Systematic chromatin state comparison of epigenomes associated with diverse properties including sex and tissue type
Epigenomic data sets provide critical information about the dynamic role of chromatin states in gene regulation, but a key question of how chromatin state segmentations vary under different conditions across the genome has remained unaddressed. Here we present ChromDiff, a group-wise chromatin state...
| Main Authors: | , |
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| Format: | Article |
| Language: | en_US |
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Nature Publishing Group
2015
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| Online Access: | http://hdl.handle.net/1721.1/100499 https://orcid.org/0000-0001-5951-9358 |
| _version_ | 1811097533110288384 |
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| author | Yen, Angela Kellis, Manolis |
| author2 | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory |
| author_facet | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Yen, Angela Kellis, Manolis |
| author_sort | Yen, Angela |
| collection | MIT |
| description | Epigenomic data sets provide critical information about the dynamic role of chromatin states in gene regulation, but a key question of how chromatin state segmentations vary under different conditions across the genome has remained unaddressed. Here we present ChromDiff, a group-wise chromatin state comparison method that generates an information-theoretic representation of epigenomes and corrects for external covariate factors to better isolate relevant chromatin state changes. By applying ChromDiff to the 127 epigenomes from the Roadmap Epigenomics and ENCODE projects, we provide novel group-wise comparative analyses across sex, tissue type, state and developmental age. Remarkably, we find that distinct sets of epigenomic features are maximally discriminative for different group-wise comparisons, in each case revealing distinct enriched pathways, many of which do not show gene expression differences. Our methodology should be broadly applicable for epigenomic comparisons and provides a powerful new tool for studying chromatin state differences at the genome scale. |
| first_indexed | 2024-09-23T17:00:53Z |
| format | Article |
| id | mit-1721.1/100499 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T17:00:53Z |
| publishDate | 2015 |
| publisher | Nature Publishing Group |
| record_format | dspace |
| spelling | mit-1721.1/1004992022-10-03T09:51:05Z Systematic chromatin state comparison of epigenomes associated with diverse properties including sex and tissue type Yen, Angela Kellis, Manolis Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science Yen, Angela Kellis, Manolis Epigenomic data sets provide critical information about the dynamic role of chromatin states in gene regulation, but a key question of how chromatin state segmentations vary under different conditions across the genome has remained unaddressed. Here we present ChromDiff, a group-wise chromatin state comparison method that generates an information-theoretic representation of epigenomes and corrects for external covariate factors to better isolate relevant chromatin state changes. By applying ChromDiff to the 127 epigenomes from the Roadmap Epigenomics and ENCODE projects, we provide novel group-wise comparative analyses across sex, tissue type, state and developmental age. Remarkably, we find that distinct sets of epigenomic features are maximally discriminative for different group-wise comparisons, in each case revealing distinct enriched pathways, many of which do not show gene expression differences. Our methodology should be broadly applicable for epigenomic comparisons and provides a powerful new tool for studying chromatin state differences at the genome scale. National Science Foundation (U.S.). Graduate Research Fellowship National Institutes of Health (U.S.) (U54 HG006991) National Institutes of Health (U.S.) (U41 HG007000) National Institutes of Health (U.S.) (5U01ES017156) National Institutes of Health (U.S.) (RC1-HG005334) National Institutes of Health (U.S.) (HG004570) National Institutes of Health (U.S.) (HG006911) National Institutes of Health (U.S.) (R01 HG004037) 2015-12-23T16:06:28Z 2015-12-23T16:06:28Z 2015-08 2015-01 Article http://purl.org/eprint/type/JournalArticle 2041-1723 http://hdl.handle.net/1721.1/100499 Yen, Angela, and Manolis Kellis. “Systematic Chromatin State Comparison of Epigenomes Associated with Diverse Properties Including Sex and Tissue Type.” Nat Comms 6 (August 18, 2015): 7973. © 2015 Macmillan Publishers Limited https://orcid.org/0000-0001-5951-9358 en_US http://dx.doi.org/10.1038/ncomms8973 Nature Communications Creative Commons Attribution http://creativecommons.org/licenses/by/4.0/ application/pdf Nature Publishing Group Nature Publishing Group |
| spellingShingle | Yen, Angela Kellis, Manolis Systematic chromatin state comparison of epigenomes associated with diverse properties including sex and tissue type |
| title | Systematic chromatin state comparison of epigenomes associated with diverse properties including sex and tissue type |
| title_full | Systematic chromatin state comparison of epigenomes associated with diverse properties including sex and tissue type |
| title_fullStr | Systematic chromatin state comparison of epigenomes associated with diverse properties including sex and tissue type |
| title_full_unstemmed | Systematic chromatin state comparison of epigenomes associated with diverse properties including sex and tissue type |
| title_short | Systematic chromatin state comparison of epigenomes associated with diverse properties including sex and tissue type |
| title_sort | systematic chromatin state comparison of epigenomes associated with diverse properties including sex and tissue type |
| url | http://hdl.handle.net/1721.1/100499 https://orcid.org/0000-0001-5951-9358 |
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