Systems Approach to Integrative Biology: An Overview of Statistical Methods to Elucidate Association and Architecture

• Published in: Integrative and comparative biology Vol. 54; no. 2; pp. 296 - 306
• Main Authors: Ciaccio, Mark F, Justin D. Finkle, Albert Y. Xue, Neda Bagheri
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01-07-2014; Oxford Publishing Limited (England)
• Subjects: A New Organismal Systems Biology: How Animals Walk the Tight Rope between Stability and Change; algorithms; Animals; case studies; Cells; data collection; ecosystems; Genomics; Models, Biological; Mollusks; mussels; Mytilus - physiology; Mytilus galloprovincialis; Organisms; phenotype; physiological response; prediction; Proteomics; Signal Transduction; statistical analysis; Systems Biology - methods; Temperature
• ISSN: 1540-7063; 1557-7023
• DOI: 10.1093/icb/icu037

An organism’s ability to maintain a desired physiological response relies extensively on how cellular and molecular signaling networks interpret and react to environmental cues. The capacity to quantitatively predict how networks respond to a changing environment by modifying signaling regulation and phenotypic responses will help inform and predict the impact of a changing global enivronment on organisms and ecosystems. Many computational strategies have been developed to resolve cue–signal–response networks. However, selecting a strategy that answers a specific biological question requires knowledge both of the type of data being collected, and of the strengths and weaknesses of different computational regimes. We broadly explore several computational approaches, and we evaluate their accuracy in predicting a given response. Specifically, we describe how statistical algorithms can be used in the context of integrative and comparative biology to elucidate the genomic, proteomic, and/or cellular networks responsible for robust physiological response. As a case study, we apply this strategy to a dataset of quantitative levels of protein abundance from the mussel, Mytilus galloprovincialis, to uncover the temperature-dependent signaling network.