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A Complete Pipeline for Isolating and Sequencing MicroRNAs, and Analyzing Them Using Open Source Tools
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MARTin-an open-source platform for microarray analysis.

Kai O Kreissner1, Benjamin Faller2, Ivan Talucci1,3

  • 1Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Würzburg, Germany.

Frontiers in Bioinformatics
|February 26, 2024
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Summary
This summary is machine-generated.

A new open-source software, MicroArray Rastering Tool (MARTin), offers reliable and efficient analysis for protein and peptide microarray data. This versatile tool ensures reproducible quantification across diverse array formats, enhancing data-driven discovery.

Keywords:
ImageJJavaarray analysisimage analysismicroarrayopen sourceproteomics

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Area of Science:

  • Biotechnology
  • Bioinformatics
  • Proteomics

Background:

  • Microarray technology enables high-throughput analysis of biomolecular interactions and gene expression.
  • Increasing data complexity and format variations necessitate robust quantification techniques.
  • Challenges in microarray analysis include diverse formats and potential flaws in interpretation.

Purpose of the Study:

  • To introduce MicroArray Rastering Tool (MARTin), a software for protein and peptide microarray image quantification.
  • To provide a versatile, user-friendly, and reproducible analysis solution.
  • To address challenges posed by varied microarray and imager formats.

Main Methods:

  • Development of MicroArray Rastering Tool (MARTin) software.
  • Implementation of adaptive filtering and autofit features for efficient measurements.
  • Integration of metadata management and integrity checks for quality control.

Main Results:

  • MARTIN is platform-independent and supports various microarray configurations, including high-density and custom formats.
  • The software ensures highly reproducible measurements through adaptive filtering and autofit.
  • Integrated quality control and data analysis features enhance scientific practice.

Conclusions:

  • MARTIN provides a reliable, efficient, and intuitive tool for peptidomic and proteomic array analysis.
  • The open-source software facilitates data-driven discovery across scientific disciplines.
  • MARTIN is freely available on GitHub under the GNU Affero General Public License.