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Pathway Browser

Introduction

The Pathway Browser is an interactive web-based tool designed for exploring biological pathways across multiple databases. It defines search logic, queries specific terms, and visualizes detailed pathway diagrams. This tool provides access to three major pathway databases: Reactome, Gramene, and KEGG, enabling cross-database comparisons and insights.

This functionality is located under Functional Analysis → Pathway Browser.

Interface Overview

Figure 1: Pathway Browser Overview

Side Panel Widgets

  1. Combine terms using: Select the desired search logic:

    • AND: Only pathways containing all specified terms will match.
    • OR: Pathways matching at least one term will be included.

  2. Autocomplete Input: Enter search terms (minimum 3 characters). The autocomplete feature provides suggestions based on the entered text. Wildcards (e.g., *) can be used at the end of the string for broader searches.

    • Press Enter or select a suggested term to add it to the query.

    Figure 2: Autocomplete Input

  3. Query Term List: Displays all selected terms in a text area-like format. Each term can be removed by clicking the “X” icon next to it. Adjusting the terms dynamically updates the search results.

Results Table

After submitting a query, the search runs independently across Reactome, Gramene, and KEGG. The results for each database appear in separate tabs within the results table. Pathways matching the query are listed with their respective details.

Figure 2: Results table. The total number of matches for each database is displayed in the tab title.

Context Menu and Diagram Viewer

In the results table, right-clicking a row opens a context menu with the option to view the pathway diagram ("Show pathway diagram"). Selecting this option loads a detailed diagram of the pathway, enriched with the terms included in the search query. These terms act as a "dictionary" to facilitate contextual analysis.

Figure 3: Context Menu.

Diagram Viewer

The Diagram Viewer in the Pathway Browser offers functionality similar to the Pathway Viewer found in the Combined Pathway Analysis tool). However, instead of displaying only terms associated with sequences in a project, it shows all the terms found within the pathway. This comprehensive view allows for a broader analysis of pathways, highlighting the presence of all relevant terms identified in the search query.

Figure 4: Diagram Viewer.