HiPiler: Visual Exploration of Large Genome Interaction Matrices with Interactive Small Multiples.
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| Title: | HiPiler: Visual Exploration of Large Genome Interaction Matrices with Interactive Small Multiples. |
|---|---|
| Authors: | Lekschas, Fritz1, Bach, Benjamin1, Kerpedjiev, Peter2, Gehlenborg, Nils2, Pfister, Hanspeter1 |
| Source: | IEEE Transactions on Visualization & Computer Graphics. Jan2018, Vol. 24 Issue 1, p522-531. 10p. |
| Subjects: | Computer interfaces software, Data visualization, Interactive computer systems, Gene expression, DNA repair |
| Abstract: | This paper presents an interactive visualization interface—HiPiler—for the exploration and visualization of regions-of-interest in large genome interaction matrices. Genome interaction matrices approximate the physical distance of pairs of regions on the genome to each other and can contain up to 3 million rows and columns with many sparse regions. Regions of interest (ROIs) can be defined, e.g., by sets of adjacent rows and columns, or by specific visual patterns in the matrix. However, traditional matrix aggregation or pan-and-zoom interfaces fail in supporting search, inspection, and comparison of ROIs in such large matrices. In HiPiler, ROIs are first-class objects, represented as thumbnail-like “snippets”. Snippets can be interactively explored and grouped or laid out automatically in scatterplots, or through dimension reduction methods. Snippets are linked to the entire navigable genome interaction matrix through brushing and linking. The design of HiPiler is based on a series of semi-structured interviews with 10 domain experts involved in the analysis and interpretation of genome interaction matrices. We describe six exploration tasks that are crucial for analysis of interaction matrices and demonstrate how HiPiler supports these tasks. We report on a user study with a series of data exploration sessions with domain experts to assess the usability of HiPiler as well as to demonstrate respective findings in the data. [ABSTRACT FROM PUBLISHER] |
| Copyright of IEEE Transactions on Visualization & Computer Graphics is the property of IEEE and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.) | |
| Database: | Engineering Source |
| FullText | Text: Availability: 0 |
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| Header | DbId: egs DbLabel: Engineering Source An: 126653849 AccessLevel: 6 PubType: Academic Journal PubTypeId: academicJournal PreciseRelevancyScore: 0 |
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| Items | – Name: Title Label: Title Group: Ti Data: HiPiler: Visual Exploration of Large Genome Interaction Matrices with Interactive Small Multiples. – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AR" term="%22Lekschas%2C+Fritz%22">Lekschas, Fritz</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Bach%2C+Benjamin%22">Bach, Benjamin</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Kerpedjiev%2C+Peter%22">Kerpedjiev, Peter</searchLink><relatesTo>2</relatesTo><br /><searchLink fieldCode="AR" term="%22Gehlenborg%2C+Nils%22">Gehlenborg, Nils</searchLink><relatesTo>2</relatesTo><br /><searchLink fieldCode="AR" term="%22Pfister%2C+Hanspeter%22">Pfister, Hanspeter</searchLink><relatesTo>1</relatesTo> – Name: TitleSource Label: Source Group: Src Data: <searchLink fieldCode="JN" term="%22IEEE+Transactions+on+Visualization+%26+Computer+Graphics%22">IEEE Transactions on Visualization & Computer Graphics</searchLink>. Jan2018, Vol. 24 Issue 1, p522-531. 10p. – Name: Subject Label: Subjects Group: Su Data: <searchLink fieldCode="DE" term="%22Computer+interfaces+software%22">Computer interfaces software</searchLink><br /><searchLink fieldCode="DE" term="%22Data+visualization%22">Data visualization</searchLink><br /><searchLink fieldCode="DE" term="%22Interactive+computer+systems%22">Interactive computer systems</searchLink><br /><searchLink fieldCode="DE" term="%22Gene+expression%22">Gene expression</searchLink><br /><searchLink fieldCode="DE" term="%22DNA+repair%22">DNA repair</searchLink> – Name: Abstract Label: Abstract Group: Ab Data: This paper presents an interactive visualization interface—HiPiler—for the exploration and visualization of regions-of-interest in large genome interaction matrices. Genome interaction matrices approximate the physical distance of pairs of regions on the genome to each other and can contain up to 3 million rows and columns with many sparse regions. Regions of interest (ROIs) can be defined, e.g., by sets of adjacent rows and columns, or by specific visual patterns in the matrix. However, traditional matrix aggregation or pan-and-zoom interfaces fail in supporting search, inspection, and comparison of ROIs in such large matrices. In HiPiler, ROIs are first-class objects, represented as thumbnail-like “snippets”. Snippets can be interactively explored and grouped or laid out automatically in scatterplots, or through dimension reduction methods. Snippets are linked to the entire navigable genome interaction matrix through brushing and linking. The design of HiPiler is based on a series of semi-structured interviews with 10 domain experts involved in the analysis and interpretation of genome interaction matrices. We describe six exploration tasks that are crucial for analysis of interaction matrices and demonstrate how HiPiler supports these tasks. We report on a user study with a series of data exploration sessions with domain experts to assess the usability of HiPiler as well as to demonstrate respective findings in the data. [ABSTRACT FROM PUBLISHER] – Name: AbstractSuppliedCopyright Label: Group: Ab Data: <i>Copyright of IEEE Transactions on Visualization & Computer Graphics is the property of IEEE and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.) |
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| RecordInfo | BibRecord: BibEntity: Identifiers: – Type: doi Value: 10.1109/TVCG.2017.2745978 Languages: – Code: eng Text: English PhysicalDescription: Pagination: PageCount: 10 StartPage: 522 Subjects: – SubjectFull: Computer interfaces software Type: general – SubjectFull: Data visualization Type: general – SubjectFull: Interactive computer systems Type: general – SubjectFull: Gene expression Type: general – SubjectFull: DNA repair Type: general Titles: – TitleFull: HiPiler: Visual Exploration of Large Genome Interaction Matrices with Interactive Small Multiples. Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Lekschas, Fritz – PersonEntity: Name: NameFull: Bach, Benjamin – PersonEntity: Name: NameFull: Kerpedjiev, Peter – PersonEntity: Name: NameFull: Gehlenborg, Nils – PersonEntity: Name: NameFull: Pfister, Hanspeter IsPartOfRelationships: – BibEntity: Dates: – D: 01 M: 01 Text: Jan2018 Type: published Y: 2018 Identifiers: – Type: issn-print Value: 10772626 Numbering: – Type: volume Value: 24 – Type: issue Value: 1 Titles: – TitleFull: IEEE Transactions on Visualization & Computer Graphics Type: main |
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