Slides to accompany: http://youtu.be/FtlsoM8TGGs
This video and slideshow demonstrates usage of the MouseMine computational platform for flexible batch data access. Templates, list analysis tools and custom queries made straightforward.
2. Introduction to MouseMine
Online computational platform to access MGI data
flexible queries from templates or fully customizable
queries
iterative refinement
point-and-click visual interface
list analysis tools, including enrichment statistics
integrated and compatible with other InterMOD
platforms (cross-species analysis)
downloadable reports, saving to online accounts or
forwarding to Galaxy
10. Iterative result
Filtered to only those GO
associations with “IDA /
Inferred by direct assay”
as the evidence code
Added a column for
positional coordinates
16. Summary
MouseMine allows straightforward, flexible batch-scale
querying of MGI data
Multiple useful list analysis tools
contact mgi-help@jax.org with any questions
Editor's Notes
MouseMine is an online… . It allows flexible queries from templates, or can be fully customized. A major feature is that it is iterative, meaning you can build a list, then filter to refine or add data in a series of sequential interations or analyses. It is a visual point-and click interface, so no SQL or webAPI experience is required.
To accessMouseMine from MGI, you can find a link by clicking on the Batch Data and Analysis button on the homepage, or select MouseMine directly from the options in the Search drop down menu
First, if you want to dive right in you have a quick search option for simple matches. Or you can begin by creating a list for analysis.Below, there are some templates for popular queries.Along the top, there are some quick navigation tabs as well for home, templates, lists and the query builder to design your own custom searches, more about the data, and the MyMine tab. You’ll see here you can create and log in using a personal account as well, which allows you to save or share your lists and searches. Before moving off the homepage, I’ll also just point out access to other computational tools as well.
One of the most user-friendly and powerful elements in MouseMine are the template queries. These are subdivided by data type as you can see in the tabs along the top and each has a descriptive title. Under the heading “function” we’ll explore a bit further using the Mouse Features to GO terms query.
This query, as the name suggests, will return a list of GO terms that have been annotated to a given feature, or gene. Entering a gene symbol into the Lookup box and clicking results will execute. As you can see, you also have the ability to constrain your search by a list, or add your own parameters to the template query at this stage.
Running the search returns a table with a pre-defined set of columns including ID, ontology namespace, ontology term and evidence.
Enrichment is based on a hypergeometric distribution and you have the option to set your multiple test correction to Holm-Bonferroni, Bonferroni, Benjamini-Hochberg or to skip this step. p-value and the list of genes which match – in this case, the MEDIC term – are also displayed. For more information on the statistics behind these widgets, click on the “I” next to the p-value.
