“Upstream Analysis”: An Integrated Promoter-Pathway Analysis Approach to Causal Interpretation of Microarray Data

Koschmann, Jeannette; Bhar, Anirban; Stegmaier, Philip; Kel, Alexander E.; Wingender, Edgar

doi:10.3390/microarrays4020270

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“Upstream Analysis”: An Integrated Promoter-Pathway Analysis Approach to Causal Interpretation of Microarray Data

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Xplain GmbH, D-38302 Wolfenbüttel, Germany

Institute of Bioinformatics, University Medical Center Göttingen, D-37077 Göttingen, Germany

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Academic Editor: Heather J. Ruskin

Microarrays 2015, 4(2), 270-286; https://doi.org/10.3390/microarrays4020270

Received: 17 March 2015 / Revised: 11 May 2015 / Accepted: 14 May 2015 / Published: 21 May 2015

(This article belongs to the Special Issue Computational Modeling and Analysis of Microarray Data: New Horizons)

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Abstract

A strategy is presented that allows a causal analysis of co-expressed genes, which may be subject to common regulatory influences. A state-of-the-art promoter analysis for potential transcription factor (TF) binding sites in combination with a knowledge-based analysis of the upstream pathway that control the activity of these TFs is shown to lead to hypothetical master regulators. This strategy was implemented as a workflow in a comprehensive bioinformatic software platform. We applied this workflow to gene sets that were identified by a novel triclustering algorithm in naphthalene-induced gene expression signatures of murine liver and lung tissue. As a result, tissue-specific master regulators were identified that are known to be linked with tumorigenic and apoptotic processes. To our knowledge, this is the first time that genes of expression triclusters were used to identify upstream regulators. View Full-Text

Keywords: microarray data; gene expression signatures; upstream analysis; promoter analysis; pathway analysis

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Koschmann, J.; Bhar, A.; Stegmaier, P.; Kel, A.E.; Wingender, E. “Upstream Analysis”: An Integrated Promoter-Pathway Analysis Approach to Causal Interpretation of Microarray Data. Microarrays 2015, 4, 270-286. https://doi.org/10.3390/microarrays4020270

AMA Style

Koschmann J, Bhar A, Stegmaier P, Kel AE, Wingender E. “Upstream Analysis”: An Integrated Promoter-Pathway Analysis Approach to Causal Interpretation of Microarray Data. Microarrays. 2015; 4(2):270-286. https://doi.org/10.3390/microarrays4020270

Chicago/Turabian Style

Koschmann, Jeannette, Anirban Bhar, Philip Stegmaier, Alexander E. Kel, and Edgar Wingender. 2015. "“Upstream Analysis”: An Integrated Promoter-Pathway Analysis Approach to Causal Interpretation of Microarray Data" Microarrays 4, no. 2: 270-286. https://doi.org/10.3390/microarrays4020270

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“Upstream Analysis”: An Integrated Promoter-Pathway Analysis Approach to Causal Interpretation of Microarray Data

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