New gene set analyses and views #159
Description
Summary
We currently have two views of the search result set, the taxagenomic distribution and a list of results. A suite of additional analyses would help the end user explore the result set. See thalemine's set of widgets on this page for inspiration:
https://apps.araport.org/thalemine/bagDetails.do?scope=all&bagName=Genes+with+a+Loss-of-Function+Mutant+Phenotype%3A+Morphological+-+Vegetative
Let the user choose in the settings interface which analyses to display
"Taxa-genomic" distribution
One line per genome, color coded by chromosome, all arranged by the species tree. Users can select multiple genomic intervals and create a regions filter.
Gene set enrichment analysis widget
Given a gene set (the search results) and a background set (default to all?) it is possible to identify annotations (e.g., ontology terms, domains, pathways) that are associated with the results at a higher frequency than expected. It might be necessary to perform the enrichment analysis on the server if performance on the client is too slow on mobile devices.
Homology widget
If the result set is contained within one gene tree, display the gene tree with genes from the result set visible. If multiple gene trees (<= 10 ?) , show the gene tree with the most search results and a table of gene trees with columns (tree stable id, number of genes from search result, root node taxon name, root node representative gene name(s). A user can choose different gene trees from this list to replace the one displayed initially. This widget should include actions to expand the search to all orthologs of genes in the result set.
Pathways widget
Similar to homology widget where you load the pathway with the most genes from the result set, and display a list of pathways below with descriptions.
Expression data widget
Choose a species for which we have ATLAS expression data, and generate a heat map for the result set. We can pre-calculate a clustered gene expression table for each species to eliminate the need to rerun clustering on the subset. This widget should guide users to select filters based on gene expression.
Domain architecture widget
Display the frequency of domain architectures in the result set as a table. Users can define a filter based on one of the domain architectures in the result set to limit/expand the search.