title: From proteomics toward systems biology: integration of different types of proteomics data into network models.
abstract: Living organisms are comprised of various systems at different levels, i.e., organs, tissues, and cells. Each system carries out its diverse functions in response to environmental and genetic perturbations, by utilizing biological networks, in which nodal components, such as, DNA, mRNAs, proteins, and metabolites, closely interact with each other. Systems biology investigates such systems by producing comprehensive global data that represent different levels of biological information, i.e., at the DNA, mRNA, protein, or metabolite levels, and by integrating this data into network models that generate coherent hypotheses for given biological situations. This review presents a systems biology framework, called the 'Integrative Proteomics Data Analysis Pipeline' (IPDAP), which generates mechanistic hypotheses from network models reconstructed by integrating diverse types of proteomic data generated by mass spectrometry-based proteomic analyses. The devised framework includes a serial set of computational and network analysis tools. Here, we demonstrate its functionalities by applying these tools to several conceptual examples.
authors: School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Korea. Dhhwang@postech.ac.kr
authors: Sangchul
authors: S
authors: Rho
authors: Sungyong
authors: S
authors: You
authors: Yongsoo
authors: Y
authors: Kim
authors: Daehee
authors: D
authors: Hwang
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D013058:Mass Spectrometry; D008954:Models, Biological; D008969:Molecular Sequence Data; D020543:Proteome / Q000737:chemistry; D040901:Proteomics / Q000379:methods*; D049490:Systems Biology / Q000379:methods*
chemical_list: D020543:Proteome