Pathway collages: personalized multi-pathway diagrams.
BMC Bioinformatics
; 17(1): 529, 2016 Dec 13.
Article
em En
| MEDLINE
| ID: mdl-27964719
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 an Escherichia coli metabolic model.CONCLUSIONS:
Pathway collages enable facile construction of personalized multi-pathway diagrams.Palavras-chave
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Escherichia coli
/
Metabolômica
Tipo de estudo:
Evaluation_studies
Idioma:
En
Ano de publicação:
2016
Tipo de documento:
Article