A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression [version 2; referees: 2 approved]
One commonly performed bioinformatics task is to infer functional regulation of transcription factors by observing differential expression under a knockout, and integrating DNA binding information of that transcription factor. However, until now, this task has required dedicated bioinformatics sup...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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F1000 Research Ltd
2018-01-01
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| Series: | F1000Research |
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| Online Access: | https://f1000research.com/articles/6-784/v2 |
| _version_ | 1828336947400015872 |
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| author | Daniel Carlin Kassi Kosnicki Sara Garamszegi Trey Ideker Helga Thorvaldsdóttir Michael Reich Jill Mesirov |
| author_facet | Daniel Carlin Kassi Kosnicki Sara Garamszegi Trey Ideker Helga Thorvaldsdóttir Michael Reich Jill Mesirov |
| author_sort | Daniel Carlin |
| collection | DOAJ |
| description | One commonly performed bioinformatics task is to infer functional regulation of transcription factors by observing differential expression under a knockout, and integrating DNA binding information of that transcription factor. However, until now, this task has required dedicated bioinformatics support to perform the necessary data integration. GenomeSpace provides a protocol, or “recipe”, and a user interface with inter-operating software tools to identify protein occupancies along the genome from a ChIP-seq experiment and associated differentially regulated genes from a RNA-Seq experiment. By integrating RNA-Seq and ChIP-seq analyses, a user is easily able to associate differing expression phenotypes with changing epigenetic landscapes. |
| first_indexed | 2024-04-13T22:08:17Z |
| format | Article |
| id | doaj.art-9ef975402c914b13992e177db8968b2d |
| institution | Directory Open Access Journal |
| issn | 2046-1402 |
| language | English |
| last_indexed | 2024-04-13T22:08:17Z |
| publishDate | 2018-01-01 |
| publisher | F1000 Research Ltd |
| record_format | Article |
| series | F1000Research |
| spelling | doaj.art-9ef975402c914b13992e177db8968b2d2022-12-22T02:27:51ZengF1000 Research LtdF1000Research2046-14022018-01-01610.12688/f1000research.11616.214929A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression [version 2; referees: 2 approved]Daniel Carlin0Kassi Kosnicki1Sara Garamszegi2Trey Ideker3Helga Thorvaldsdóttir4Michael Reich5Jill Mesirov6The University of California, San Diego School of Medicine, 500 Gilman Dr, La Jolla, CA, 92093, USAThe University of California, San Diego School of Medicine, 500 Gilman Dr, La Jolla, CA, 92093, USABroad Institute, Cambridge, MA, 02142, USAThe University of California, San Diego School of Medicine, 500 Gilman Dr, La Jolla, CA, 92093, USABroad Institute, Cambridge, MA, 02142, USAThe University of California, San Diego School of Medicine, 500 Gilman Dr, La Jolla, CA, 92093, USAThe University of California, San Diego School of Medicine, 500 Gilman Dr, La Jolla, CA, 92093, USAOne commonly performed bioinformatics task is to infer functional regulation of transcription factors by observing differential expression under a knockout, and integrating DNA binding information of that transcription factor. However, until now, this task has required dedicated bioinformatics support to perform the necessary data integration. GenomeSpace provides a protocol, or “recipe”, and a user interface with inter-operating software tools to identify protein occupancies along the genome from a ChIP-seq experiment and associated differentially regulated genes from a RNA-Seq experiment. By integrating RNA-Seq and ChIP-seq analyses, a user is easily able to associate differing expression phenotypes with changing epigenetic landscapes.https://f1000research.com/articles/6-784/v2BioinformaticsGenomics |
| spellingShingle | Daniel Carlin Kassi Kosnicki Sara Garamszegi Trey Ideker Helga Thorvaldsdóttir Michael Reich Jill Mesirov A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression [version 2; referees: 2 approved] F1000Research Bioinformatics Genomics |
| title | A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression [version 2; referees: 2 approved] |
| title_full | A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression [version 2; referees: 2 approved] |
| title_fullStr | A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression [version 2; referees: 2 approved] |
| title_full_unstemmed | A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression [version 2; referees: 2 approved] |
| title_short | A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression [version 2; referees: 2 approved] |
| title_sort | multi tool recipe to identify regions of protein dna binding and their influence on associated gene expression version 2 referees 2 approved |
| topic | Bioinformatics Genomics |
| url | https://f1000research.com/articles/6-784/v2 |
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