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High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions
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The EXPANDER Integrated Platform for Transcriptome Analysis.

Tom Aharon Hait1, Adi Maron-Katz2, Dorit Sagir3

  • 1The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.

Journal of Molecular Biology
|May 18, 2019
PubMed
Summary
This summary is machine-generated.

EXPANDER is a comprehensive software for transcriptomic analysis, integrating gene expression and ChIP-seq data. This user-friendly platform offers a one-stop shop for diverse analyses, enhancing biological and biomedical research.

Keywords:
Gene expression analysisRNA-seq analysisSoftware packageTranscriptomic analysis

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Genome-wide analysis of cellular transcriptomes is crucial in biological and biomedical research.
  • RNA-sequencing (RNA-seq) and expression arrays are standard tools for such analyses.
  • Efficient and comprehensive software is needed to manage and interpret large-scale expression datasets.

Purpose of the Study:

  • To present EXPANDER (EXPression ANalyzer and DisplayER), a comprehensive software package for transcriptomic data analysis.
  • To provide a "one-stop shop" platform for all stages of transcriptomic analysis, from raw data to high-level interpretation.
  • To introduce novel capabilities, including the combined analysis of gene expression and ChIP-seq data.

Main Methods:

  • EXPANDER offers a wide range of analytical modules, including preprocessing, normalization, differential expression analysis, clustering, and bi-clustering.
  • It supports supervised grouping, functional and pathway enrichment tests, and network and motif analyses.
  • The software incorporates established algorithms and novel methods, with support for 18 organisms.

Main Results:

  • EXPANDER has been continuously developed since 2003, demonstrating sustained utility and adoption.
  • The software has achieved over 18,000 downloads and 540 citations, indicating significant impact.
  • Recent versions enhance the inference of transcriptional networks and their functional interpretation through combined gene expression and ChIP-seq data analysis.

Conclusions:

  • EXPANDER provides a powerful, user-friendly platform for diverse transcriptomic analyses.
  • Its integration of gene expression and ChIP-seq data offers advanced capabilities for network inference.
  • The software is freely available, promoting accessibility and advancing biological and biomedical research.