Ways to find genes with significant expression

[mestato]

Right now it is quite difficult for a user to find the things they probably want to know. Here are three scenarios I think are likely:

• "I'm interested in gene expression of organism A. I can find the expression analysis, but are genes actually significant and if so, can I get a list of them?"
• "I'm interested in gene expression of organism A. I want to search for genes with significant expression related to GO term XXX. How do I find those?"
• "I'm interested in searching for genes with significant expression related to GO term XXX, I want them from every organism!"

Let's break down strategies to meet each user's needs.

• "I'm interested in gene expression of organism A. I can find the expression analysis, but are genes actually significant and if so, can I get a list of them?"

• From the expression analysis, show what go terms are used to tag genes (ie. "drought exposure", "temperature", "leaf", "up-regulated"

• Clicking on any of the above leads to a list of genes with those tags

• "I'm interested in gene expression of organism A. I want to search for genes with significant expression related to GO term XXX. How do I find those?"

This seems easy but is actually kind of hard because a feature_cvterm entry might come from different types of analysis. It would be nice to filter by type of evidence or type of analysis as part of the feature search.

• "I'm interested in searching for genes with significant expression related to GO term XXX, I want them from every organism!"

Ditta above but in a general all genes search page instead of an organism-specific gene search. We could check out other modules for this like Tripal MegaSearch

[florence-77]

See this page.

This page is linked to from the 'keyword' column in the significant expression tab. It now prints the CV term, definition, and vocabulary in a table at the top of the page, then in another table below lists all of the organism's features that express response to the cvterm. The table has three columns: feature name, p-value, and expression relationship. Feature name links to that feature page. It can be sorted alphabetically by feature name or grouped by relationship.

To-do: currently, when clicked on the p-value column sorts itself by ASCII order, does not recognize scientific notation.

[florence-77]

See this page.

Analysis/gene profile pages now have a table listing attached features, as well as associated keyword, relationship, and p-value. Feature names link to the feature page, and keyword links to the previously added page which displays cv term, definition, vocabulary, and all of the organism's features that express response to the cv term.