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Plant Synthetic Promoters

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Cover of 'Plant Synthetic Promoters'

Table of Contents

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    Book Overview
  2. Altmetric Badge
    Chapter 1 Plant Synthetic Promoters
  3. Altmetric Badge
    Chapter 2 Quantitative Analysis of Cis-Regulatory Element Activity Using Synthetic Promoters in Transgenic Plants
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    Chapter 3 The Identification of Cis-Regulatory Sequence Motifs in Gene Promoters Based on SNP Information
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    Chapter 4 Plant Synthetic Promoters
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    Chapter 5 Analyzing Synthetic Promoters Using Arabidopsis Protoplasts
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    Chapter 6 Selecting Hypomethylated Genomic Regions Using MRE-Seq
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    Chapter 7 Spatio-Temporal Imaging of Promoter Activity in Intact Plant Tissues
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    Chapter 8 Novel Synthetic Promoters from the Cestrum Yellow Leaf Curling Virus
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    Chapter 9 Fast and Efficient Cloning of Cis-Regulatory Sequences for High-Throughput Yeast One-Hybrid Analyses of Transcription Factors
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    Chapter 10 The Physcomitrella patens System for Transient Gene Expression Assays
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    Chapter 11 Analysis of Microbe-Associated Molecular Pattern-Responsive Synthetic Promoters with the Parsley Protoplast System
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    Chapter 12 A Framework for Discovering, Designing, and Testing MicroProteins to Regulate Synthetic Transcriptional Modules
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    Chapter 13 Simultaneous Analysis of Multiple Promoters: An Application of the PC-GW Binary Vector Series
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    Chapter 14 Plant Synthetic Promoters
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    Chapter 15 Bioinformatic Identification of Conserved Cis-Sequences in Coregulated Genes
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    Chapter 16 In Silico Expression Analysis
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    Chapter 17 FootprintDB: Analysis of Plant Cis-Regulatory Elements, Transcription Factors, and Binding Interfaces
  19. Altmetric Badge
    Chapter 18 RSAT::Plants: Motif Discovery Within Clusters of Upstream Sequences in Plant Genomes
  20. Altmetric Badge
    Chapter 19 Plant Synthetic Promoters
Attention for Chapter 17: FootprintDB: Analysis of Plant Cis-Regulatory Elements, Transcription Factors, and Binding Interfaces
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Chapter title
FootprintDB: Analysis of Plant Cis-Regulatory Elements, Transcription Factors, and Binding Interfaces
Chapter number 17
Book title
Plant Synthetic Promoters
Published in
Methods in molecular biology, January 2016
DOI 10.1007/978-1-4939-6396-6_17
Pubmed ID
Book ISBNs
978-1-4939-6394-2, 978-1-4939-6396-6
Authors

Bruno Contreras-Moreira, Alvaro Sebastian, Contreras-Moreira, Bruno, Sebastian, Alvaro

Editors

Reinhard Hehl

Abstract

FootprintDB is a database and search engine that compiles regulatory sequences from open access libraries of curated DNA cis-elements and motifs, and their associated transcription factors (TFs). It systematically annotates the binding interfaces of the TFs by exploiting protein-DNA complexes deposited in the Protein Data Bank. Each entry in footprintDB is thus a DNA motif linked to the protein sequence of the TF(s) known to recognize it, and in most cases, the set of predicted interface residues involved in specific recognition. This chapter explains step-by-step how to search for DNA motifs and protein sequences in footprintDB and how to focus the search to a particular organism. Two real-world examples are shown where this software was used to analyze transcriptional regulation in plants. Results are described with the aim of guiding users on their interpretation, and special attention is given to the choices users might face when performing similar analyses.

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X Demographics

The data shown below were collected from the profile of 1 X user who shared this research output. Click here to find out more about how the information was compiled.
Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 18 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
China 1 6%
Unknown 17 94%

Demographic breakdown

Readers by professional status Count As %
Researcher 7 39%
Student > Ph. D. Student 4 22%
Student > Master 3 17%
Student > Bachelor 1 6%
Student > Doctoral Student 1 6%
Other 0 0%
Unknown 2 11%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 7 39%
Agricultural and Biological Sciences 7 39%
Nursing and Health Professions 1 6%
Computer Science 1 6%
Social Sciences 1 6%
Other 0 0%
Unknown 1 6%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 26 August 2016.
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#18,467,727
of 22,883,326 outputs
Outputs from Methods in molecular biology
#7,923
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Outputs of similar age
#284,559
of 393,702 outputs
Outputs of similar age from Methods in molecular biology
#845
of 1,471 outputs
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