Part I. Cardiac Gene Expression Profiling; The Global Perspective

Microarray Analysis of Gene Expression in Murine Cardiac Graft Infiltrating Cells
Yurong Liang, Xin Lu, and David L. Perkins

Expression Profiling Using Affymetrix GeneChip¿ Probe Arrays
Martina Schinke-Braun, and Jennifer A. Couget

Serial Analysis of Gene Expression (SAGE): A Useful Tool to Analyze the Cardiac Transcriptome
Kirill V. Tarasov, Sheryl A. Brugh, Yelena S. Tarasova, and Kenneth R. Boheler

Functional Genomics by cDNA Subtractive Hybridization
Christophe Depre

Statistical Methods in Cardiac Gene Expression Profiling: From Image to Function
Sek Won Kong

Part II. Cardiac Gene Regulation-Gene-Specific mRNA Measurement in the Myocardium

Measurement of Cardiac Gene Expression by Reverse Transcription Polymerase Chain Reaction (RT-PCR)
Nicola King

Quantitative (Real-Time) RT-PCR in Cardiovascular Research
Kevin John Ashton and John Patrick Headrick

RNase Protection Assay for Quantifying Gene Expression Levels
Yongxia Qu and Mohamed Boutjdir

In Situ Hybridization: A Technique to Study Localization of Cardiac Gene Expression
Thierry P. Calmels and David Mazurais

Part III. Cardiac Gene Regulation-Promoter Characterization in the Myocardium

Characterization of Cis-Regulatory Elements and Transcription Factor Binding: Gel Mobility Shift Assay
Jim Jung-Ching Lin, Shaun E. Grosskurth, Shannon M. Jaacks, Elisabeth A. Gustafson-Wagner, and Qin Wang

Mapping Transcriptional Start Sites and in silico DNA Footprinting
Martin E Cullen and Paul JR Barton

Characterization of Cardiac Gene Promoter Activity: Reporter Constructs and Heterologous Promoter Studies
Hsiao-Huei Chen and Alexandre F. R. Stewart

Part IV. In Silico Assessment of Regulatory Cis-Elements and GeneRegulation

Comparative Genomics: A Tool to Functionally Annotate Human DNA
Jan-Fang Cheng, James R. Priest, and Len A. Pennacchio

Developing Computational Resources in Cardiac Gene Expression
Michael B. Bober and Raimond Winslow

Part V. Cardiac Single Nucleotide Polymorphisms

In Silico Analysis of SNPs and Other High Throughput Data
Neema Jamshidi, Thuy D. Vo, and Bernhard O. Palsson

Discovery and Identification of Sequence Polymorphisms and Mutations With MALDI-TOF Ms
Dirk van den Boom and Mathias Ehrich

Part VI. Gene Overexpression and Targeting in the Myocardium

Conditional Targeting: Inducible Deletion by Cre Recombinase
Kelly R. O'Neal and Ramtin Agah

Cardiomyocyte Preparation, Culture, and Gene Transfer
Alexander H. Maass and Massimo Buvoli

Adeno-Associated Viral Vector Delivered Hypoxia-Inducible Gene Expression in Ischemic Hearts
Hua Su and Yuet Wai Kan

Virus-Mediated Gene Expression-Lentivisus
Jing Zhao and Andrew ML Lever

Cardiac Gene Expression: Methods and Protocols presents both cutting-edge and established methods for studying cardiac gene expression. The protocols provide a template for solid research, and cover the process through screening, analysis, characterization, and functional confirmation of novel genes or known genes with a new function.
Section I, Cardiac Gene Expression Profiling: The Global Perspective, discusses several different approaches to examining, identifying, and analyzing changes in transcriptome gene expression. Section II, Cardiac Gene Regulation: Gene-Specific mRNA Measurement in the Myocardium, outlines more sensitive and gene-targeted expression methods. Section III, Cardiac Gene Regulation: Promoter Characterization in the Myocardium, provides protocols for the study of underlying gene regulation mechanisms by focusing on the interaction of transcription factors with their cognate cis binding elements. Section IV, In Silico Assessment of Regulatory cis-Elements and Gene Regulation, and Section V, Cardiac Single Network Polymorphisms, emphasize new analytical approaches for deciphering the functional elements buried in the 3 billion nucleotides of the human genome and other model genomes. The concluding section, Gene Overexpression and Targeting in the Myocardium, highlights methods that facilitate overexpression or cardiac-specific targeted gene deletion.