Expander: From expression microarrays to networks and functions

Igor Ulitsky, Adi Maron-Katz, Seagull Shavit, Dorit Sagir, Chaim Linhart, Ran Elkon, Amos Tanay, Roded Sharan, Yosef Shiloh, Ron Shamir*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

A major challenge in the analysis of gene expression microarray data is to extract meaningful biological knowledge out of the huge volume of raw data. Expander (EXPression ANalyzer and DisplayER) is an integrated software platform for the analysis of gene expression data, which is freely available for academic use. It is designed to support all the stages of microarray data analysis, from raw data normalization to inference of transcriptional regulatory networks. The microarray analysis described in this protocol starts with importing the data into Expander 5.0 and is followed by normalization and filtering. Then, clustering and network-based analyses are performed. The gene groups identified are tested for enrichment in function (based on Gene Ontology), co-regulation (using transcription factor and microRNA target predictions) or co-location. The results of each analysis step can be visualized in a number of ways. The complete protocol can be executed in ∼1 h.

Original languageEnglish
Pages (from-to)303-322
Number of pages20
JournalNature Protocols
Volume5
Issue number2
DOIs
StatePublished - Feb 2010

Funding

FundersFunder number
Seventh Framework Programme223575, 200767
Israel Science Foundation802/08
Tel Aviv University
Seventh Framework ProgrammeHEALTH-F4-2007-200767, HEALTH-F4-2009-223575

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