Published 2010
Table of Contents:
“…Cover -- Half-title -- Title -- Copyright -- Contents -- Contributors -- Introduction -- 1 Network views of the cell -- 1.1 The network hypothesis -- 1.2 The central dogma and gene regulatory networks -- 1.3 Proteinprotein interaction networks -- 1.4 Metabolic networks -- 1.5 Signaling networks -- 1.6 Networked networks and cell functionality -- 1.7 Concluding remarks -- 2 Transcriptional regulatory networks -- 2.1 Introduction -- 2.2 Transcriptional regulation in prokaryotes and eukaryotes -- 2.3 Structure of transcriptional regulatory networks -- 2.3.1 Global level -- 2.3.2 Modular level -- 2.3.3 Local level -- 2.4 Evolution of transcriptional regulatory networks -- 2.4.1 Evolution of transcription factors and
cis-regulatory elements -- 2.4.2 Transcriptional network evolution within an organism -- 2.4.3 Transcriptional network evolution across organisms -- 2.5 Dynamics of transcriptional regulatory networks -- 2.5.1 Temporal dynamics of transcriptional networks -- 2.5.2 Dynamics of individual regulatory interactions -- 2.6 Conclusions -- Acknowledgments -- 3 Transcription factors and gene regulatory networks -- 3.1 Introduction -- 3.2 Promoters' complexity/eukaryotic gene promoters -- 3.2.1 Human promoters -- 3.3 Transcription factors -- 3.3.1 bZIP transcription factors -- 3.3.2 Helix-turn-helix domains -- 3.3.3 Zinc-coordinating domains -- 3.4 Bioinformatics of regulatory networks -- 3.4.1 Transcription factors identification -- 3.4.2 Motif finding -- 4 Experimental methods for protein interaction identification -- 4.1 Introduction -- 4.1.1 Complex versus binary interactions -- 4.1.2 The biological relevance of detected proteinprotein interactions -- 4.1.3 Proteinprotein interactions are incompletely studied -- 4.2 Protein complementation techniques -- 4.2.1 The yeast two-hybrid system -- 4.2.2 Other fragment complementation techniques -- 4.3 Affinity purification methods -- 4.3.1 GST pulldown -- 4.3.2 Co-immunoprecipitation -- 4.4 Protein complex purification and mass spectrometry -- 4.4.1 Purification of proteins using affinity tags -- 4.4.2 Tandem affinity tagging -- 4.4.3 Genetics and cloning of affinity tagged proteins -- 4.4.4 Isolation of protein complexes -- 4.4.5 Proteomics by mass spectrometry -- 4.4.6 Identifying interacting proteins using mass spectrometry -- 4.4.7 Quantitative proteomics -- 4.5 Protein and peptide chips -- 4.6 Other methods for interaction detection and functional analysis -- Genetic interactions -- Functional interactions such as post-translational modifications -- 4.7 Quality of large-scale interaction data -- 4.8 Comparison of methods -- 4.8.1 Y2H vs. co-AP/MS -- 4.8.2 coAP/MS vs. protein chips -- 4.9 Conclusions -- 5 Modeling protein interaction networks -- 5.1 Introduction -- 5.2 Scaling laws and network topology -- 5.2.1 Evolution and duplication of proteins -- 5.2.2 Protein binding physical models -- 5.3 Predicting protein interactions -- 5.3.1 Genome analysis and expression -- 5.4 Towards models at an atomic level of resolution -- 5.4.1 Proteinprotein docking -- 5.4.2 Modeling by homology -- 5.5 Concluding remarks -- 6 Dynamics and evolution of metabolic networks -- 6.1 Introduction -- 6.2 Cellular metabolism and its regulation -- 6.3 Metabolism across disciplines -- Origin and ev.…”
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