi software provides researchers with accessible tools for identifying miRNA-mRNA interactions associated with binary phenotypes.
  • This integrated approach allows for more comprehensive analysis of miRNA-mRNA regulatory networks.
  • The software facilitates the discovery of novel miRNA-mRNA signatures relevant to various biological conditions.