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Help: ChemComps


ChemComps presents the chemicals with the most comparable sets of interacting genes as the page's subject chemical.

Filter by interaction type

By default, this page shows Comps calculated using all 70 chemical–gene interaction types. You can perform a more focused similarity calculation by choosing a specific interaction type and one or more degrees to limit the interactions considered.

Similarity Index

Similarity (or comparability) is measured by the Jaccard index—the size of the intersection of interacting genes for chemical A and chemical B divided by the size of the union of those genes:
Jaccard Index formula: A∩B / A∪B

Chemical

The chemicals with comparable interacting gene sets as the page's subject chemical.

Common Interacting Genes

You may view the common interacting genes between the page's subject chemical and a chemical of interest by clicking a link in this column. This link will take you to results generated using the VennViewer tool.

The common interacting genes are also included in the downloadable files.

Download

Save these data into a comma-separated values (CSV), Excel, XML, or tab-separated values (TSV) file by clicking a Download link at the bottom of the table.

Pathway View

You may view the network of common interacting genes for the top 10-ranked comparable chemicals by either (1) downloading the XGMML file into Cytoscape, or (2) using our online visualization (for smaller networks only; your browser must support both JavaScript and Flash). More than 10 chemicals are included when more than one shares an identical Similarity Index.

The XGMML file can be viewed using Cytoscape, an open-source pathway visualization application:

  1. Download and install Cytoscape.
  2. Launch Cytoscape.
  3. Import the downloaded XGMML file by going to File > Import > Network (Multiple File Types) > Local (or Ctrl+L) and selecting your file. See also: Cytoscape Manual
  4. Use the Layout menu to view different arrangements of the network. We suggest the Cytoscape > Force-Directed Layout as a starting point.
  5. To view additional details about the nodes and edges within a pathway, select the Node or Edge Attribute Browser and click the Select All Attributes button in the Data Panel.
    Cytoscape Data Panel: Select All Attributes button