UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein-DNA interactions
The Universal PBM Resource for Oligonucleotide Binding Evaluation (UniPROBE) serves as a convenient source of information on published data generated using universal protein-binding microarray (PBM) technology, which provides in vitro data about the relative DNA-binding preferences of transcription...
| Main Authors: | , , , |
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| Other Authors: | |
| Format: | Article |
| Language: | en_US |
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Oxford University Press
2014
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| Online Access: | http://hdl.handle.net/1721.1/92531 https://orcid.org/0000-0002-4472-4209 |
| _version_ | 1811075510021652480 |
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| author | Barrera, Luis Alberto Bulyk, Martha L. Hume, Maxwell A. Gisselbrecht, Stephen S. |
| author2 | Harvard University--MIT Division of Health Sciences and Technology |
| author_facet | Harvard University--MIT Division of Health Sciences and Technology Barrera, Luis Alberto Bulyk, Martha L. Hume, Maxwell A. Gisselbrecht, Stephen S. |
| author_sort | Barrera, Luis Alberto |
| collection | MIT |
| description | The Universal PBM Resource for Oligonucleotide Binding Evaluation (UniPROBE) serves as a convenient source of information on published data generated using universal protein-binding microarray (PBM) technology, which provides in vitro data about the relative DNA-binding preferences of transcription factors for all possible sequence variants of a length k (‘k-mers’). The database displays important information about the proteins and displays their DNA-binding specificity data in terms of k-mers, position weight matrices and graphical sequence logos. This update to the database documents the growth of UniPROBE since the last update 4 years ago, and introduces a variety of new features and tools, including a new streamlined pipeline that facilitates data deposition by universal PBM data generators in the research community, a tool that generates putative nonbinding (i.e. negative control) DNA sequences for one or more proteins and novel motifs obtained by analyzing the PBM data using the BEEML-PBM algorithm for motif inference. The UniPROBE database is available at http://uniprobe.org. |
| first_indexed | 2024-09-23T10:07:15Z |
| format | Article |
| id | mit-1721.1/92531 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T10:07:15Z |
| publishDate | 2014 |
| publisher | Oxford University Press |
| record_format | dspace |
| spelling | mit-1721.1/925312022-09-26T15:50:08Z UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein-DNA interactions Barrera, Luis Alberto Bulyk, Martha L. Hume, Maxwell A. Gisselbrecht, Stephen S. Harvard University--MIT Division of Health Sciences and Technology Barrera, Luis Alberto Bulyk, Martha L. The Universal PBM Resource for Oligonucleotide Binding Evaluation (UniPROBE) serves as a convenient source of information on published data generated using universal protein-binding microarray (PBM) technology, which provides in vitro data about the relative DNA-binding preferences of transcription factors for all possible sequence variants of a length k (‘k-mers’). The database displays important information about the proteins and displays their DNA-binding specificity data in terms of k-mers, position weight matrices and graphical sequence logos. This update to the database documents the growth of UniPROBE since the last update 4 years ago, and introduces a variety of new features and tools, including a new streamlined pipeline that facilitates data deposition by universal PBM data generators in the research community, a tool that generates putative nonbinding (i.e. negative control) DNA sequences for one or more proteins and novel motifs obtained by analyzing the PBM data using the BEEML-PBM algorithm for motif inference. The UniPROBE database is available at http://uniprobe.org. National Institutes of Health (U.S.) (R01 HG003985) National Science Foundation (U.S.). Graduate Research Fellowship Program 2014-12-29T19:06:59Z 2014-12-29T19:06:59Z 2014-11 2014-09 Article http://purl.org/eprint/type/JournalArticle 0305-1048 1362-4962 http://hdl.handle.net/1721.1/92531 Hume, Maxwell A., Luis A. Barrera, Stephen S. Gisselbrecht, and Martha L. Bulyk. “UniPROBE, Update 2015: New Tools and Content for the Online Database of Protein-Binding Microarray Data on Protein-DNA Interactions.” Nucleic Acids Research (November 5, 2014). https://orcid.org/0000-0002-4472-4209 en_US http://dx.doi.org/10.1093/nar/gku1045 Nucleic Acids Research Creative Commons Attribution http://creativecommons.org/licenses/by-nc/4.0 application/pdf Oxford University Press Oxford University Press |
| spellingShingle | Barrera, Luis Alberto Bulyk, Martha L. Hume, Maxwell A. Gisselbrecht, Stephen S. UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein-DNA interactions |
| title | UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein-DNA interactions |
| title_full | UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein-DNA interactions |
| title_fullStr | UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein-DNA interactions |
| title_full_unstemmed | UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein-DNA interactions |
| title_short | UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein-DNA interactions |
| title_sort | uniprobe update 2015 new tools and content for the online database of protein binding microarray data on protein dna interactions |
| url | http://hdl.handle.net/1721.1/92531 https://orcid.org/0000-0002-4472-4209 |
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