VISIONET: intuitive visualisation of overlapping transcription factor networks, with applications in cardiogenic gene discovery.
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.
Systems Biology Institute (SBI) Australia, Monash University, Clayton, VIC, 3800, Australia. hieu.nim@monash.edu.|Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, 3800, Australia. hieu.nim@monash.edu.
Hieu T
HT
Nim
Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, 3800, Australia. milena.furtado@monash.edu.
Milena B
MB
Furtado
Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, 3800, Australia. mauro.dacosta@monash.edu.
Mauro W
MW
Costa
Systems Biology Institute (SBI) Australia, Monash University, Clayton, VIC, 3800, Australia. nadia.rosenthal@monash.edu.|Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, 3800, Australia. nadia.rosenthal@monash.edu.|National Heart and Lung Institute, Imperial College London, London, W12 0NN, UK. nadia.rosenthal@monash.edu.
Nadia A
NA
Rosenthal
Systems Biology Institute (SBI) Australia, Monash University, Clayton, VIC, 3800, Australia. kitano@sbi.jp.|Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, 3800, Australia. kitano@sbi.jp.|Sony Computer Science Laboratories, Inc., Higashigotanda, Shinagawa, Tokyo, Japan. kitano@sbi.jp.|Okinawa Institute of Science and Technology, Onna, Onna-son, Kunigami, Okinawa, Japan. kitano@sbi.jp.
Hiroaki
H
Kitano
Systems Biology Institute (SBI) Australia, Monash University, Clayton, VIC, 3800, Australia. sarah.boyd@monash.edu.|Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, 3800, Australia. sarah.boyd@monash.edu.
Sarah E
SE
Boyd
D000328:Adult; D002478:Cells, Cultured; D003196:Computer Graphics; D005347:Fibroblasts / Q000166:cytology / Q000378:metabolism; D050991:GATA4 Transcription Factor / Q000235:genetics; D018507:Gene Expression Regulation, Developmental; D053263:Gene Regulatory Networks; D056726:Genetic Association Studies; D006321:Heart / Q000502:physiology*; D006801:Humans; D012984:Software; D020825:T-Box Domain Proteins / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics*
D050991:GATA4 Transcription Factor; C484170:GATA4 protein, human; D020825:T-Box Domain Proteins; C420984:TBX20 protein, human; D014157:Transcription Factors