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ABioTrans: A Biostatistical Tool for Transcriptomics Analysis.

Yutong Zou1, Thuy Tien Bui2, Kumar Selvarajoo2

  • 1Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore.

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|June 20, 2019
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Summary
This summary is machine-generated.

ABioTrans is a new R tool for analyzing RNA-Seq gene expression data. It simplifies complex bioinformatics tasks, enabling researchers to explore gene expression patterns and classifications from the Gene Expression Omnibus database.

Keywords:
DEG (differentially expressed genes)RNA-seqclusteringcorrelationentropygene expression datanoisetranscriptomics

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Area of Science:

  • Bioinformatics and Computational Biology
  • Genomics and Transcriptomics
  • Statistical Genetics

Background:

  • Gene expression analysis is crucial for understanding biological processes.
  • Accessing and analyzing data from repositories like the Gene Expression Omnibus (GEO) can be complex.
  • Bioinformatic tools are needed to streamline RNA-Seq data interpretation.

Purpose of the Study:

  • To introduce ABioTrans, a novel R package for comprehensive gene expression analysis.
  • To provide researchers with an accessible tool for processing RNA-Seq data from public databases.
  • To facilitate various statistical and clustering analyses for gene expression data.

Main Methods:

  • Development of ABioTrans using the R programming language.
  • Integration with the Gene Expression Omnibus (GEO) database for direct data retrieval.
  • Implementation of statistical analyses including distribution fitting, correlation, PCA, and clustering (k-means, hierarchical).
  • Inclusion of differential expression analysis, entropy, noise calculations, and Gene Ontology classification.

Main Results:

  • ABioTrans offers a user-friendly interface accessible via web browsers.
  • The tool supports direct import of RNA-Seq data from GEO.
  • It enables a wide range of analyses, from basic statistics to advanced bioinformatics classifications.
  • Facilitates exploration of gene expression patterns and biological functions.

Conclusions:

  • ABioTrans provides a versatile and accessible platform for RNA-Seq gene expression analysis.
  • The tool empowers researchers to conduct complex bioinformatics analyses efficiently.
  • It enhances the utility of public gene expression datasets for biological discovery.