Analyzing cellular biochemistry in terms of molecular networks
- PMID:15189167
- DOI: 10.1146/annurev.biochem.73.011303.073950
Analyzing cellular biochemistry in terms of molecular networks
Abstract
One way to understand cells and circumscribe the function of proteins is through molecular networks. These networks take a variety of forms including webs of protein-protein interactions, regulatory circuits linking transcription factors and targets, and complex pathways of metabolic reactions. We first survey experimental techniques for mapping networks (e.g., the yeast two-hybrid screens). We then turn our attention to computational approaches for predicting networks from individual protein features, such as correlating gene expression levels or analyzing sequence coevolution. All the experimental techniques and individual predictions suffer from noise and systematic biases. These problems can be overcome to some degree through statistical integration of different experimental datasets and predictive features (e.g., within a Bayesian formalism). Next, we discuss approaches for characterizing the topology of networks, such as finding hubs and analyzing subnetworks in terms of common motifs. Finally, we close with perspectives on how network analysis represents a preliminary step toward a systems approach for modeling cells.
Similar articles
- METANNOGEN: compiling features of biochemical reactions needed for the reconstruction of metabolic networks.Gille C, Hoffmann S, Holzhütter HG.Gille C, et al.BMC Syst Biol. 2007 Jan 9;1:5. doi: 10.1186/1752-0509-1-5.BMC Syst Biol. 2007.PMID:17408512Free PMC article.
- Quantitative modeling of biochemical networks.Hofestädt R, Thelen S.Hofestädt R, et al.In Silico Biol. 1998;1(1):39-53.In Silico Biol. 1998.PMID:11471241
- Interaction networks: from protein functions to drug discovery. A review.Chautard E, Thierry-Mieg N, Ricard-Blum S.Chautard E, et al.Pathol Biol (Paris). 2009 Jun;57(4):324-33. doi: 10.1016/j.patbio.2008.10.004. Epub 2008 Dec 13.Pathol Biol (Paris). 2009.PMID:19070972Review.
- Analyzing protein interaction networks using structural information.Kiel C, Beltrao P, Serrano L.Kiel C, et al.Annu Rev Biochem. 2008;77:415-41. doi: 10.1146/annurev.biochem.77.062706.133317.Annu Rev Biochem. 2008.PMID:18304007Review.
- Implicit methods for qualitative modeling of gene regulatory networks.Garg A, Mohanram K, De Micheli G, Xenarios I.Garg A, et al.Methods Mol Biol. 2012;786:397-443. doi: 10.1007/978-1-61779-292-2_22.Methods Mol Biol. 2012.PMID:21938638
Cited by
- Navigating the network: signaling cross-talk in hematopoietic cells.Fraser ID, Germain RN.Fraser ID, et al.Nat Immunol. 2009 Apr;10(4):327-31. doi: 10.1038/ni.1711. Epub 2009 Mar 19.Nat Immunol. 2009.PMID:19295628Free PMC article.Review.
- Identification of key signaling pathways in cerebral small vessel disease using differential pathway network analysis.Zheng G, Zheng Q, Xu Q.Zheng G, et al.Exp Ther Med. 2017 Nov;14(5):4371-4376. doi: 10.3892/etm.2017.5104. Epub 2017 Sep 5.Exp Ther Med. 2017.PMID:29104648Free PMC article.
- Biological Resource Centers and Systems Biology.Wang Y, Lilburn TG.Wang Y, et al.Bioscience. 2009 Feb 11;59(2):113-125. doi: 10.1525/bio.2009.59.2.5.Bioscience. 2009.PMID:20157346Free PMC article.
- Protein interaction networks in plants.Uhrig JF.Uhrig JF.Planta. 2006 Sep;224(4):771-81. doi: 10.1007/s00425-006-0260-x. Epub 2006 Mar 31.Planta. 2006.PMID:16575597Review.
- The G protein-coupled receptor heterodimer network (GPCR-HetNet) and its hub components.Borroto-Escuela DO, Brito I, Romero-Fernandez W, Di Palma M, Oflijan J, Skieterska K, Duchou J, Van Craenenbroeck K, Suárez-Boomgaard D, Rivera A, Guidolin D, Agnati LF, Fuxe K.Borroto-Escuela DO, et al.Int J Mol Sci. 2014 May 14;15(5):8570-90. doi: 10.3390/ijms15058570.Int J Mol Sci. 2014.PMID:24830558Free PMC article.
Publication types
MeSH terms
Substances
Grants and funding
LinkOut - more resources
Full Text Sources
Molecular Biology Databases