Modeling Transcriptional Regulation: Methods and Protocols

ISBN-13: 9781071615331 / Angielski / Twarda / 2021 / 307 str.

Shahid Mukhtar

Spis treści

1. Co-expression Networks in Predicting Transcriptional Gene Regulation

Synan F. AbuQamar, Khaled A. El-Tarabily, and Arjun Sham

 

2. Inference of Gene Coexpression Networks from Bulk-based RNA-Sequencing Data

Running-title: Inference of GCNs from bulk-based RNA-Seq

Alicia T. Lamere

 

3. Genomic Footprinting Analyses from DNase-seq data to Construct Gene Regulatory Networks

Tomás C. Moyano, Rodrigo A. Gutiérrez, and José M. Alvarez

 

4. Spatiotemporal Gene Expression Profiling and Network Inference: A Roadmap For Analysis, Visualization, and Key Gene Identification

Ryan Spurney, Michael Schwartz, Mariah Gobble, Rosangela Sozzani, and Lisa Van den Broeck

 

5. Dynamic Modeling of Transcriptional Gene Regulatory Networks

Joanna E Handzlik, Yen Lee Loh, and Manu

 

6. Mathematical Programming for Modelling Expression of a Gene using Gurobi Optimizer to Identify its Transcriptional Regulators

Vijaykumar Yogesh Muley

 

7. Multiscale Modeling of Cross-Regulatory Transcript and Protein Influences

Megan L. Matthews and Cranos M. Williams

 

8. Biological Network Mining

Zongliang Yue, Da Yan, Guimu Guo, Jake Y. Chen

 

9. Identification of Gene Regulatory Networks from Single-Cell Expression Data

Song Li, Haidong Yan, and Jiyoung Lee

 

10. Inference of Gene Regulatory Network From Single-Cell Transcriptomic Data using pySCENIC

Nilesh Kumar, Bharat Mishra, Mohammad Athar, M. Shahid Mukhtar

 

11.          Modeling Immune Dynamics in Plants using JIMENA-package

Özge Osmanoglu, Shabana Shams, Thomas Dandekar, and Muhammad Naseem

 

12. Dynamic Regulatory Event Mining by iDREM in Large Scale Multi-Omics Datasets during Biotic and Abiotic Stress in Plants

Bharat Mishra, Nilesh Kumar, Jinbao Liu, and Karolina M. Pajerowska-Mukhtar

 

13. A semi-in vivo Transcriptional Assay to Dissect Plant Defense Regulatory Modules

Fatimah Aljedaani, Naganand Rayapuram, and Ikram Blilou

 

14. Assessing Global Circadian Rhythm through Single-Time-Point Transcriptomic Analysis

Xingwei Wang, Yufeng Xu, Mian Zhou, and Wei Wang

 

15. High-throughput Targeted Transcriptional Profiling of Defense Genes using RNA-mediated oligonucleotide Annealing, Selection, and Ligation with next-generation sequencing in Arabidopsi

Sung-Il Kim, Yogendra Bordiya, Ji-Chul Nam, José Mayorga, and Hong-Gu Kang

 

16. Rapid Validation of Transcriptional Enhancers Using a Transient Reporter Assay

Yuan Lin and Jiming Jiang

 

17. Computational Identification of ceRNA and Reconstruction of ceRNA Regulatory Network Based on RNA-seq and Small RNA-seq Data in Plants

Xiangyuan Wan and Ziwen Li

 

18. In Silico Prediction for ncRNAs in Prokaryotes

Amanda Carvalho Garcia

 

19. Mathematical Linear Programming to Model MicroRNAs-Mediated Gene Regulation Using Gurobi Optimizer

Vijaykumar Yogesh Muley

Blurb

This book provides methods and techniques used in construction of global transcriptional regulatory networks in diverse systems, various layers of gene regulation and mathematical as well as computational modeling of transcriptional gene regulation. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

 

Authoritative and cutting-edge, Modeling Transcriptional Regulation: Methods and Protocols aims to provide an in depth understanding of new techniques in transcriptional gene regulation for specialized audience.