HiBrowse: multi-purpose statistical analysis of genome-wide chromatin 3D organization
Recently developed methods that couple next-generation sequencing with chromosome conformation capture-based techniques, such as Hi-C and ChIA-PET, allow for characterization of genome-wide chromatin 3D structure. Understanding the organization of chromatin in three dimensions is a crucial next step...
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| Veröffentlicht in: | Bioinformatics 2014-06, Vol.30 (11), p.1620-1622 |
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| container_title | Bioinformatics |
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| creator | Paulsen, Jonas Sandve, Geir Kjetil Gundersen, Sveinung Lien, Tonje G Trengereid, Kai Hovig, Eivind |
| description | Recently developed methods that couple next-generation sequencing with chromosome conformation capture-based techniques, such as Hi-C and ChIA-PET, allow for characterization of genome-wide chromatin 3D structure. Understanding the organization of chromatin in three dimensions is a crucial next step in the unraveling of global gene regulation, and methods for analyzing such data are needed. We have developed HiBrowse, a user-friendly web-tool consisting of a range of hypothesis-based and descriptive statistics, using realistic assumptions in null-models.
HiBrowse is supported by all major browsers, and is freely available at http://hyperbrowser.uio.no/3d. Software is implemented in Python, and source code is available for download by following instructions on the main site. |
| doi_str_mv | 10.1093/bioinformatics/btu082 |
| format | Article |
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HiBrowse is supported by all major browsers, and is freely available at http://hyperbrowser.uio.no/3d. Software is implemented in Python, and source code is available for download by following instructions on the main site.</description><subject>Applications Notes</subject><subject>Bioinformatics</subject><subject>Chromatin - chemistry</subject><subject>Chromosomes</subject><subject>Computer programs</subject><subject>Data Interpretation, Statistical</subject><subject>Gene expression</subject><subject>Genome</subject><subject>Genomics - methods</subject><subject>High-Throughput Nucleotide Sequencing</subject><subject>Organizations</subject><subject>Software</subject><subject>Statistics</subject><subject>Three dimensional</subject><issn>1367-4803</issn><issn>1367-4811</issn><issn>1460-2059</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2014</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>3HK</sourceid><recordid>eNqFUk1P3DAQtSqq8tH-hLY59pIyjjOOwwEJKGUrrcQFzpbXmSyuEnuxExD99U20sIITp_HIM-_Nm3mMfeXwk0MtjlcuON-G2JvB2XS8GkZQxQd2wIWs8lJxvrd7g9hnhyn9BQAElJ_YflEi56DggN0u3HkMj4lOsn7sBpdvxrgJibI0TMBpwjZdZrzpnpJLWWizNfnQU_7oGsrsXQwzv8_EryzEtfHu35QG_5l9bE2X6MtzPGK3vy9vLhb58vrqz8XZMrcIfMhbg1Cpuq5IWStUY1RhG1VWUKOx1EqOSklEoKZVlmMhaiplWUhCrE2FUhyx0y3uZlz11FjyQzSd3kTXm_ikg3H67Y93d3odHnQJRQ0lTADftwA2zmK99iEaPa0GCz0xlzPFj2eKGO5HSoPuXbLUdcZTGJPmsuKSSyHx_VIU02HqWcj7pYUSQio5D4AvI4aUIrU7eRz0bAX91gp6a4Wp79vr3ey6Xm4v_gN8cbSw</recordid><startdate>20140601</startdate><enddate>20140601</enddate><creator>Paulsen, Jonas</creator><creator>Sandve, Geir Kjetil</creator><creator>Gundersen, Sveinung</creator><creator>Lien, Tonje G</creator><creator>Trengereid, Kai</creator><creator>Hovig, Eivind</creator><general>Oxford University Press</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>7QO</scope><scope>7TM</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>7SC</scope><scope>JQ2</scope><scope>L7M</scope><scope>L~C</scope><scope>L~D</scope><scope>3HK</scope><scope>5PM</scope></search><sort><creationdate>20140601</creationdate><title>HiBrowse: multi-purpose statistical analysis of genome-wide chromatin 3D organization</title><author>Paulsen, Jonas ; Sandve, Geir Kjetil ; Gundersen, Sveinung ; Lien, Tonje G ; Trengereid, Kai ; Hovig, Eivind</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c501t-fa5078997e8cc38da82cd847095acef615886550edf8c15239e46426e559a7563</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2014</creationdate><topic>Applications Notes</topic><topic>Bioinformatics</topic><topic>Chromatin - chemistry</topic><topic>Chromosomes</topic><topic>Computer programs</topic><topic>Data Interpretation, Statistical</topic><topic>Gene expression</topic><topic>Genome</topic><topic>Genomics - methods</topic><topic>High-Throughput Nucleotide Sequencing</topic><topic>Organizations</topic><topic>Software</topic><topic>Statistics</topic><topic>Three dimensional</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Paulsen, Jonas</creatorcontrib><creatorcontrib>Sandve, Geir Kjetil</creatorcontrib><creatorcontrib>Gundersen, Sveinung</creatorcontrib><creatorcontrib>Lien, Tonje G</creatorcontrib><creatorcontrib>Trengereid, Kai</creatorcontrib><creatorcontrib>Hovig, Eivind</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>Biotechnology Research Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Computer and Information Systems Abstracts</collection><collection>ProQuest Computer Science Collection</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>Computer and Information Systems Abstracts Academic</collection><collection>Computer and Information Systems Abstracts Professional</collection><collection>NORA - Norwegian Open Research Archives</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Bioinformatics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Paulsen, Jonas</au><au>Sandve, Geir Kjetil</au><au>Gundersen, Sveinung</au><au>Lien, Tonje G</au><au>Trengereid, Kai</au><au>Hovig, Eivind</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>HiBrowse: multi-purpose statistical analysis of genome-wide chromatin 3D organization</atitle><jtitle>Bioinformatics</jtitle><addtitle>Bioinformatics</addtitle><date>2014-06-01</date><risdate>2014</risdate><volume>30</volume><issue>11</issue><spage>1620</spage><epage>1622</epage><pages>1620-1622</pages><issn>1367-4803</issn><eissn>1367-4811</eissn><eissn>1460-2059</eissn><abstract>Recently developed methods that couple next-generation sequencing with chromosome conformation capture-based techniques, such as Hi-C and ChIA-PET, allow for characterization of genome-wide chromatin 3D structure. Understanding the organization of chromatin in three dimensions is a crucial next step in the unraveling of global gene regulation, and methods for analyzing such data are needed. We have developed HiBrowse, a user-friendly web-tool consisting of a range of hypothesis-based and descriptive statistics, using realistic assumptions in null-models.
HiBrowse is supported by all major browsers, and is freely available at http://hyperbrowser.uio.no/3d. Software is implemented in Python, and source code is available for download by following instructions on the main site.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>24511080</pmid><doi>10.1093/bioinformatics/btu082</doi><tpages>3</tpages><oa>free_for_read</oa></addata></record> |
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| source | PubMed (Medline); OUP_牛津大学出版社OA刊; MEDLINE; NORA - Norwegian Open Research Archives; Alma/SFX Local Collection; EZB Electronic Journals Library |
| subjects | Applications Notes Bioinformatics Chromatin - chemistry Chromosomes Computer programs Data Interpretation, Statistical Gene expression Genome Genomics - methods High-Throughput Nucleotide Sequencing Organizations Software Statistics Three dimensional |
| title | HiBrowse: multi-purpose statistical analysis of genome-wide chromatin 3D organization |
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