Sequence analysis of chromatin immunoprecipitation data for factors
Chromatin immunoprecipitation (ChIP) experiments allow the location of transcription factors to be determined across the genome. Subsequent analysis of the sequences of the identified regions allows binding to be localized at a higher resolution than can be achieved by current high-throughput experi...
| Main Authors: | , |
|---|---|
| Other Authors: | |
| Format: | Article |
| Language: | en_US |
| Published: |
Springer Science + Business Media
2012
|
| Online Access: | http://hdl.handle.net/1721.1/69229 https://orcid.org/0000-0001-9249-8181 |
| _version_ | 1811087688560803840 |
|---|---|
| author | MacIsaac, Kenzie Daniel Fraenkel, Ernest |
| author2 | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory |
| author_facet | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory MacIsaac, Kenzie Daniel Fraenkel, Ernest |
| author_sort | MacIsaac, Kenzie Daniel |
| collection | MIT |
| description | Chromatin immunoprecipitation (ChIP) experiments allow the location of transcription factors to be determined across the genome. Subsequent analysis of the sequences of the identified regions allows binding to be localized at a higher resolution than can be achieved by current high-throughput experiments without sequence analysis and may provide important insight into the regulatory programs enacted by the protein of interest. In this chapter we review the tools, workflow, and common pitfalls of such analyses and recommend strategies for effective motif discovery from these data. |
| first_indexed | 2024-09-23T13:50:26Z |
| format | Article |
| id | mit-1721.1/69229 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T13:50:26Z |
| publishDate | 2012 |
| publisher | Springer Science + Business Media |
| record_format | dspace |
| spelling | mit-1721.1/692292022-10-01T17:26:14Z Sequence analysis of chromatin immunoprecipitation data for factors MacIsaac, Kenzie Daniel Fraenkel, Ernest Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology. Department of Biological Engineering Fraenkel, Ernest Fraenkel, Ernest MacIsaac, Kenzie Daniel Chromatin immunoprecipitation (ChIP) experiments allow the location of transcription factors to be determined across the genome. Subsequent analysis of the sequences of the identified regions allows binding to be localized at a higher resolution than can be achieved by current high-throughput experiments without sequence analysis and may provide important insight into the regulatory programs enacted by the protein of interest. In this chapter we review the tools, workflow, and common pitfalls of such analyses and recommend strategies for effective motif discovery from these data. 2012-02-28T17:24:51Z 2012-02-28T17:24:51Z 2010-01 Article http://purl.org/eprint/type/JournalArticle 9781607618546 1607618540 978-1-60761-853-9 1064-3745 http://hdl.handle.net/1721.1/69229 MacIsaac, Kenzie D., and Ernest Fraenkel. “Sequence Analysis of Chromatin Immunoprecipitation Data for Transcription Factors.” Chapter 11 of Computational Biology of Transcription Factor Binding. Ed. Istvan Ladunga. Totowa, NJ: Humana Press, 2010. 179–193. (Methods in Molecular Biology ; Vol. 674) https://orcid.org/0000-0001-9249-8181 en_US http://dx.doi.org/10.1007/978-1-60761-854-6_11 Computational Biology of Transcription Factor Binding Creative Commons Attribution-Noncommercial-Share Alike 3.0 http://creativecommons.org/licenses/by-nc-sa/3.0/ application/pdf Springer Science + Business Media Prof. Fraenkel via Howard Silver |
| spellingShingle | MacIsaac, Kenzie Daniel Fraenkel, Ernest Sequence analysis of chromatin immunoprecipitation data for factors |
| title | Sequence analysis of chromatin immunoprecipitation data for factors |
| title_full | Sequence analysis of chromatin immunoprecipitation data for factors |
| title_fullStr | Sequence analysis of chromatin immunoprecipitation data for factors |
| title_full_unstemmed | Sequence analysis of chromatin immunoprecipitation data for factors |
| title_short | Sequence analysis of chromatin immunoprecipitation data for factors |
| title_sort | sequence analysis of chromatin immunoprecipitation data for factors |
| url | http://hdl.handle.net/1721.1/69229 https://orcid.org/0000-0001-9249-8181 |
| work_keys_str_mv | AT macisaackenziedaniel sequenceanalysisofchromatinimmunoprecipitationdataforfactors AT fraenkelernest sequenceanalysisofchromatinimmunoprecipitationdataforfactors |