Next generation microarray bioinformatics: methods and protocols
Gespeichert in:
| Weitere Verfasser: | |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
New York, NY [u.a.]
Humana Press, Springer
2012
|
| Schriftenreihe: | Methods in molecular biology
802 |
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | Literaturangaben |
| Beschreibung: | XVI, 401 S. Ill., graph. Darst. |
| ISBN: | 9781617793998 |
Internformat
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Datensatz im Suchindex
| _version_ | 1804148567878664192 |
|---|---|
| adam_text | Titel: Next generation microarray bioinformatics
Autor: Wang, Junbai
Jahr: 2012
Contents
Preface..................................................................... v
Contributors................................................................ xiii
Part I Introduction and Resources for Microarray Bioinformatics
1 A Primer on the Current State of Microarray Technologies.................... 3
Alexander J. Trachtenberg, Jae-Hyung Robert, Azza E. Abdalla,
Andrew Eraser, Steven Y. He, Jessica N. Lacy, Chiara Rivas-Morello,
Allison Truong, Gary Hardiman, Lucila Ohno-Machado,
Fang Liu, Eivind Hovig, and Winston Patrick Kuo
2 The KEGG Databases and Tools Facilitating Omics Analysis: Latest
Developments Involving Human Diseases and Pharmaceuticals................. 19
Masaaki Kotera, Mika Hirakawa, Toshiaki Tokimatsu,
Susumu Goto, and Minoru Kanehisa
3 Strategies to Explore Functional Genomics Data Sets
in NCBI s GEO Database................................................ 41
Stephen E. Wilhite and Tanya Barrett
Part II Microarray Data Analysis (Top-Down Approach)
4 Analyzing Cancer Samples with SNP Arrays................................. 57
Peter Van Loo, Gro Nilsen, Silje H. Nordgard,
Hans Kristian Moen Vollan, Anne-Lise Berresen-Dale,
Vessela N. Kristensen, and Ole Christian Lingjssrde
5 Classification Approaches for Microarray Gene Expression Data Analysis......... 73
Leo Wang-Kit Cheung
6 Biclustering of Time Series Microarray Data................................. 87
Jia Meng and Yufei Huang
7 Using the Bioconductor GeneAnswers Package
to Interpret Gene Lists................................................... 101
Gang Feng, Pamela Shaw, Steven T. Rosen,
Simon M. Lin, and Warren A. Kibbe
8 Analysis of Isoform Expression from Splicing Array
Using Multiple Comparisons.............................................. 113
T. Murlidharan Nair
9 Functional Comparison of Microarray Data Across Multiple
Platforms Using the Method of Percentage of Overlapping Functions........... 123
Zhiguang Li, Joshua C. Kwekel, and Tao Chen
10 Performance Comparison of Multiple Microarray Platforms
for Gene Expression Profiling............................................. 141
Fang Liu, Winston P. Kuo, Tor-Kristian Jenssen, and Eivind Hovig
11 Integrative Approaches for Microarray Data Analysis.......................... 157
Levi Waldron, Hilary A. Coller, and Curtis Huttenhower
ix
x Contents
Part III Microarray Bioinformatics in Systems Biology
(Bottom-Up Approach)
12 Modeling Gene Regulation Networks Using Ordinary
Differential Equations................................................... 185
Jiguo Cao, Xin Qi, and Hongyu Zhao
13 Nonhomogeneous Dynamic Bayesian Networks in Systems Biology............. 199
Sophie Lebre, Frank Dondelinger, and Dirk Husmeier
14 Inference of Regulatory Networks from Microarray Data
with R. and the Bioconductor Package qpgraph.............................. 215
Robert Castelo and Alberto Roverato
15 Effective Non-linear Methods for Inferring Genetic Regulation
from Time-Series Microarray Gene Expression Data.......................... 235
Junbai Wang and Tianhai Tian
Part IV Next Generation Sequencing Data Analysis
16 An Overview of the Analysis of Next Generation Sequencing Data.............. 249
Andreas Gogol-Doring and Wei Chen
17 How to Analyze Gene Expression Using RNA-Sequencing Data................ 259
Daniel Ramskbld, Ersen Kavak, and Rickard Sandberg
18 Analyzing ChlP-seq Data: Preprocessing, Normalization,
Differential Identification, and Binding Pattern Characterization............... 275
Cenny Taslim, Kun Huang, Tim Huang, and Shili Lin
19 Identifying Differential Histone Modification Sites from ChlP-seq Data......... 293
Han Xu and Wing-Kin Sung
20 ChlP-Seq Data Analysis: Identification of Protein-DNA Binding
Sites with SISSRs Peak-Finder............................................. 305
Leelavati Narlikar and Rajajothi
21 Using ChlPMotifs for De Novo Motif Discovery of OCT4
and ZNF263 Based on ChlP-Based High-Throughput Experiments............ 323
Brian A. Kennedy, Xun Lan, Tim H.-M. Huang,
Peggy J. Farnham, and Victor X. Jin
Part V Emerging Applications of Microarray and
Next Generation Sequencing
22 Hidden Markov Models for Controlling False Discovery Rate
in Genome-Wide Association Analysis...................................... 337
Zhi Wei
23 Employing Gene Set Top Scoring Pairs to Identify Deregulated
Pathway-Signatures in Dilated Cardiomyopathy from Integrated
Microarray Gene Expression Data.......................................... 345
Aik Choon Tan
Contents xi
24 JAMIE: A Software Tool for Jointly Analyzing Multiple
ChlP-chip Experiments.................................................. 363
Hao Wu and Hongkai Ji
25 Epigenetic Analysis: ChlP-chip and ChlP-seq................................ 377
Matteo Pellegrini and Roberto Ferrari
26 BiNGS!SL-seq: A Bioinformatics Pipeline for the Analysis
and Interpretation of Deep Sequencing Genome-Wide
Synthetic Lethal Screen.................................................. 389
Jihye Kim andAik Choon Tan
Index...................................................................... 399
|
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| title | Next generation microarray bioinformatics methods and protocols |
| title_auth | Next generation microarray bioinformatics methods and protocols |
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