Genotet

An interactive web-based visual exploration framework to support validation of gene regulatory networks

Bowen Yu, Harish Doraiswamy, Xi Chen, Emily Miraldi, Mario Luis Arrieta-Ortiz, Christoph Hafemeister, Aviv Madar, Richard Bonneau, Claudio T. Silva

Research output: Contribution to journalArticle

Abstract

Elucidation of transcriptional regulatory networks (TRNs) is a fundamental goal in biology, and one of the most important components of TRNs are transcription factors (TFs), proteins that specifically bind to gene promoter and enhancer regions to alter target gene expression patterns. Advances in genomic technologies as well as advances in computational biology have led to multiple large regulatory network models (directed networks) each with a large corpus of supporting data and gene-annotation. There are multiple possible biological motivations for exploring large regulatory network models, including: validating TF-target gene relationships, figuring out co-regulation patterns, and exploring the coordination of cell processes in response to changes in cell state or environment. Here we focus on queries aimed at validating regulatory network models, and on coordinating visualization of primary data and directed weighted gene regulatory networks. The large size of both the network models and the primary data can make such coordinated queries cumbersome with existing tools and, in particular, inhibits the sharing of results between collaborators. In this work, we develop and demonstrate a web-based framework for coordinating visualization and exploration of expression data (RNA-seq, microarray), network models and gene-binding data (ChIP-seq). Using specialized data structures and multiple coordinated views, we design an efficient querying model to support interactive analysis of the data. Finally, we show the effectiveness of our framework through case studies for the mouse immune system (a dataset focused on a subset of key cellular functions) and a model bacteria (a small genome with high data-completeness).

Original languageEnglish (US)
Article number6876028
Pages (from-to)1903-1912
Number of pages10
JournalIEEE Transactions on Visualization and Computer Graphics
Volume20
Issue number12
DOIs
StatePublished - Dec 31 2014

Fingerprint

Genes
Transcription factors
Visualization
Immune system
Microarrays
Set theory
RNA
Gene expression
Data structures
Bacteria
Proteins

Keywords

  • gene regulatory network
  • Web-based visualization

ASJC Scopus subject areas

  • Computer Graphics and Computer-Aided Design
  • Software
  • Computer Vision and Pattern Recognition
  • Signal Processing

Cite this

Genotet : An interactive web-based visual exploration framework to support validation of gene regulatory networks. / Yu, Bowen; Doraiswamy, Harish; Chen, Xi; Miraldi, Emily; Arrieta-Ortiz, Mario Luis; Hafemeister, Christoph; Madar, Aviv; Bonneau, Richard; Silva, Claudio T.

In: IEEE Transactions on Visualization and Computer Graphics, Vol. 20, No. 12, 6876028, 31.12.2014, p. 1903-1912.

Research output: Contribution to journalArticle

Yu, Bowen ; Doraiswamy, Harish ; Chen, Xi ; Miraldi, Emily ; Arrieta-Ortiz, Mario Luis ; Hafemeister, Christoph ; Madar, Aviv ; Bonneau, Richard ; Silva, Claudio T. / Genotet : An interactive web-based visual exploration framework to support validation of gene regulatory networks. In: IEEE Transactions on Visualization and Computer Graphics. 2014 ; Vol. 20, No. 12. pp. 1903-1912.
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