TY - JOUR
T1 - From proteomics toward systems biology
T2 - Integration of different types of proteomics data into network models
AU - Rho, Sangchul
AU - You, Sungyong
AU - Kim, Yongsoo
AU - Hwang, Daehee
PY - 2008/3/1
Y1 - 2008/3/1
N2 - 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.
AB - 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.
KW - Data integration
KW - Network analysis
KW - Network modeling
KW - Proteomics
KW - Systems biology
UR - http://www.scopus.com/inward/record.url?scp=42049115910&partnerID=8YFLogxK
M3 - Short survey
C2 - 18377721
SN - 1225-8687
VL - 41
SP - 184
EP - 193
JO - Journal of Biochemistry and Molecular Biology
JF - Journal of Biochemistry and Molecular Biology
IS - 3
ER -