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Entering Seed Genes

You can autofill seed genes, manually type into the “Seed Genes” textbox, or upload a txt file.

• Autofill seed genes: You can simply switch the toggle and enter the number of seed genes you want. Then you will see the seed genes with your desired number are automatically filled in the textbox.
• Autofill seed genes
• Type into textbox: Manually type in seed gene names or their Ensembl IDs to generate the network. You can also mix gene names and Ensembl IDs together. The format is line-separated.
• Upload a txt file: The gene names or Ensembl IDs can also be uploaded as txt format. The format is the same as the “Seed Genes” textbox.

The seed genes are the foundation of the network generation, your network will be expanded based on the seed genes you provided. Once you determine the seed genes, you can proceed to Step 2 to generate your own network.

Selecting Preferable Options

Now you can select different options from different parameters to integrate your own feature styles into your network. We offer 4 parameters here — Disease Map, Order, Interaction Type and Min Interaction Score. Let’s go through them one by one:

• Disease Map: You can determine your network falls into which disease category, and no worries, if you want to change the disease after generating the network, you can easily change it on the left panel of the network visualization page. We offer over 20,000 different diseases, all from Open Targets Platform. You can simply type in the disease name to search for your desired disease.

• Order: Based on the seed genes you provided, you can expand the network from different perspective. We provide 3 different orders:

  • Zero order: This option only gives you the interactions among the seed genes.
  • First order: This option involves the neighbors of the seed genes. Besides the interactions among the seed genes in Zero order, it also gives the interactions among seed genes and their neighbors.
  • Second order: This option is a combination of First order and Zero order. It not only contains the interactions among seed genes themselves & the interactions among the seed genes and their neighbors, it also contains the interactions among the neighbors of seed genes.

• Interaction Type: We provide 3 different interaction types for you to construct your own network, you can select one or more interaction types to make your network more comprehensive.

  • STRING: Protein-protein interactions from STRING database.
  • IntAct: Molecular Interaction Database interactions.
  • BioGrid: Biological General Repository for Interaction Datasets interactions.

• Min Interaction Score: Each interaction has its own score, from computer science perspective, we also call it edge weight. You can select the cutoff here to make your network thinner or fatter. There are 4 different cutoff available: Low (0.15), Medium (0.4), High (0.7) and Highest (0.9).

Clicking “Submit” Button

After click “Submit”, a confirmation page will pop up. There are 2 tabs available in the pop-up window: Found and Not-Found.

• Found: The listed genes are available in our database, you can confirm the information of seed genes. You can also click on the link of each ENSG ID and Gene Name, which directs you to the corresponding Ensembl page and corresponding HGNC page, respectively.

Found genes

• Not-Found: The listed genes have no records in our database. You probably entered a wrong name or wrong Ensembl ID, you mignt want to go back to the “Seed Genes” textbox or your uploaded file to make the corresponding changes and submit again. Or you can simply click “Submit” button and proceed to the Network Visualization page.

Not-Found genes

You can also download the Found genes and/or Not-Found genes by clicking the download button on the Results Preview window.