The EXPANDER Integrated Platform for Transcriptome Analysis

Tom Aharon Hait, Adi Maron-Katz, Dorit Sagir, David Amar, Igor Ulitsky, Chaim Linhart, Amos Tanay, Roded Sharan, Yosef Shiloh, Ran Elkon, Ron Shamir

Research output: Contribution to journalArticlepeer-review

Abstract

Genome-wide analysis of cellular transcriptomes using RNA-seq or expression arrays is a major mainstay of current biological and biomedical research. EXPANDER (EXPression ANalyzer and DisplayER) is a comprehensive software package for analysis of expression data, with built-in support for 18 different organisms. It is designed as a “one-stop shop” platform for transcriptomic analysis, allowing for execution of all analysis steps starting with gene expression data matrix. Analyses offered include low-level preprocessing and normalization, differential expression analysis, clustering, bi-clustering, supervised grouping, high-level functional and pathway enrichment tests, and networks and motif analyses. A variety of options is offered for each step, using established algorithms, including many developed and published by our laboratory. EXPANDER has been continuously developed since 2003, having to date over 18,000 downloads and 540 citations. One of the innovations in the recent version is support for combined analysis of gene expression and ChIP-seq data to enhance the inference of transcriptional networks and their functional interpretation. EXPANDER implements cutting-edge algorithms and makes them accessible to users through user-friendly interface and intuitive visualizations. It is freely available to users at http://acgt.cs.tau.ac.il/expander/.

Original languageEnglish
Pages (from-to)2398-2406
Number of pages9
JournalJournal of Molecular Biology
Volume431
Issue number13
DOIs
StatePublished - 14 Jun 2019

Keywords

  • Gene expression analysis
  • RNA-seq analysis
  • Software package
  • Transcriptomic analysis

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