Book Volume 815 2012

Functional Genomics

Methods and Protocols

Editors:

ISBN: 978-1-61779-423-0 (Print) 978-1-61779-424-7 (Online)

Table of contents (29 protocols)

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  1. Front Matter

    Pages i-xv

  2. Bioinformatics

    1. Front Matter

      Pages 1-1

    2. No Access

      Protocol

      Pages 3-13

      Prediction of Protein Tertiary Structures Using MUFOLD

    3. No Access

      Protocol

      Pages 15-24

      Prediction of Protein Functions

    4. No Access

      Protocol

      Pages 25-38

      Genome-Wide Screens for Expressed Hypothetical Proteins

    5. No Access

      Protocol

      Pages 39-47

      Self-Custom-Made SFP Arrays for Nonmodel Organisms

  3. DNA analysis

    1. Front Matter

      Pages 49-49

    2. No Access

      Protocol

      Pages 51-65

      Construction and Analysis of Full-Length and Normalized cDNA Libraries from Citrus

    3. No Access

      Protocol

      Pages 67-78

      Assembling Linear DNA Templates for In Vitro Transcription and Translation

    4. No Access

      Protocol

      Pages 79-87

      Automated Computational Analysis of Genome-Wide DNA Methylation Profiling Data from HELP-Tagging Assays

  4. RNA analysis

    1. Front Matter

      Pages 89-89

    2. No Access

      Protocol

      Pages 91-102

      Detection of RNA Editing Events in Human Cells Using High-Throughput Sequencing

    3. No Access

      Protocol

      Pages 103-119

      Comparative Study of Differential Gene Expression in Closely Related Bacterial Species by Comparative Hybridization

    4. No Access

      Protocol

      Pages 121-130

      Whole-Genome RT-qPCR MicroRNA Expression Profiling

    5. No Access

      Protocol

      Pages 131-145

      Using Quantitative Real-Time Reverse Transcriptase Polymerase Chain Reaction to Validate Gene Regulation by PTTG

    6. No Access

      Protocol

      Pages 147-159

      FRET-Based Real-Time DNA Microarrays

  5. Protein analysis I: quantification and identification

    1. Front Matter

      Pages 161-161

    2. No Access

      Protocol

      Pages 163-173

      2-D Gel Electrophoresis: Constructing 2D-Gel Proteome Reference Maps

    3. No Access

      Protocol

      Pages 175-185

      The Use of Antigen Microarrays in Antibody Profiling

    4. No Access

      Protocol

      Pages 187-198

      Limited Proteolysis in Proteomics Using Protease-Immobilized Microreactors

    5. No Access

      Protocol

      Pages 199-225

      Mass Spectrometry for Protein Quantification in Biomarker Discovery

  6. Protein analysis II: functional characterization

    1. Front Matter

      Pages 227-227

    2. No Access

      Protocol

      Pages 229-239

      High-Throughput Microtitre Plate-Based Assay for DNA Topoisomerases

    3. No Access

      Protocol

      Pages 241-252

      Microscale Thermophoresis as a Sensitive Method to Quantify Protein: Nucleic Acid Interactions in Solution

    4. No Access

      Protocol

      Pages 253-263

      Bioluminescence Resonance Energy Transfer: An Emerging Tool for the Detection of Protein–Protein Interaction in Living Cells

    5. No Access

      Protocol

      Pages 265-275

      LuMPIS: Luciferase-Based MBP-Pull-Down Protein Interaction Screening System

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