Computational prediction of protein complexes from protein interaction networks / (Record no. 883)
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| 000 -LEADER | |
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| fixed length control field | 06818nam a2200601 i 4500 |
| 001 - CONTROL NUMBER | |
| control field | 011453064650 |
| 003 - CONTROL NUMBER IDENTIFIER | |
| control field | MOCL |
| 005 - DATE AND TIME OF LATEST TRANSACTION | |
| control field | 20260609132937.0 |
| 006 - FIXED-LENGTH DATA ELEMENTS--ADDITIONAL MATERIAL CHARACTERISTICS | |
| fixed length control field | m eo d |
| 007 - PHYSICAL DESCRIPTION FIXED FIELD--GENERAL INFORMATION | |
| fixed length control field | cr cn |||m|||a |
| 008 - FIXED-LENGTH DATA ELEMENTS--GENERAL INFORMATION | |
| fixed length control field | 170810s2017 nyua fob 000 0deng d |
| 020 ## - INTERNATIONAL STANDARD BOOK NUMBER | |
| International Standard Book Number | 9781970001532 |
| Qualifying information | ebook |
| 020 ## - INTERNATIONAL STANDARD BOOK NUMBER | |
| Canceled/invalid ISBN | 9781970001549 |
| Qualifying information | ePub |
| 020 ## - INTERNATIONAL STANDARD BOOK NUMBER | |
| Canceled/invalid ISBN | 9781970001525 |
| Qualifying information | paperback |
| 020 ## - INTERNATIONAL STANDARD BOOK NUMBER | |
| Canceled/invalid ISBN | 9781970001556 |
| Qualifying information | hardcover |
| 024 7# - OTHER STANDARD IDENTIFIER | |
| Standard number or code | 10.1145/3064650 |
| Source of number or code | doi |
| 035 ## - SYSTEM CONTROL NUMBER | |
| System control number | (CaBNVSL)swl00407728 |
| 035 ## - SYSTEM CONTROL NUMBER | |
| System control number | (OCoLC)1000387350 |
| 040 ## - CATALOGING SOURCE | |
| Original cataloging agency | CaBNVSL |
| Language of cataloging | eng |
| Description conventions | rda |
| Transcribing agency | CaBNVSL |
| Modifying agency | CaBNVSL |
| 050 #4 - LIBRARY OF CONGRESS CALL NUMBER | |
| Classification number | QP551.5 |
| Item number | .S753 2017 |
| 082 04 - DEWEY DECIMAL CLASSIFICATION NUMBER | |
| Classification number | 572.64 |
| Edition information | 23 |
| 100 1# - MAIN ENTRY--PERSONAL NAME | |
| Personal name | Srihari, Sriganesh, |
| Relator term | author. |
| 245 10 - TITLE STATEMENT | |
| Title | Computational prediction of protein complexes from protein interaction networks / |
| Statement of responsibility, etc. | Sriganesh Srihari, Chern Han Yong, Limsoon Wong. |
| 250 ## - EDITION STATEMENT | |
| Edition statement | First edition. |
| 264 #1 - PRODUCTION, PUBLICATION, DISTRIBUTION, MANUFACTURE, AND COPYRIGHT NOTICE | |
| Place of production, publication, distribution, manufacture | [New York] : |
| Name of producer, publisher, distributor, manufacturer | Association for Computing Machinery ; |
| Place of production, publication, distribution, manufacture | [San Rafael, California] : |
| Name of producer, publisher, distributor, manufacturer | Morgan & Claypool, |
| Date of production, publication, distribution, manufacture, or copyright notice | 2017. |
| 300 ## - PHYSICAL DESCRIPTION | |
| Extent | 1 PDF (xiv, 281 pages) : |
| Other physical details | illustrations. |
| 336 ## - CONTENT TYPE | |
| Content type term | text |
| Source | rdacontent |
| 337 ## - MEDIA TYPE | |
| Media type term | electronic |
| Source | isbdmedia |
| 338 ## - CARRIER TYPE | |
| Carrier type term | online resource |
| Source | rdacarrier |
| 490 1# - SERIES STATEMENT | |
| Series statement | ACM books, |
| International Standard Serial Number | 2374-6777 ; |
| Volume/sequential designation | #16 |
| 538 ## - SYSTEM DETAILS NOTE | |
| System details note | Mode of access: World Wide Web. |
| 538 ## - SYSTEM DETAILS NOTE | |
| System details note | System requirements: Adobe Acrobat Reader. |
| 504 ## - BIBLIOGRAPHY, ETC. NOTE | |
| Bibliography, etc. note | Includes bibliographical references (pages 233-278). |
| 505 0# - FORMATTED CONTENTS NOTE | |
| Formatted contents note | 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 -- |
| 505 8# - FORMATTED CONTENTS NOTE | |
| Formatted contents note | 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 -- |
| 505 8# - FORMATTED CONTENTS NOTE | |
| Formatted contents note | 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 -- |
| 505 8# - FORMATTED CONTENTS NOTE | |
| Formatted contents note | 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 -- |
| 505 8# - FORMATTED CONTENTS NOTE | |
| Formatted contents note | 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 -- |
| 505 8# - FORMATTED CONTENTS NOTE | |
| Formatted contents note | 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 -- |
| 505 8# - FORMATTED CONTENTS NOTE | |
| Formatted contents note | 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 -- |
| 505 8# - FORMATTED CONTENTS NOTE | |
| Formatted contents note | 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 -- |
| 505 8# - FORMATTED CONTENTS NOTE | |
| Formatted contents note | 9. Conclusion -- References -- Authors' biographies. |
| 520 3# - SUMMARY, ETC. | |
| Summary, etc. | 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. |
| 530 ## - ADDITIONAL PHYSICAL FORM AVAILABLE NOTE | |
| Additional physical form available note | Also available in print. |
| 588 ## - SOURCE OF DESCRIPTION NOTE | |
| Source of description note | Title from PDF title page (viewed on August 10, 2017). |
| 650 #0 - SUBJECT ADDED ENTRY--TOPICAL TERM | |
| Topical term or geographic name entry element | Protein-protein interactions |
| General subdivision | Computer simulation. |
| 655 #0 - INDEX TERM--GENRE/FORM | |
| Genre/form data or focus term | Electronic books. |
| 700 1# - ADDED ENTRY--PERSONAL NAME | |
| Personal name | Yong, Chern Han, |
| Relator term | author. |
| 700 1# - ADDED ENTRY--PERSONAL NAME | |
| Personal name | Wong, Limsoon, |
| Dates associated with a name | 1965-, |
| Relator term | author. |
| 776 08 - ADDITIONAL PHYSICAL FORM ENTRY | |
| Relationship information | Print version: |
| International Standard Book Number | 9781970001556 |
| -- | 9781970001525 |
| 830 #0 - SERIES ADDED ENTRY--UNIFORM TITLE | |
| Uniform title | ACM books ; |
| Volume/sequential designation | #16. |
| International Standard Serial Number | 2374-6777 |
| 856 48 - ELECTRONIC LOCATION AND ACCESS | |
| Materials specified | Abstract with links to full text |
| Uniform Resource Identifier | <a href="http://dx.doi.org/10.1145/3064650">http://dx.doi.org/10.1145/3064650</a> |
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