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Transcription Factor Regulatory Networks

  • Book
  • © 2023

Overview

Editors:
  1. Qi Song

    1. Computational Biology Department, Carnegie Mellon University, Pittsburgh, USA

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    You can also search for this editor in PubMed   Google Scholar

  2. Zhipeng Tao

    1. Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, USA

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge techniques
  • Provides step-by-step detail essential for reproducible results
  • Contains key implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2594)

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Table of contents (16 protocols)

  1. Front Matter

    Pages i-xii
    Download chapter PDF

  2. The TARGET System: Rapid Identification of Direct Targets of Transcription Factors by Gene Regulation in Plant Cells

    • Matthew D. Brooks, Kelsey M. Reed, Gabriel Krouk, Gloria M. Coruzzi, Bastiaan O. R. Bargmann
    Pages 1-12

  3. The Method of Screening and Identification of Transcription Factor in Klebsiella

    • Qiang Wu, Gao-Qiang Liu, Jiang-Shan Ma, Qiang Li
    Pages 13-28

  4. Genome-Wide Identification of Open Chromatin in Plants Using MH-Seq

    • Aicen Zhang, Xinxu Li, Hainan Zhao, Jiming Jiang, Wenli Zhang
    Pages 29-43

  5. Post-bisulfite Adaptor Tagging with a Highly Efficient Single-Stranded DNA Ligation Technique

    • Fumihito Miura, Takashi Ito
    Pages 45-57

  6. Perturbation of Gene Regulation by Genome Editing

    • Nan Cher Yeo, George M. Church
    Pages 59-68

  7. Analysis of Neutrophil Morphology and Function Under Genetic Perturbation of Transcription Factors In Vitro

    • Julia Salafranca, Zhichao Ai, Lihui Wang, Irina A. Udalova, Erinke van Grinsven
    Pages 69-86

  8. Detection of TP53 Mutation in Acute Myeloid Leukemia by RT-PCR-Based Sanger Sequencing

    • Emily R. Novak, Anagha Deshpande, Darren Finlay, James R. Mason, Aniruddha J. Deshpande, Peter D. Adams et al.
    Pages 87-95

  9. Assessing the Activity of Transcription Factor FoxO1

    • Limin Shi, Zhipeng Tao, Zhiyong Cheng
    Pages 97-106

  10. Targeting Transcription Factors in Cancer: From “Undruggable” to “Druggable”

    • Zhipeng Tao, Xu Wu
    Pages 107-131

  11. A Survey of Transcription Factors in Cell Fate Control

    • Emal Lesha, Haydy George, Mark M. Zaki, Cory J. Smith, Parastoo Khoshakhlagh, Alex H. M. Ng
    Pages 133-141

  12. Single-Cell mRNA-Seq of In Vitro-Derived Human Neurons Using Smart-Seq2

    • Christoph Schweingruber, Jik Nijssen, Julio Aguila Benitez, Eva Hedlund
    Pages 143-164

  13. Computational Analysis of Single-Cell RNA-Seq Data

    • Byungjin Hwang
    Pages 165-172

  14. Database for Plant Transcription Factor Binding Sites

    • Wen-Chi Chang, Chi-Nga Chow
    Pages 173-183

  15. MicroRNA Regulatory Network Analysis Using miRNet 2.0

    • Le Chang, Jianguo Xia
    Pages 185-204

  16. Modeling Plant Transcription Factor Networks Using ConSReg

    • Qi Song, Song Li
    Pages 205-215

  17. Identification of Plant Co-regulatory Modules Using CoReg

    • Qi Song, Song Li
    Pages 217-223

  18. Back Matter

    Pages 225-226
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Keywords

About this book

This book covers various state-of-the-art techniques regarding the associations between transcription factors (TFs) and genes, with a focus on providing methodological and practical references for researchers. The contents cover diverse protocols and summaries of TFs including screening of TF-DNA interactions, detection of open chromatin regions, identification of epigenetic regulations, engineering TFs with genome editing tools, detection of transcriptional activities, computational analysis of TF networks, functions and druggabilities of TFs in biomedical research, and much more. Written for the highly successful Methods in Molecular Biology series, chapters feature the kind of detailed implementation advice from the experts to ensure successful research results. 

Authoritative and cutting-edge, Transcription Factor Regulatory Networks aims to benefit readers who are interested in using state-of-the-art techniques to study TFs and their myriad effects in cellular life.

Editors and Affiliations

  • Computational Biology Department, Carnegie Mellon University, Pittsburgh, USA

    Qi Song

  • Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, USA

    Zhipeng Tao

Bibliographic Information

  • Book Title: Transcription Factor Regulatory Networks

  • Editors: Qi Song, Zhipeng Tao

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-2815-7

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2023

  • Hardcover ISBN: 978-1-0716-2814-0Published: 21 October 2022

  • Softcover ISBN: 978-1-0716-2817-1Published: 21 October 2023

  • eBook ISBN: 978-1-0716-2815-7Published: 20 October 2022

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XII, 226

  • Number of Illustrations: 11 b/w illustrations, 51 illustrations in colour

  • Topics: Genetics and Genomics, Biological Techniques

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