VISIONET: intuitive visualisation of overlapping transcription factor networks, with applications in cardiogenic gene discovery.
Document Type
Article
Publication Date
5-1-2015
JAX Source
BMC Bioinformatics 2015 May 1; 16:141.
Volume
16
First Page
141
Last Page
141
ISSN
1471-2105
PMID
25929466
Abstract
BACKGROUND: Existing de novo software platforms have largely overlooked a valuable resource, the expertise of the intended biologist users. Typical data representations such as long gene lists, or highly dense and overlapping transcription factor networks often hinder biologists from relating these results to their expertise.
RESULTS: VISIONET, a streamlined visualisation tool built from experimental needs, enables biologists to transform large and dense overlapping transcription factor networks into sparse human-readable graphs via numerically filtering. The VISIONET interface allows users without a computing background to interactively explore and filter their data, and empowers them to apply their specialist knowledge on far more complex and substantial data sets than is currently possible. Applying VISIONET to the Tbx20-Gata4 transcription factor network led to the discovery and validation of Aldh1a2, an essential developmental gene associated with various important cardiac disorders, as a healthy adult cardiac fibroblast gene co-regulated by cardiogenic transcription factors Gata4 and Tbx20.
CONCLUSIONS: We demonstrate with experimental validations the utility of VISIONET for expertise-driven gene discovery that opens new experimental directions that would not otherwise have been identified.
BMC Bioinformatics 2015 May 1; 16:141.
Recommended Citation
Nim H,
Furtado M,
Costa M,
Rosenthal NA,
Kitano H,
Boyd S.
VISIONET: intuitive visualisation of overlapping transcription factor networks, with applications in cardiogenic gene discovery. BMC Bioinformatics 2015 May 1; 16:141.