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GOBO: Gene Expression-Based Outcome for Breast Cancer Online

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  • Markus Ringnér
  • Erik Fredlund
  • Jari Häkkinen
  • Åke Borg
  • Johan Staaf

Abstract

Microarray-based gene expression analysis holds promise of improving prognostication and treatment decisions for breast cancer patients. However, the heterogeneity of breast cancer emphasizes the need for validation of prognostic gene signatures in larger sample sets stratified into relevant subgroups. Here, we describe a multifunctional user-friendly online tool, GOBO (http://co.bmc.lu.se/gobo), allowing a range of different analyses to be performed in an 1881-sample breast tumor data set, and a 51-sample breast cancer cell line set, both generated on Affymetrix U133A microarrays. GOBO supports a wide range of applications including: 1) rapid assessment of gene expression levels in subgroups of breast tumors and cell lines, 2) identification of co-expressed genes for creation of potential metagenes, 3) association with outcome for gene expression levels of single genes, sets of genes, or gene signatures in multiple subgroups of the 1881-sample breast cancer data set. The design and implementation of GOBO facilitate easy incorporation of additional query functions and applications, as well as additional data sets irrespective of tumor type and array platform.

Suggested Citation

  • Markus Ringnér & Erik Fredlund & Jari Häkkinen & Åke Borg & Johan Staaf, 2011. "GOBO: Gene Expression-Based Outcome for Breast Cancer Online," PLOS ONE, Public Library of Science, vol. 6(3), pages 1-11, March.
    • Handle: RePEc:plo:pone00:0017911
    DOI: 10.1371/journal.pone.0017911
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    1. Charles M. Perou & Therese Sørlie & Michael B. Eisen & Matt van de Rijn & Stefanie S. Jeffrey & Christian A. Rees & Jonathan R. Pollack & Douglas T. Ross & Hilde Johnsen & Lars A. Akslen & Øystein Flu, 2000. "Molecular portraits of human breast tumours," Nature, Nature, vol. 406(6797), pages 747-752, August.
    2. Andy J. Minn & Gaorav P. Gupta & Peter M. Siegel & Paula D. Bos & Weiping Shu & Dilip D. Giri & Agnes Viale & Adam B. Olshen & William L. Gerald & Joan Massagué, 2005. "Genes that mediate breast cancer metastasis to lung," Nature, Nature, vol. 436(7050), pages 518-524, July.
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    1. Masoumeh Moslemi & Ehsan Sohrabi & Nemamali Azadi & Ali Zekri & Hamed Afkhami & Mansoor Khaledi & Ehsan Razmara, 2020. "Expression Analysis of EEPD1 and MUS81 Genes in Breast Cancer," Biomedical Journal of Scientific & Technical Research, Biomedical Research Network+, LLC, vol. 29(4), pages 22556-22564, August.

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