Causal analysis approaches in Ingenuity Pathway Analysis
Top Cited Papers
Open Access
- 13 December 2013
- journal article
- research article
- Published by Oxford University Press (OUP) in Bioinformatics
- Vol. 30 (4), 523-530
- https://doi.org/10.1093/bioinformatics/btt703
Abstract
Motivation: Prior biological knowledge greatly facilitates the meaningful interpretation of gene-expression data. Causal networks constructed from individual relationships curated from the literature are particularly suited for this task, since they create mechanistic hypotheses that explain the expression changes observed in datasets. Results: We present and discuss a suite of algorithms and tools for inferring and scoring regulator networks upstream of gene-expression data based on a large-scale causal network derived from the Ingenuity Knowledge Base. We extend the method to predict downstream effects on biological functions and diseases and demonstrate the validity of our approach by applying it to example datasets. Availability: The causal analytics tools ‘Upstream Regulator Analysis', ‘Mechanistic Networks', ‘Causal Network Analysis' and ‘Downstream Effects Analysis' are implemented and available within Ingenuity Pathway Analysis (IPA, http://www.ingenuity.com). Supplementary information: Supplementary material is available at Bioinformatics online.Keywords
This publication has 20 references indexed in Scilit:
- Parity induces differentiation and reduces Wnt/Notch signaling ratio and proliferation potential of basal stem/progenitor cells isolated from mouse mammary epitheliumBreast Cancer Research, 2013
- Assessment of network perturbation amplitudes by applying high-throughput data to causal biological networksBMC Systems Biology, 2012
- Assessing statistical significance in causal graphsBMC Bioinformatics, 2012
- Excessive bone formation in a mouse model of ankylosing spondylitis is associated with decreases in Wnt pathway inhibitorsArthritis Research & Therapy, 2012
- 2009 pandemic H1N1 influenza virus elicits similar clinical course but differential host transcriptional response in mouse, macaque, and swine infection modelsBMC Genomics, 2012
- Causal reasoning identifies mechanisms of sensitivity for a novel AKT kinase inhibitor, GSK690693BMC Genomics, 2010
- Comparative study of gene set enrichment methodsBMC Bioinformatics, 2009
- Whole-Genome Cartography of Estrogen Receptor α Binding SitesPLoS Genetics, 2007
- A Computational Model to Define the Molecular Causes of Type 2 Diabetes MellitusDiabetes Technology & Therapeutics, 2005
- The Anti-estrogenic Effect of All-trans-retinoic Acid on the Breast Cancer Cell Line MCF-7 Is Dependent on HES-1 ExpressionOnline Journal of Public Health Informatics, 2002