Pathway collages: personalized multi-pathway diagrams. Issue 1 (December 2016)
- Record Type:
- Journal Article
- Title:
- Pathway collages: personalized multi-pathway diagrams. Issue 1 (December 2016)
- Main Title:
- Pathway collages: personalized multi-pathway diagrams
- Authors:
- Paley, Suzanne
O'Maille, Paul E.
Weaver, Daniel
Karp, Peter D. - Abstract:
- Abstract Background Metabolic pathway diagrams are a classical way of visualizing a linked cascade of biochemical reactions. However, to understand some biochemical situations, viewing a single pathway is insufficient, whereas viewing the entire metabolic network results in information overload. How do we enable scientists to rapidly construct personalized multi-pathway diagrams that depict a desired collection of interacting pathways that emphasize particular pathway interactions? Results We define software for constructing personalized multi-pathway diagrams called pathway-collages using a combination of manual and automatic layouts. The user specifies a set of pathways of interest for the collage from a Pathway/Genome Database. Layouts for the individual pathways are generated by the Pathway Tools software, and are sent to a Javascript Pathway Collage application implemented using Cytoscape.js. That application allows the user to re-position pathways; define connections between pathways; change visual style parameters; and paint metabolomics, gene expression, and reaction flux data onto the collage to obtain a desired multi-pathway diagram. We demonstrate the use of pathway collages in two application areas: a metabolomics study of pathogen drug response, and anEscherichia coli metabolic model. Conclusions Pathway collages enable facile construction of personalized multi-pathway diagrams.
- Is Part Of:
- BMC bioinformatics. Volume 17:Issue 1(2016)
- Journal:
- BMC bioinformatics
- Issue:
- Volume 17:Issue 1(2016)
- Issue Display:
- Volume 17, Issue 1 (2016)
- Year:
- 2016
- Volume:
- 17
- Issue:
- 1
- Issue Sort Value:
- 2016-0017-0001-0000
- Page Start:
- 1
- Page End:
- 10
- Publication Date:
- 2016-12
- Subjects:
- Metabolic pathways -- Visualization -- Pathway diagram
Bioinformatics -- Periodicals
Computational biology -- Periodicals
570.285 - Journal URLs:
- http://www.biomedcentral.com/bmcbioinformatics/ ↗
http://www.pubmedcentral.nih.gov/tocrender.fcgi?journal=13 ↗
http://link.springer.com/ ↗ - DOI:
- 10.1186/s12859-016-1382-1 ↗
- Languages:
- English
- ISSNs:
- 1471-2105
- Deposit Type:
- Legaldeposit
- View Content:
- Available online (eLD content is only available in our Reading Rooms) ↗
- Physical Locations:
- British Library DSC - BLDSS-3PM
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British Library HMNTS - ELD Digital store - Ingest File:
- 9974.xml