Data Mining for Systems Biology: Methods and Protocols

ISBN-13: 9781627031066 / Angielski / Twarda / 2012 / 279 str.

Charles Delisi; Minoru Kanehisa; Hiroshi Mamitsuka

Opis

The post-genomic revolution is witnessing the generation of petabytes of data annually, with deep implications ranging across evolutionary theory, developmental biology, agriculture, and disease processes. Data Mining for Systems Biology: Methods and Protocols, surveys and demonstrates the science and technology of converting an unprecedented data deluge to new knowledge and biological insight. The volume is organized around two overlapping themes, network inference and functional inference. Written in the highly successful Methods in Molecular Biology(TM) series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Data Mining for Systems Biology: Methods and Protocols also seeks to aid researchers in the further development of databases, mining and visualization systems that are central to the paradigm altering discoveries being made with increasing frequency.

Spis treści

1. Dense Module Enumeration in Biological Networks

Koji Tsuda and Elisabeth Georgii

 2. Discovering Interacting Domains and Motifs in Protein-Protein Interactions

Hugo Willy, Wing-Kin Sung, and See-Kiong Ng.

 3. Global Alignment of Protein-Protein Interaction Networks

Misael Mongiov__ Roded Sharan

 4. Structure Learning for Bayesian Networks as Models of Biological Networks

Antti Larjo, Ilya Shmulevich, and Harri L¨ahdesm¨aki

 5. Supervised Inference of Gene Regulatory Networks from Positive Examples

Fantine Mordelet and Jean-Phillippe Vert

6. Mining Regulatory Network Connections by Ranking Transcription Factor Target Genes using Time Series Expression Data

Annti Honkela, Magnus Rattray, and Neil D. Lawrence

 7. Identifying Pathways of Co-ordinated Gene Expression

Timothy Hancock, Ichigaku Takigawa, and Hiroshi Mamitsuka

8. Mining Frequent Subtrees in Glcan Data using the RINGS Glycan Miner Tool

Kiyoko Flora Aoki-Kinoshita

 9. Chemogenomic Approaches to Infer Drug-target Interaction Networks

Yoshihiro Yamanishi

 10. Localization Prediction and Structure-based in Silico Analysis of Bacterial Proteins- with Emphasis on Outer Membrane Proteins

Kenichiro Imai, Sikander Hayat, Noriyuki Sakiyama, Naoya Fujita, Kentaro Tomii, Arne Elofsson, and Paul Horton

11. Analysis Strategy of Protein-Protein Interaction Networks

Zhenjun Hu

 12. Data Mining in the MetaCyc Family of Pathway Databases

Peter D. Karp, Suzanne Paley, and Tomer Altman

13. Gene Set/Pathway Enrichment Analysis

Jui-Hung Hung

 

14. Construction of Functional Linkage Gene Networks by Data Integration

Bolan Linghu, Eric A. Franzosa, Yu Xia 

 

15. Genome-Wide Association Studies

Tun-Hsiang Yang, Mark Kon, Charles DeLisi

 

16. Viral Genome Analysis and Knowledge Management

Carla Kuiken, Hyejin Yoon, Werner Abfalterer, Brian Gaschen, Chienchi Lo, Bette Korber

 17. Molecular Network Analysis of Diseases and Drugs in KEGG

Minoru Kanehisa

Blurb

The post-genomic revolution is witnessing the generation of petabytes of data annually, with deep implications ranging across evolutionary theory, developmental biology, agriculture, and disease processes. Data Mining for Systems Biology: Methods and Protocols, surveys and demonstrates the science and technology of converting an unprecedented data deluge to new knowledge and biological insight. The volume is organized around two overlapping themes, network inference and functional inference. Written in the highly successful Methods in Molecular Biology™ series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and key tips on troubleshooting and avoiding known pitfalls.

 

Authoritative and practical, Data Mining for Systems Biology: Methods and Protocols also seeks to aid researchers in the further development of databases, mining and visualization systems that are central to the paradigm altering discoveries being made with increasing frequency.