SYSTEMS AND COMPUTATIONAL BIOLOGY – MOLECULAR AND CELLULAR EXPERIMENTAL SYSTEMS Edited by Ning-Sun Yang Systems and Computational Biology – Molecular and Cellular Experimental Systems Edited by Ning-Sun Yang Published by InTech Janeza Trdine 9, 51000 Rijeka, Croatia Copyright © 2011 InTech All chapters are Open Access articles distributed under the Creative Commons Non Commercial Share Alike Attribution 3.0 license, which permits to copy, distribute, transmit, and adapt the work in any medium, so long as the original work is properly cited. After this work has been published by InTech, authors have the right to republish it, in whole or part, in any publication of which they are the author, and to make other personal use of the work. Any republication, referencing or personal use of the work must explicitly identify the original source. Statements and opinions expressed in the chapters are these of the individual contributors and not necessarily those of the editors or publisher. No responsibility is accepted for the accuracy of information contained in the published articles. The publisher assumes no responsibility for any damage or injury to persons or property arising out of the use of any materials, instructions, methods or ideas contained in the book. Publishing Process Manager Davor Vidic Technical Editor Teodora Smiljanic Cover Designer Jan Hyrat Image Copyright OPIS, 2011. Used under license from Shutterstock.com First published September, 2011 Printed in Croatia A free online edition of this book is available at www.intechopen.com Additional hard copies can be obtained from [email protected] Systems and Computational Biology – Molecular and Cellular Experimental Systems, Edited by Ning-Sun Yang p. cm. ISBN 978-953-307-280-7 free online editions of InTech Books and Journals can be found at www.intechopen.com Contents Preface IX Part 1 Approaches for Studying Genomes, Transcriptomes, and Proteomes 1 Chapter 1 Gene Expression Analysis Using RNA-Seq from Organisms Lacking Substantial Genomic Resources 3 Yingjia Shen, Tzintzuni Garcia and Ronald B. Walter Chapter 2 Linguistic Approaches for Annotation, Visualization and Comparison of Prokaryotic Genomes and Environmental Sequences 27 Oliver Bezuidt, Hamilton Ganesan, Phillip Labuschange, Warren Emmett, Rian Pierneef and Oleg N. Reva Chapter 3 On the Structural Characteristics of the Protein Active Sites and Their Relation to Thermal Fluctuations 53 Shao-Wei Huang and Jenn-Kang Hwang Chapter 4 Decomposition of Intramolecular Interactions Between Amino-Acids in Globular Proteins - A Consequence for Structural Classes of Proteins and Methods of Their Classification 69 Boris Fackovec and Jiri Vondrasek Chapter 5 The Prediction and Analysis of Inter- and Intra-Species Protein-Protein Interaction 83 Theresa Tsun-Hui Tsao, Chen-Hsiung Chan, Chi-Ying F. Huang and Sheng-An Lee Chapter 6 Computational Prediction of Post-Translational Modification Sites in Proteins 105 Yu Xue, Zexian Liu, Jun Cao and Jian Ren Chapter 7 Protein Networks: Generation, Structural Analysis and Exploitation 125 Enrico M. Bucci, Massimo Natale and Alice Poli VI Contents Part 2 Gene Regulation, Networking and Signaling in and Between Genomes 147 Chapter 8 Prediction and Analysis of Gene Regulatory Networks in Prokaryotic Genomes 149 Richard Münch, Johannes Klein and Dieter Jahn Chapter 9 Mining Host-Pathogen Interactions 163 Dmitry Korkin, Thanh Thieu, Sneha Joshi and Samantha Warren Chapter 10 Prediction of Novel Pathway Elements and Interactions Using Bayesian Networks 185 Andrew P. Hodges, Peter Woolf and Yongqun He ξ Chapter 11 MicroRNA Identification Based on Bioinformatics Approaches 205 Malik Yousef, Naim Najami and Walid Khaleifa Chapter 12 Motif Discovery with Compact Approaches - Design and Applications 217 Cinzia Pizzi Part 3 Omics-Based Molecular and Cellular Experimental Systems - Examples and Applications 235 Chapter 13 Data Mining Pubmed Using Natural Language Processing to Generate the β-Catenin Biological Association Network 237 Fengming Lan, Xiao Yue, Lei Han, Peiyu Pu and Chunsheng Kang Chapter 14 In Silico Identification of Plant-Derived Antimicrobial Peptides 249 Maria Clara Pestana-Calsa and Tercilio Calsa Jr. Chapter 15 Mining Effector Proteins in Phytopathogenic Fungi 273 Li Cheng-yun and Yang Jing Chapter 16 Immuno-Modulatory Effects of Phytomedicines Evaluated Using Omics Approaches 289 Shu-Yi Yin and Ning-Sun Yang Chapter 17 High Content and Throughput Drug Discovery 315 Quin Wills Preface Immediately after the first drafts of the human genome sequence were reported almost a decade ago, the importance of genomics and functional genomics studies became well recognized across the broad disciplines of biological sciences research. The initiatives of Leroy Hood and other pioneers on developing systems biology approaches for evaluating or addressing global and integrated biological activities, mechanisms, and network systems have motivated many of us, as bioscientists, to re- examine or revisit a whole spectrum of our previous experimental findings or observations in a much broader, link-seeking and cross-talk context. Soon thereafter, these lines of research efforts generated interesting, fancy and sometimes misleading new names for the now well-accepted “omics” research areas, including functional genomics, (functional) proteomics, metabolomics, transcriptomics, glycomics, lipidomics, and cellomics. It may be interesting for us to try to relate these “omics” approaches to one of the oldest omics studies that we all may be quite familiar with, and that is “economics”, in a way that all “omics” indeed seemed to have meant to address the mechanisms/activities/constituents in a global, inter-connected and regulated way or manner. The advancement of a spectrum of technological methodologies and assay systems for various omics studies has been literally astonishing, including next-generation DNA sequencing platforms, whole transcriptome microarrays, micro-RNA arrays, various protein chips, polysaccharide or glycomics arrays, advanced LC-MS/MS, GC-MS/MS, MALDI-TOF, 2D-NMR, FT-IR, and other systems for proteome and metabolome research and investigations on related molecular signaling and networking bioactivities. Even more excitingly and encouragingly, many outstanding researchers previously trained as mathematicians, information or computation scientists have courageously re-educated themselves and turned into a new generation of bioinformatics scientists. The collective achievements and breakthroughs made by our colleagues have created a number of wonderful database systems which are now routinely and extensively used by not only young but also “old” researchers. It is very difficult to miss the overwhelming feeling and excitement of this new era in systems biology and computational biology research. It is now estimated, with good supporting evidence by omics information, that there are approximately 25,000 genes in the human genome, about 45,000 total proteins in the human proteome, and around 3000 species of primary and between 3000 and 6000 X Preface species of secondary metabolites, respectively, in the human body fluid/tissue metabolome. These numbers and their relative levels to each other are now helping us to construct a more comprehensive and realistic view of human biology systems. Likewise, but maybe to a lesser extent, various baseline omics databases on mouse, fruit fly, Arabidopsis plant, yeast, and E. coli systems are being built to serve as model systems for molecular, cellular and systems biology studies; these efforts are projected to result in very interesting and important research findings in the coming years. Good findings in a new research area may not necessarily translate quickly into good or high-impact benefits pertaining to socio-economic needs, as may be witnessed now by many of us with regard to research and development in omics science/technology. To some of us, the new genes, novel protein functions, unique metabolite profiles or PCA clusters, and their signaling systems that we have so far revealed seemed to have yielded less than what we have previously (only some 5 to 10 years ago) expected, in terms of new targets or strategies for drug or therapeutics development in medical sciences, or for improvement of crop plants in agricultural science. Nonetheless, some useful new tools for diagnosis and personalized medicine have been developed as a result of genomics research. Recent reviews on this subject have helped us more realistically and still optimistically to address such issues in a socially responsible academic exercise. Therefore, whereas some “microarray” or “bioinformatics” scientists among us may have been criticized as doing “cataloging research”, the majority of us believe that we are sincerely exploring new scientific and technological systems to benefit human health, human food and animal feed production, and environmental protections. Indeed, we are humbled by the complexity, extent and beauty of cross-talks in various biological systems; on the other hand, we are becoming more educated and are able to start addressing honestly and skillfully the various important issues concerning translational medicine, global agriculture, and the environment. I am very honored to serve as the editor of these two volumes on Systems and Computational Biology: (I) Molecular and Cellular Experimental Systems, and (II) Bioinformatics and Computational Modeling. I believe that we have collectively contributed a series of high-quality research or review articles in a timely fashion to this emerging research field of our scientific community. I sincerely hope that our colleagues and readers worldwide will help us in future similar efforts, by providing us feedback in the form of critical comments, interdisciplinary ideas and innovative suggestions on our book chapters, as a way to pay our high respect to the biological genomes on planet earth. Dr. Ning-Sun Yang Agricultural Biotechnology Research Center, Academia Sinica Taiwan, R.O.C