| Chapter title |
Plant Synthetic Promoters
|
|---|---|
| Chapter number | 19 |
| Book title |
Plant Synthetic Promoters
|
| Published in |
Methods in molecular biology, January 2016
|
| DOI | 10.1007/978-1-4939-6396-6_19 |
| Pubmed ID | |
| Book ISBNs |
978-1-4939-6394-2, 978-1-4939-6396-6
|
| Authors |
Castro-Mondragon, Jaime A, Rioualen, Claire, Contreras-Moreira, Bruno, van Helden, Jacques, Jaime A. Castro-Mondragon, Claire Rioualen, Bruno Contreras-Moreira, Jacques van Helden |
| Editors |
Reinhard Hehl |
| Abstract |
In this protocol, we explain how to run ab initio motif discovery in order to gather putative transcription factor binding motifs (TFBMs) from sets of genomic regions returned by ChIP-seq experiments. The protocol starts from a set of peak coordinates (genomic regions) which can be either downloaded from ChIP-seq databases, or produced by a peak-calling software tool. We provide a concise description of the successive steps to discover motifs, cluster the motifs returned by different motif discovery algorithms, and compare them with reference motif databases. The protocol is documented with detailed notes explaining the rationale underlying the choice of options. The interpretation of the results is illustrated with an example from the model plant Arabidopsis thaliana. |
X Demographics
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| France | 2 | 67% |
| Norway | 1 | 33% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Scientists | 2 | 67% |
| Members of the public | 1 | 33% |
Mendeley readers
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| France | 1 | 10% |
| Unknown | 9 | 90% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Researcher | 4 | 40% |
| Other | 1 | 10% |
| Professor | 1 | 10% |
| Lecturer | 1 | 10% |
| Student > Master | 1 | 10% |
| Other | 1 | 10% |
| Unknown | 1 | 10% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 6 | 60% |
| Computer Science | 2 | 20% |
| Biochemistry, Genetics and Molecular Biology | 1 | 10% |
| Unknown | 1 | 10% |