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Expander: from expression microarrays to networks and functions

Nature Protocols volume 5, pages 303–322 (2010)Cite this article

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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.

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Figure 1: Flow chart of the Expander workflow.
Figure 3: Expander views.
Figure 2: Data sheet view.
Figure 4: Clustering solution visualization.
Figure 5: Enrichment analysis results.
Figure 6: MATISSE results.

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Acknowledgements

We thank Israel Steinfeld for his role in the early development of Expander, Metsada Pasmanik-Chor for useful discussions and Akshay Krishnamurthy for commenting on an early version of the protocol. Igor Ulitsky was partially supported by the Edmond J Safra Bioinformatics Program at Tel Aviv University and by the Legacy Heritage Fund. Yosef Shiloh is a Research Professor of the Israel Cancer Research Fund. This study was supported in part by the Israel Science Foundation (Grant No. 802/08) and by the European Community's Seventh Framework Programme (Grants HEALTH-F4-2007-200767 for the APO-SYS project and HEALTH-F4-2009-223575 for the TRIREME project).

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  1. Igor Ulitsky

    Present address: Current address: Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA.,

Authors and Affiliations

  1. Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel

    Igor Ulitsky, Adi Maron-Katz, Seagull Shavit, Chaim Linhart, Roded Sharan & Ron Shamir

  2. Department of Human Molecular Genetics and Biochemistry, Tel Aviv University, Tel Aviv, Israel

    Dorit Sagir & Yosef Shiloh

  3. Division of Gene Regulation, The Netherlands Cancer Institute, Amsterdam, The Netherlands

    Ran Elkon

  4. Faculty of Mathematics and Computer Science, Weizmann Institute of Science, Rehovot, Israel

    Amos Tanay

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Contributions

R.S. conceived and led the project; A.M.-K., S.S. and D.S. developed Expander using software code contributed by R.S., A.T., C.L., R.E. and I.U.; I.U. and R.S. wrote the paper. All the authors contributed to the design of Expander, and all have read and approved the paper.

Corresponding author

Correspondence to Ron Shamir.

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Competing interests

Expander is available for commercial licensing through Tel Aviv University's technology transfer company.

Supplementary information

Supplementary Data 1

BMM.txt contains a microarray dataset constructed by the Innate Immunity Systems Biology project (http://www.innateimmunity-systemsbiology.org/), in which expression profiles were recorded in murine bone marrow-derived macrophage cells (BMMs) at several time points after exposure to six agents. (TXT 15753 kb)

Supplementary Data 2

MG430_2.0_Probe2EntrezGene.txt contains a mapping of Affymetrix Murine Genome (MG) U430 2.0 probes to Entrez Gene identifiers, taken from BioMart24. (TXT 573 kb)

Supplementary Data 3

Mir155.txt contains a microarray dataset due to Rodriguez et al.22, in which five repeats of Th1 cells deficient for mir-155 are compared with five controls (obtained from the ArrayExpress database, accession number E-TABM-232). (TXT 3337 kb)

Supplementary Data 4

mouse.IntAct.sif a mouse PPI network taken from the IntAct database43, in SIF format. (TXT 35 kb)

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Ulitsky, I., Maron-Katz, A., Shavit, S. et al. Expander: from expression microarrays to networks and functions. Nat Protoc 5, 303–322 (2010). https://doi.org/10.1038/nprot.2009.230

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