Computational prediction of protein complexes from protein interaction networks / Sriganesh Srihari, Chern Han Yong, Limsoon Wong.

Format:

Book

Author/Creator:

Srihari, Sriganesh, author.

Yong, Chern Han, author.

Wong, Limsoon, 1965- author.

Series:

ACM books ; 2374-6777 #16.

ACM books, 2374-6777 ; #16

Language:

English

Subjects (All):

Protein-protein interactions--Computer simulation.

Protein-protein interactions.

Genre:

Electronic books.

Physical Description:

1 online resource (xiv, 281 pages) : illustrations.

Edition:

First edition.

Place of Publication:

[New York] : Association for Computing Machinery ; [San Rafael, California] : Morgan & Claypool, 2017.

System Details:

Mode of access: World Wide Web.

System requirements: Adobe Acrobat Reader.

Summary:

Complexes of physically interacting proteins constitute fundamental functional units that drive almost all biological processes within cells. A faithful reconstruction of the entire set of protein complexes (the "complexosome") is therefore important not only to understand the composition of complexes but also the higher level functional organization within cells. Advances over the last several years, particularly through the use of high-throughput proteomics techniques, have made it possible to map substantial fractions of protein interactions (the "interactomes") from model organisms including Arabidopsis thaliana (a flowering plant), Caenorhabditis elegans (a nematode), Drosophila melanogaster (fruit fly), and Saccharomyces cerevisiae (budding yeast). These interaction datasets have enabled systematic inquiry into the identification and study of protein complexes from organisms. Computational methods have played a significant role in this context, by contributing accurate, efficient, and exhaustive ways to analyze the enormous amounts of data. These methods have helped to compensate for some of the limitations in experimental datasets including the presence of biological and technical noise and the relative paucity of credible interactions. In this book, we systematically walk through computational methods devised to date (approximately between 2000 and 2016) for identifying protein complexes from the network of protein interactions (the protein-protein interaction (PPI) network). We present a detailed taxonomy of these methods, and comprehensively evaluate them for protein complex identification across a variety of scenarios including the absence of many true interactions and the presence of false-positive interactions (noise) in PPI networks. Based on this evaluation, we highlight challenges faced by the methods, for instance in identifying sparse, sub-, or small complexes and in discerning overlapping complexes, and reveal how a combination of strategies is necessary to accurately reconstruct the entire complexosome.

Contents:

1. Introduction to protein complex prediction

1.1 From protein interactions to protein complexes

1.2 Databases for protein complexes

1.3 Organization of the rest of the book

2. Constructing reliable protein-protein interaction (PPI) networks

2.1 High-throughput experimental systems to infer PPIs

2.2 Data sources for PPIs

2.3 Topological properties of PPI networks

2.4 Theoretical models for PPI networks

2.5 Visualizing PPI networks

2.6 Building high-confidence PPI networks

2.7 Enhancing PPI networks by integrating functional interactions

3. Computational methods for protein complex prediction from PPI networks

3.1 Basic definitions and terminologies

3.2 Taxonomy of methods for protein complex prediction

3.3 Methods based solely on PPI network clustering

3.4 Methods incorporating core-attachment structure

3.5 Methods incorporating functional information

4. Evaluating protein complex prediction methods

4.1 Evaluation criteria and methodology

4.2 Evaluation on unweighted yeast PPI networks

4.3 Evaluation on weighted yeast PPI networks

4.4 Evaluation on human PPI networks

4.5 Case study: prediction of the human mechanistic target of Rapamycin complex

4.6 Take-home lessons from evaluating prediction methods

5. Open challenges in protein complex prediction

5.1 Three main challenges in protein complex prediction

5.2 Identifying sparse protein complexes

5.3 Identifying overlapping protein complexes

5.4 Identifying small protein complexes

5.5 Identifying protein sub-complexes

5.6 An integrated system for identifying challenging protein complexes

5.7 Recent methods for protein complex prediction

5.8 Identifying membrane-protein complexes

6. Identifying dynamic protein complexes

6.1 Dynamism of protein interactions and protein complexes

6.2 Identifying temporal protein complexes

6.3 Intrinsic disorder in proteins

6.4 Intrinsic disorder in protein interactions and protein complexes

6.5 Identifying fuzzy protein complexes

7. Identifying evolutionarily conserved protein complexes

7.1 Inferring evolutionarily conserved PPIs (interologs)

7.2 Identifying conserved complexes from interolog networks, I

7.3 Identifying conserved complexes from interolog networks, II

8. Protein complex prediction in the era of systems biology

8.1 Constructing the network of protein complexes

8.2 Identifying protein complexes across phenotypes

8.3 Identifying protein complexes in diseases

8.4 Enhancing quantitative proteomics using PPI networks and protein complexes

8.5 Systems biology tools and databases to analyze biomolecular networks

9. Conclusion

References

Authors' biographies.

Notes:

Includes bibliographical references (pages 233-278).

Title from PDF title page (viewed on August 10, 2017).

Other Format:

Print version:

ISBN:

9781970001532

OCLC:

1000387350

Access Restriction:

Restricted for use by site license.