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ePlant3 Interactions View Blueprint and Requirements

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Vincent Lau edited this page Dec 5, 2024 · 1 revision

ePlant3 Interactions View Blueprint and Requirements

by V. Lau (reviewed by N. Provart)

Introduction

Genes and their gene products (proteins) can interact with other genes and gene products. The most common types of interactions are Protein-DNA Interactions (PDIs, ) where proteins up- or down-regulate the expression of its target (DNA) gene, and Protein-Protein Interactions (PPIs) whereby two proteins bind together to achieve their functions. PDIs and PPIs can be discovered via targetted assays but more generally via high-throughput methods such as Protein Microarrays, Chromatin Immunoprecipation Sequencing (ChIP-Seq) Rao, V. S., Srinivas, K., Sujini, G. N., & Kumar, G. N. (2014);Furey, T. S. (2012);Paiano, A., Margiotta, A., De Luca, M., & Bucci, C. (2019). One succinet method to display this high-throughput data is via a graph (or network) whereby nodes (genes) connect to each via edges (lines). At the BAR, we host over 2.8 million PDIs and PPIs for Arabidopsis Dong, S., Lau, V., Song, R., Ierullo, M., Esteban, E., Wu, Y., ... & Provart, N. J. (2019). They can viewed via the Arabidopsis Interactions Viewer 2 (AIV2, see below). Note that AIV2 allows for multiple genes to be searched (i.e. whether two genes interact with one another) versus ePlant which is a single-gene approach.

image AIV2 display multiple searched GOIs (larger nodes), whereby protein interactors are shown via circular nodes (the doughnut pie-chart denotes cellularrlocalization) and DNA interactors are collapsed into square boxes which can be viewed with a tooltip image Current ePlant2 Interactions Viewer. Note it follows a similar design and colour scheme but only contains one search gene, which again is large. Other genes whcih are loaded into ePlant currently are also darker grey.

Purpose

Users will wish to see at a glance, for their gene of interest (GOI); what interaction partners exist. This shall be visualized via a graph (i.e. gene network).

Intended Audience

  • ePlant Users
    • Plant biologists
    • Bioinformaticians
    • Students

Product Scope and Value

The addition of this module to ePlant will allow users to focus on interactors of their GOI. From there, they may discover additional GOIs and learn how their gene is modulated. Moreover, genes that modulate the GOI may also interact with each other as we source PDI and PPI information from more than one source. Shown visually, this will help the researcher discover novel information.

Abbreviations

  • PPI: Protein-Protein Interaction
  • PDI: Protein-DNA Interaction
  • GOI: Gene of Interest
  • AIV2: Arabidopsis Interactions Viewer 2

System and Functional Requirements

  • This module should easily be replicated and generalized for other species when we receive PPI and PDI data for other species
  • The module must load the gene network view in a organized manner to visualize all genes at a glance
    • Protein interacting genes will be visualized by circular nodes
    • Protein-DNA interacting genes will be 'collapsed' into their respective chromosomes (see above ePlant2 example)
    • Interactions are denoted via edges (i.e. lines) with a specific colour coding
      • Such as predicted interactions are shown by a dashed line
    • Colour coding will be specified by a legend (we can reuse the old legend to keep consistency across our applications)
  • The user can view information about and load additional interactors upon hovering over the gene
  • The user can click on a call-to-action (i.e. button) to download the raw data
  • The user can apply filters pertaining to confidence and correlation to simplify the view; the view shall be updated instantly.

External Interface Requirements

  • User Interface: The network view should take up as much resolution of the available panel as possible
  • Hardware Interface: Optimize this for desktop and large format tablet visualization (resolution >960px); mobile visualization on graphs is unrealistic.
  • Software Interface: Use your existing ePlant3 module logic to create this view. You will need to use our existing webservices such as this one to grab the interactors. You should use Cytoscape.js as the graphing library.
  • Communication Interfaces: Standard communication on Github Issues, and weekly discussions. Please link to this issue for any features, bugs pertaining to the Gene Network view and label it with the 'Inteactions Viewer view' label on Github.

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