Analyzing cellular biochemistry in terms of molecular networks Journal Article
| Authors: | Xia, Y.; Yu, H.; Jansen, R.; Seringhaus, M.; Baxter, S.; Greenbaum, D.; Zhao, H.; Gerstein, M. |
| Article Title: | 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. |
| Keywords: | protein array analysis; sequence analysis; review; nonhuman; proteins; protein analysis; gene expression; models, biological; protein protein interaction; data base; quantitative analysis; gene interaction; intermethod comparison; chemical structure; yeast; databases, factual; biochemistry; systems theory; cytochemistry; fungal protein; protein dna interaction; macromolecular substances; two-hybrid system techniques; mathematical analysis; cells; regulatory networks; noise; experimentation; coevolution; priority journal; genome-wide high-throughput experiments; integration and prediction; network topology; protein-protein interaction networks |
| Journal Title: | Annual Review of Biochemistry |
| Volume: | 73 |
| ISSN: | 0066-4154 |
| Publisher: | Annual Reviews |
| Date Published: | 2004-01-01 |
| Start Page: | 1051 |
| End Page: | 1087 |
| Language: | English |
| DOI: | 10.1146/annurev.biochem.73.011303.073950 |
| PROVIDER: | scopus |
| PUBMED: | 15189167 |
| DOI/URL: | |
| Notes: | Annu. Rev. Biochem. -- Cited By (since 1996):91 -- Export Date: 16 June 2014 -- CODEN: ARBOA -- Source: Scopus |
