The Evidence View provides a table-based view of all the node types (concepts) linked to your search results.
Evidence View table header definitions:
| Header | Description |
|---|---|
| Select | Select evidence (for creating networks*) |
| Type | Evidence type |
| Node label | Evidence name/description |
| P-Value | Statistical significance (P-Value) |
| Genes | Genes in Knowledge Graph related to your search |
| Gene List | Genes in your Gene List related to your search |
* Available only when searching with a gene list. Use Refine Search to add a Gene List automatically (see below).
Filtering results
The various evidence node types (GO, TO, phenotype, pathway, gene, publication, etc.) matching the search terms are summarised in the key/legend, with a count of how many of each. The key is interactive and can be used to filter the results by selecting one or multiple evidence types in the key.
Table ordering explained
The results are default ordered according to P-Value->Gene List->Genes. Whichever is available.
This is because when the user did not provide a Gene List, the P-Value and Gene List columns are not available.
Refine Search
Refine search allows you to recursively refine your search results by re-searching KnetMiner using the selected Evidences. Note that clicking Refine search will purge your existing search by replacing it. By using Recursive Search in Evidence view, when you searched without a Gene list; the list of Genes related to an evidence will be used to populate a Gene List Search, and your Keywords will be transferred. Thereafter you will be able to create a network from Evidence view.
Creating a Network
Select one or more concepts and click “Create Network”. This may be unavailable if you did not search using a Gene List. See Refine Search above.
Gene List functionality
The “Genes” column now contains a clickable ‘File’ icon beside each row’s count.
Clicking the button displays a table containing a list of genes in the full knowledge graph, found to be matching the graph node specified under “Node label”. Copying the gene accessions allows for easy pasting into the Gene List search box on KnetMiner, for querying again. Note that this is similar to what the Refine Search functionality does for you. Alternatively you can download this data as a .tsv by clicking the download button.
