TargetMine Exercise and Tutorial
AIST KANSAIJanuary 20th 2012
Copyright  2012 The Mizuguchi laboratory (www.mizuguchi.org), NIBIOCONTENTS
I. Quick Search and report pages
II. Lists and List Analysis pages
III.
Template queries
IV. Query Builder

Go to the TargetMine web site: targetmine.nibio.go.jp
All features are accessible from the toolbar on each TargetMine webpage:

I. Quick Search and report pages
A search function may be found at the upper left corner of the top page orappears at the left side of menu bar on all pages. A user may enter any text
(such as a gene name, identifier or a keyword) in the quick search box tosearch for the related content in TargetMine.
For example,Run a quick search for a word ‘apolipoprotein’:1orNOTE: Use wildcard character '*' for partial matching.
The search results may then further be filtered using different features.
Clicking on the search result will direct the user to the report page for thatobject. The report page for a particular object in the TargetMine databaseprovides all the stored information for that object. All report pages have thesame basic structure:•The upper half displays the basic information about the object. The lower
parts provide more detailed information corresponding to the data2

categories in TargetMine (which can be viewed on the home page). This
information includes the classes associated with the object and the query
results of a set of predefined queries known as templates (see below)
related to specific data categories which are executed for the object on thefly.

II. Lists and List Analysis pages
The ‘list’ function in TargetMine enables queries on user-supplied list(s) ofobjects (e.g., a list of genes/proteins). The user may either save lists fromresults pages or create them by uploading lists of identifiers. Lists can beused to constrain queries, either a template query or in the query builder(see below), to perform logical operations (union, intersect, subtract) andexported. The users may also search and copy the lists.
The Lists page is accessible via the 'Lists' tab on the TargetMine menu bar.
The 'Upload' tab on the Lists page permits the user to create a list of objects
either by ‘Type/Paste in identifiers’ or upload a file containing a list ofobjects.

A list can be created of only one ‘type’ of objects (e.g., genes, proteins), which
can be set from the drop-down list. However, it is possible for the list tocontain a mixture of identifier types (e.g., gene symbols and gene IDs).
Optionally, the user may also set the organism for the list of identifiers.
This tutorial will deal with uploading an example list of genes. The list willthen be used to view the ‘List Analysis page’, run a template query, save afurther list from the results and employ the lists for a customised queryusing the query builder.
•Click on ‘click to see an example’ link, to input an example genelist.
3•Click on the “Create List” button.

•List Confirmation

Before a list is created it is checked against the TargetMine database andany discrepancies are reported in the ‘Verify identifier matches’. Theuser may either assign a name to the list or use the default name generated
by the system. For the purpose of this tutorial, the users are advised to namethe list as ‘demo’, and click on the save button.

•List Analysis Page

Details of the contents of the lists together with additional information about
a list can be viewed through the ‘List Analysis’ page. The analysis page is
automatically displayed when a list is created. It can also be accessed atother times by clicking on the list name on the ‘list page’.
List Analysis page consists of three sections: A summary of the contents of the list includes a table with thefirst 10 objects of the list, a list description, List Info, Convert tools
and Link outs (if available). Above the table, there are4

Display/Export/Use options and a find box. Searching a list is casesensitive and wild cards cannot be used.
A series of ‘widgets’ providing more information about the list, forexample, overrepresented KEGG pathways, Gene Ontology (GO)terms, Drug and Disease Ontology associations, Protein-protein
interactions (PPIs) and Associated Drugs.

A set of template queries that have been pre-run on the set ofobjects in the list.

III. Template queries
To enable the users to quickly and easily carry out diverse queries acrossdata sources, TargetMine includes a library of predefined Template
queries. These consist of a query form in which certain variables can bechanged by imposing constraints (filters) on certain data types so as torestrict the queries to certain subsets of data.

5Template queries can be accessed in different ways
•
•
•

•

Each data category page has a set of templates related to that datatype.
Templates appear on report pages and list analysis pages.
Templates can be searched using the Quick Search available on everyTargetMine page, by changing the drop-down list from ‘Identifiers’ to‘Templates’.
The templates page, accessible from the TargetMine home page or via
tabs in the menu bar, allows the users to search or browse for templates.

For example, search the template queries for ‘transcription’:and select the template ‘Gene(s) --> Upstream Transcription
Factors’:

Now that we have created a list the template query gives us the option to use
it instead of entering an identifier.
Click the checkbox to select the demo list "demo" saved earlier,and then click on "Show Results" to run the query.

6The results table shows the transcription factors that target the genes fromour original list.
The user can also create new lists from results tables. We can save a list of
the transcription factors from this query to view in the list analysis page or
to use in more templates.
Click on the checkbox by 'Source > ncbiGeneNumber' to select all
genes

Click on the tab 'CREATE LIST' and choose a name for the saved
list. For example, name it as 'upstream_TFs'. Then click 'Save
selected' to save.

Using lists is an excellent way to retrieve information about a whole list ofdata. For example the users can also retrieve:Interactions for these genes
Disease Ontology (DO) annotation for these genes

7Please try it yourself.

IV. Query Builder
Aimed mostly at advanced users, the ‘Query Builder’ allows the users to• construct new queries across multiple data sources in TargetMine• modify the existing template queries to change the output or add a
constraint as may be understood from the following example.
Find the template ' Gene(s) --> Upstream Transcription Factors'
as described in previous section. Click 'Edit Query' to bring up theQuery Builder:The ‘Model browser’ on the left permits the user to navigate theTargetMine data model. In this example, the model browser displays theinitial Gene class and all its attributes (e.g., Name, Symbol) and relatedclasses (e.g., Organism, Proteins). TargetMine uses an object based datamodel; biological types are termed 'classes' and individual entries are termed'objects'.
The user can click to open related classes and see their attributes. Thetab may be used to add fields to the output. Thetab allows
the user to add constraints (filters).

8Underneath the model browser, the ‘Fields selected for output’ displays
the fields selected by the user to be displayed in the results. Each field isrepresented by a box which eventually corresponds to a column in the results
table. The order of the fields in the column may be changed by drag and drop.

The ‘Query Overview’ section shows the constraints applied to this query.
Notice that one of them says 'Gene' then 'LOOKUP 10121 IN H. sapiens'.
This indicates that the query is restricted to a human gene with theidentifier 10121.
What if the user wants to search for all genes in TargetMine for any
upstream transcription factor that may regulate their gene expression? Theuser may simply remove this constraint and run the query again.
Click on thebutton next to 'LOOKUP 10121 IN H. sapiens' toremove the constraint:

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Now click 'Show results' to run the query:

The results table now shows all the upstream transcription factors inTargetMine and their target genes.
The user may click the summary buttonon the 'Source >symbol' and 'Target > symbol' columns to find more information
about the column.

Let's try something further.
Click on 'Query' in the Trail to revert to the query builder.

Now, try to use the 'Model browser' and find the attribute at the following
path 'Gene -> Protein DNA Interactions -> Data Sets -> Name'. Click the10tab beside to bring out a pop-up window. Select 'ORegAnno' fromthe dropdown list then click 'Add to query' to make the constraint.

Model browser
Query overview
Click 'Show results' to run the query again. The results will only show thetranscription factors retrieved from the ORegAnno database.
The users are highly encouraged to play around with the QueryBuilder
themselves.

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