"Upstream Analysis": An Integrated Promoter-Pathway Analysis Approach to Causal Interpretation of Microarray Data.

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 kno

SUBMITTER: Koschmann J 

PROVIDER: S-EPMC4996392 | biostudies-literature | 2015 May

REPOSITORIES: biostudies-literature