What is PathwayViz? Launch PathwayViz Now

PathwayViz is a web-based tool for users to upload their gene expression comparison data and overlay it on three gene pathway diagrams: WikiPathways, Reactome Pathways, and KEGG Pathways.



How to use PathwayViz?

Getting Started with PathwayViz:

  1. Input Your Data
    • Upload your own comparison files or try the demo file to explore
  2. Define Your Data Structure
    • Identify the type of data in each column
  3. Configure Pathway Settings
    • Choose your species of interest
    • Select the pathway type
    • Pick a specific pathway from the available options
  4. Launch Visualization
    • Click "View WikiPathways" to generate your pathway visualization

What data file is supported in PathwayViz?

PathwayViz supports CSV files with a header row containing column names, and the first column should contain Gene Symbols.
Typically, the first colunn name can be "Symbol". Other column names can be in this format: <Comparison Name>_<Data Type>. The typical data types are: logFC, P.Val and adj.P.Val.

Overview of gene pathway databases

Gene pathway databases are crucial resources in bioinformatics and systems biology. They provide structured information about biological processes, gene interactions, and molecular functions. Here's an overview of major gene pathway databases:

1. WikiPathways

WikiPathways is a collaborative platform for creating, editing, and sharing biological pathways.

2. Reactome

Reactome is a free, open-source, curated and peer-reviewed pathway database.

3. KEGG (Kyoto Encyclopedia of Genes and Genomes)

KEGG is a comprehensive database resource for understanding high-level functions and utilities of biological systems.

Comparison of Major Databases

Feature WikiPathways Reactome KEGG
Access Free, open Free, open Free for academic use
Curation Community Expert-curated Expert-curated
Species coverage Multiple Primarily human Wide range
Integration High High High
Visualization tools Yes Yes Yes
API availability Yes Yes Yes

Each of these databases offers unique features and strengths. Researchers often use a combination of these resources for comprehensive pathway analysis and interpretation. The choice of database often depends on the specific research question, organism of interest, and the type of pathway information required.

It's important to note that many of these databases integrate data from each other and from primary literature sources. Therefore, using multiple databases can provide a more comprehensive view of biological pathways and gene interactions.