The Gene View displays identified candidate genes sorted by the KnetScore in a table. Please note that the gene ranking KnetScore is not normalised and cannot be used to 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 |
|---|---|
| Select | Select gene (for creating networks – see below for more information) |
| Accession | Gene accession |
| Gene name | Gene name (click arrow to view synonyms) |
| Location | Chromosome location:Nucleotide start |
| Gene length | Length of gene in Nucleotides |
| KnetScore | Non-normalised Gene Ranking score (see below for more information) |
| Evidence | Supporting evidence and counts (click icons to expand and view details + Distance to gene) |
Filtering results
The various evidence node types (GO, TO, phenotype, pathway, gene, publication, etc.) matching the search terms are summarised in the key/legend at the top of Gene View. The key is interactive and can be used to filter the results by selecting one or multiple evidence types in the key.
Filters also exist on a per-header basis.
Location filter: select the Chromosome to clamp to, and optionally drag the sliders to the region to clamp the search within.
KnetScore: use the sliders to filter the table results.
Evidence: the evidence filter is more complex. It allows for filtering based on P-Value and/or distance (edges/hops away from gene). The P-Value cutoff is set globally for all evidences whereas the Distance can be set either Globally (Global Distance) or based on a particular node type. Filters set in this column are considered when creating a network from Gene View to prioritise showing relevant nodes in the Network View, and hiding the less relevant ones (according to your own filters) by default.
Refine Search
Refine search allows you to recursively refine your search results by re-searching KnetMiner using the selected Genes. Note that clicking Refine search will purge your existing search by replacing it.
Creating a Network
There are two ways to make networks from Gene View:
1. Click a Gene Accession to create a network using that particular gene.
2. Select one or more genes with the tickboxes on the left 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, if there are any.
Downloading the table
Hovering over the the Download button (top right) provides you a choice in download format: TSV and Json. Download whichever format suits you.
