An Interactive Analysis and Exploration Tool for Epigenomic Data
In this design study, we present an analysis and ion of the data and tasks related to the domain of epigenomics, and the design and implementation of an interactive tool to facilitate data analysis and visualization in this domain. Epigenomic data can be grouped into subsets either by k‐means cluste...
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| Veröffentlicht in: | Computer graphics forum Jg. 32; H. 3pt1; S. 91 - 100 |
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| Format: | Journal Article |
| Sprache: | Englisch |
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Oxford, UK
Blackwell Publishing Ltd
01.06.2013
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| ISSN: | 0167-7055, 1467-8659 |
| Online-Zugang: | Volltext |
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| Abstract | In this design study, we present an analysis and ion of the data and tasks related to the domain of epigenomics, and the design and implementation of an interactive tool to facilitate data analysis and visualization in this domain. Epigenomic data can be grouped into subsets either by k‐means clustering or by querying for combinations of presence or absence of signal (on/off) in different epigenomic experiments. These steps can easily be interleaved and the comparison of different workflows is explicitly supported. We took special care to contain the exponential expansion of possible on/off combinations by creating a novel querying interface. An interactive heat map facilitates the exploration and comparison of different clusters. We validated our iterative design by working closely with two groups of biologists on different biological problems. Both groups quickly found new insight into their data as well as claimed that our tool would save them several hours or days of work over using existing tools. |
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| AbstractList | In this design study, we present an analysis and abstraction of the data and tasks related to the domain of epigenomics, and the design and implementation of an interactive tool to facilitate data analysis and visualization in this domain. Epigenomic data can be grouped into subsets either by k-means clustering or by querying for combinations of presence or absence of signal (on/off) in different epigenomic experiments. These steps can easily be interleaved and the comparison of different workflows is explicitly supported. We took special care to contain the exponential expansion of possible on/off combinations by creating a novel querying interface. An interactive heat map facilitates the exploration and comparison of different clusters. We validated our iterative design by working closely with two groups of biologists on different biological problems. Both groups quickly found new insight into their data as well as claimed that our tool would save them several hours or days of work over using existing tools [PUBLICATION ABSTRACT]. In this design study, we present an analysis and abstraction of the data and tasks related to the domain of epigenomics, and the design and implementation of an interactive tool to facilitate data analysis and visualization in this domain. Epigenomic data can be grouped into subsets either by k-means clustering or by querying for combinations of presence or absence of signal (on/off) in different epigenomic experiments. These steps can easily be interleaved and the comparison of different workflows is explicitly supported. We took special care to contain the exponential expansion of possible on/off combinations by creating a novel querying interface. An interactive heat map facilitates the exploration and comparison of different clusters. We validated our iterative design by working closely with two groups of biologists on different biological problems. Both groups quickly found new insight into their data as well as claimed that our tool would save them several hours or days of work over using existing tools. In this design study, we present an analysis and ion of the data and tasks related to the domain of epigenomics, and the design and implementation of an interactive tool to facilitate data analysis and visualization in this domain. Epigenomic data can be grouped into subsets either by k‐means clustering or by querying for combinations of presence or absence of signal (on/off) in different epigenomic experiments. These steps can easily be interleaved and the comparison of different workflows is explicitly supported. We took special care to contain the exponential expansion of possible on/off combinations by creating a novel querying interface. An interactive heat map facilitates the exploration and comparison of different clusters. We validated our iterative design by working closely with two groups of biologists on different biological problems. Both groups quickly found new insight into their data as well as claimed that our tool would save them several hours or days of work over using existing tools. |
| Author | Cullum, R. Jones, S.J.M. Younesy, H. Lorincz, M.C. Möller, T. Alder, O. Karimi, M.M. Nielsen, C.B. |
| Author_xml | – sequence: 1 givenname: H. surname: Younesy fullname: Younesy, H. organization: School of Computing Science, Simon Fraser University – sequence: 2 givenname: C.B. surname: Nielsen fullname: Nielsen, C.B. organization: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency – sequence: 3 givenname: T. surname: Möller fullname: Möller, T. organization: School of Computing Science, Simon Fraser University – sequence: 4 givenname: O. surname: Alder fullname: Alder, O. organization: Terry Fox Laboratory, British Columbia Cancer Agency – sequence: 5 givenname: R. surname: Cullum fullname: Cullum, R. organization: Terry Fox Laboratory, British Columbia Cancer Agency – sequence: 6 givenname: M.C. surname: Lorincz fullname: Lorincz, M.C. organization: Department of Medical Genetics, Life Sciences Institute, The University of British Columbia – sequence: 7 givenname: M.M. surname: Karimi fullname: Karimi, M.M. organization: Department of Medical Genetics, Life Sciences Institute, The University of British Columbia – sequence: 8 givenname: S.J.M. surname: Jones fullname: Jones, S.J.M. organization: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency |
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| Cites_doi | 10.1186/gb-2010-11-8-r86 10.1038/ng1966 10.1186/gb-2011-12-8-r83 10.1073/pnas.082249499 10.1038/nmeth0810-573 10.1038/nmeth.1937 10.1111/j.1467-8659.2012.03110.x 10.1038/nbt.1662 10.1038/nature07829 10.1145/1385569.1385609 10.1371/journal.pcbi.1000201 10.1111/j.1467-8659.2009.01710.x 10.1109/TVCG.2010.137 10.1093/nar/gkr1012 10.1080/00401706.1987.10488204 10.1038/nbt.1505 10.1198/tas.2009.0033 10.1007/978-3-540-24595-7_44 10.1038/nature11247 10.1145/142750.143054 10.1101/gr.104356.109 10.1038/nbt1010-1045 10.1093/nar/gkq1287 10.1038/nmeth.1422 |
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| Copyright | 2013 The Author(s) Computer Graphics Forum © 2013 The Eurographics Association and Blackwell Publishing Ltd. |
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| References_xml | – reference: Hoffman M. , Buske O. , Wang J. , Weng Z. , Bilmes J. , Noble W. : Unsupervised pattern discovery in human chromatin structure through genomic segmentation . Nature Methods 9 , 5 ( 2012 ), 473 - 476 . 3 . – reference: Heintzman N. , Stuart R. , Hon G. , Fu Y. , Ching C. , Hawkins R. , et al. : Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome . Nature genetics 39 , 3 ( 2007 ), 311 - 318 . 3, 7 . – reference: Wilkinson L. , Friendly M. : The history of the cluster heat map . The American Stat. 63 , 2 ( 2009 ), 179 - 184 . 6 . – reference: The ENCODE Project Consortium : An integrated encyclopedia of DNA elements in the human genome . Nature 489 ( 2012 ), 57 - 74 . 1 . – reference: Bernstein B. , Stamatoyannopoulos J. , Costello J. , Ren B. , Milosavljevic A. , et al. : The NIH Roadmap Epigenomics Mapping Consortium . Nature biotechnology 28 , 10 ( 2010 ), 1045 - 1048 . 1 . – reference: Hon G. , Ren B. , Wang W. : ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome . PLoS Computational Biology 4 , 10 ( Oct 2008 ), e1000201 . 2, 3 . – reference: Wong B. : Points of view: Color coding . Nature Methods 7 , 8 ( Aug 2010 ), 573 - 573 . 6 . – reference: Nielsen C. B. , Cantor M. , Dubchak I. , Gordon D. , Wang T. : Visualizing genomes: techniques and challenges . Nature Methods 7 , 3 Suppl ( Mar 2010 ), S5 - S15 . 3 . – reference: Ji H. , Jiang H. , Ma W. , Johnson D. S. , Myers R. M. , Wong W. H. : An integrated software system for analyzing ChIP-chip and ChIP-seq data . Nat Biotechnol 26 , 11 ( Nov 2008 ), 1293 - 1300 . 3 . – reference: Ernst J. , Kellis M. : Discovery and characterization of chromatin states for systematic annotation of the human genome . Nat Biotechnol 28 , 8 ( Aug 2010 ), 817 - 825 . 3 . – reference: Rosenbloom K. , Dreszer T. , Long J. , Malladi V. , Sloan C. , et al. : ENCODE whole-genome data in the UCSC Genome Browser: update 2012 . Nucleic acids research 40 , D1 ( 2012 ), D912 - D917 . 3 . – reference: Meyer M. , Munzner T. , DePace A. , Pfister H. : MulteeSum: A tool for comparative spatial and temporal gene expression data . IEEE Transactions on Visualization and Computer Graphics 16 ( 2010 ), 908 - 917 . 6 . – reference: Heintzman N. , Hon G. , Hawkins R. , Kheradpour P. , Stark A. , Harp L. , et al. : Histone modifications at human enhancers reflect global cell-type-specific gene expression . Nature 459 , 7243 ( 2009 ), 108 - 112 . 3 . – reference: Bernstein B. , Humphrey E. , Erlich R. , Schneider R. , Bouman P. , Liu J. , Kouzarides T. , Schreiber S. : Methylation of histone H3 Lys 4 in coding regions of active genes . Proceedings of the National Academy of Sciences 99 , 13 ( 2002 ), 8695 - 8700 . 8 . – reference: Goecks J. , Nekrutenko A. , Taylor J. , The Galaxy Team : Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences . Genome Bio. 11 , 8 ( 2010 ), R86 . 3, 7 . – reference: Liu T. , Ortiz J. , Taing L. , Meyer C. , Lee B. , Zhang Y. , Shin H. , Wong S. , Ma J. , Lei Y. , et al. : Cistrome: an integrative platform for transcriptional regulation studies . Genome Biology 12 , 8 ( 2011 ), R83 . 3 . – reference: Meyer M. , Wong B. , Styczynski M. , Munzner T. , Pfister H. : Pathline: A tool for comparative functional genomics . Computer Graphics Forum 29 , 3 ( 2010 ), 1043 - 1052 . 6 . – reference: Hoffman B. , Robertson G. , Zavaglia B. , Beach M. , Cullum R. , et al. : Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver . Genome research 20 , 8 ( 2010 ), 1037 - 1051 . 7, 8 . – reference: Becker R. A. , Cleveland W. S. : Brushing Scatterplots . Technometrics 29 , 2 ( May 1987 ), 127 - 142 . URL : http://www.jstor.org/stable/1269768 . 4 . – reference: Lex A. , Streit M. , Schulz H. , Partl C. , Schmalstieg D. , Park P. J. , Gehlenborg N. : StratomeX: Visual analysis of Large-Scale heterogeneous genomics data for cancer subtype characterization . Computer Graphics Forum (EuroVis '12) 31 , 3 ( 2012 ), 1175 - 1184 . 3 . – reference: Ye T. , Krebs A. R. , Choukrallah M. A. , Keime C. , Plewniak F. , Davidson I. , Tora L. : seqMINER: an integrated ChIP-seq data interpretation platform . Nucleic Acids Res 39 , 6 ( Mar 2011 ). 3 . – volume: 11 start-page: R86 issue: 8 year: 2010 article-title: Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences publication-title: Genome Bio. – start-page: 243 year: 2008 end-page: 250 – volume: 40 start-page: D912 issue: D1 year: 2012 end-page: D917 article-title: ENCODE whole‐genome data in the UCSC Genome Browser: update 2012 publication-title: Nucleic acids research – volume: 459 start-page: 108 issue: 7243 year: 2009 end-page: 112 article-title: Histone modifications at human enhancers reflect global cell‐type‐specific gene expression publication-title: Nature – volume: 16 start-page: 908 year: 2010 end-page: 917 article-title: MulteeSum: A tool for comparative spatial and temporal gene expression data publication-title: IEEE Transactions on Visualization and Computer Graphics – volume: 12 start-page: R83 issue: 8 year: 2011 article-title: Cistrome: an integrative platform for transcriptional regulation studies publication-title: Genome Biology – volume: 4 start-page: e1000201 issue: 10 year: Oct 2008 article-title: ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome publication-title: PLoS Computational Biology – volume: 9 start-page: 473 issue: 5 year: 2012 end-page: 476 article-title: Unsupervised pattern discovery in human chromatin structure through genomic segmentation publication-title: Nature Methods – volume: 39 start-page: 3 issue: 6 year: Mar 2011 article-title: seqMINER: an integrated ChIP‐seq data interpretation platform publication-title: Nucleic Acids Res – volume: 26 start-page: 1293 issue: 11 year: Nov 2008 end-page: 1300 article-title: An integrated software system for analyzing ChIP‐chip and ChIP‐seq data publication-title: Nat Biotechnol – volume: 29 start-page: 1043 issue: 3 year: 2010 end-page: 1052 article-title: Pathline: A tool for comparative functional genomics 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| SubjectTerms | Analysis Biologists Clusters Computer graphics Data processing Design engineering Environmental monitoring Exploration H.5.m [Information Systems]: Information Interfaces and Presentation-Miscellaneous I.3.8 [Computing Methodologies]: Computer Graphics-Applications Interactive Studies Tasks Visualization |
| Title | An Interactive Analysis and Exploration Tool for Epigenomic Data |
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