Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

Summary

The Inherent Dynamics Visualizer is an interactive visualization package that connects to a gene regulatory network inference tool for enhanced, streamlined generation of functional network models. The visualizer can be used to make more informed decisions for parameterizing the inference tool, thus increasing confidence in the resulting models.

Abstract

Developing gene regulatory network models is a major challenge in systems biology. Several computational tools and pipelines have been developed to tackle this challenge, including the newly developed Inherent Dynamics Pipeline. The Inherent Dynamics Pipeline consists of several previously published tools that work synergistically and are connected in a linear fashion, where the output of one tool is then used as input for the following tool. As with most computational techniques, each step of the Inherent Dynamics Pipeline requires the user to make choices about parameters that don't have a precise biological definition. These choices can substantially impact gene regulatory network models produced by the analysis. For this reason, the ability to visualize and explore the consequences of various parameter choices at each step can help increase confidence in the choices and the results.The Inherent Dynamics Visualizer is a comprehensive visualization package that streamlines the process of evaluating parameter choices through an interactive interface within a web browser. The user can separately examine the output of each step of the pipeline, make intuitive changes based on visual information, and benefit from the automatic production of necessary input files for the Inherent Dynamics Pipeline. The Inherent Dynamics Visualizer provides an unparalleled level of access to a highly intricate tool for the discovery of gene regulatory networks from time series transcriptomic data.

Introduction

Many important biological processes, such as cell differentiation and environmental response, are governed by sets of genes that interact with each other in a gene regulatory network (GRN). These GRNs produce the transcriptional dynamics needed for activating and maintaining the phenotype they control, so identifying the components and topological structure of the GRN is key to understanding many biological processes and functions. A GRN may be modeled as a set of interacting genes and/or gene products described by a network whose nodes are the genes and whose edges describe the direction and form of interaction (e.g., activation/repression of transcription, post-tran....

Protocol

1. Install the IDP and IDV

NOTE: This section assumes that docker, conda, pip, and git are installed already (Table of materials).

1. In a terminal, enter the command: git clone https://gitlab.com/biochron/inherent_dynamics_pipeline.git.
2. Follow the install instructions in the IDP's README file.
3. In a terminal, enter the command: git clone https://gitlab.com/bertfordley/inherent_dynamics_visualizer.git.
   NOTE: Cloning of the IDV should happen outside of the IDP's top-level directory.
4. Follow the install instructions in the IDV'....

Results

The steps described textually above and graphically in Figure 1 were applied to the core oscillating GRN of the yeast cell-cycle to see if it is possible to discover functional GRN models that are capable of producing the dynamics observed in time series gene expression data collected in a yeast cell-cycle study¹⁶. To illustrate how the IDV can clarify and improve IDP output, the results, after performing this analysis in two ways, were compared: 1) running all steps .......

Discussion

The inference of GRNs is an important challenge in systems biology. The IDP generates model GRNs from gene expression data using a sequence of tools that utilize the data in increasingly complex ways. Each step requires decisions about how to process the data and what elements (genes, functional interactions) will be passed to the next layer of the IDP. The impacts of these decisions on IDP results are not as obvious. To help in this regard, the IDV provides useful interactive visualizations of the outputs from individua.......

Materials

Name	Company	Catalog Number	Comments
Docker			https://docs.docker.com/get-docker/
Git			https://git-scm.com/
Inherent Dynamics Pipeline			https://gitlab.com/biochron/inherent_dynamics_pipeline
Inherent Dynamics Visualizer			https://gitlab.com/bertfordley/inherent_dynamics_visualizer
Miniconda			https://docs.conda.io/en/latest/miniconda.html
Pip			https://pip.pypa.io/en/stable/