The Gene View displays identified candidate genes sorted by the KnetScore in a table (Figure 1). As of KnetMiner 5.6 we are displaying the KnetScore column within the table, however, please note that the gene ranking score is not normalised and cannot be used a score across multiple searches. Instead, it can be used as an approximated sorter for existing genes based on your query and the data available.
Gene View table header definitions:
| Header | Description |
|---|---|
| Accession | Gene accession |
| Gene | Gene name (click arrow to view synonyms) |
| Chr | Chromosome name |
| Nt start | Nucleotide start position |
| Evidence | Supporting evidence and counts (click icons to expand) |
| KnetScore | Non-normalised Gene Ranking score (see below for more information) |
| Select | Select gene (for creating networks – see below for more information) |
Filtering results
The various evidence node types (GO, TO, phenotype, pathway, gene, publication, etc.) matching the search terms are summarised in the key/legend. The key is interactive and can be used to filter the results by selecting one or multiple evidence types in the key. Clicking the refresh button resets all filters.
Bottom left of the table are three boxes:
1. “All Genes” dropdown allows users to select how many genes to view in the table.
2. “Unlinked Genes” button filters results in the table to match genes found in the knowledge graph which match the keyword search but not genes supplied by the user in the Gene List Search box. The button will only be visible when a user has inputted a Gene List.
3. “Linked Genes” button filters table results to only match genes supplied by the user in the Gene List Search box. The button will only be visible when a user has inputted a Gene List.
Figure 1 – Gene View
Creating a Network
There are two ways to make networks from Gene View:
1. Click the Accession number (in green) to create a network using the selected gene.
2. Select one or more genes with the tickboxes on the right of the row and click the “Create Network” button.
Gene synonym viewer
Clicking the arrow beside any Gene name in the Gene column, lists all synonyms for the selected gene (Figure 2).
Figure 2 – Gene synonym viewer
Downloading the table
Clicking the Download button (top right, above table and in line with Views buttons), downloads the queried table in .tsv format (Figure 3).
Figure 3 – Download button
