TargetMine Exercise and Tutorial
AIST KANSAIJanuary 28th 2011
Copyright  2010 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 every TargetMine page:

I. Quick Search and report pages
A quick search box appears in the menu bar of all pages. Entering any object
identifier (such as a gene name or identifier) in the quick search box will
direct the user straight to the report page for that object. For example
Run a quick search for an ensembl id 'ENSG00000084674':

The report page for a particular object in the TargetMine database provides
all the information that TargetMine has for that object. All report pages havethe same basic structure1•The upper half summarises the information associated with each object•The lower half ‘Further information by category’ provides more detailed
information corresponding to data categories in TargetMine (which canbe seen on the home page). This information is derived from a set ofpredefined queries known as templates (see below) related to specific data
categories which are pre-run on the object of query.

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.

2The Lists page is accessible via the 'Lists' tab on the TargetMine menu bar.
The 'Upload' tab in 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, protein), which
can be set from the drop-down list. However, it is possible for the list tocontain a mix 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.
••

Find the sample gene list at http://targetmine.nibio.go.jp/workshop/hych
Select and copy the gene list and paste in "Type/Paste in identifiers" box.
Then click on the "Create List" tab.

• List Confirmation Page
Before a list is created it is checked against the TargetMine database andany discrepancies are reported in the ‘list confirmation page’. The user must3

assign a name to the list. For example, the uploaded list contains 32 genes
and for the purpose of this tutorial is saved as ‘hych’.

• 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 isautomatically 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 the first
10 objects of the list, a list description, List Info, Convert tools and
Link outs (if available). Above the table, there are
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 on the list, forexample, overrepresented KEGG pathway, Gene Ontology (GO),Drug and Disease Ontology associations, Protein-proteininteractions (PPIs) and Associated Drugs.

4

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 be changed byimposing constraints (filters) on certain data types so as to restrict thequeries to certain subsets of data.
Template queries can be accessed in different ways•••

Each data category page has a set of templates related to that data type.
Templates appear on report pages and list analysis pages.
Templates can be searched using the Quick Search available on every
TargetMine 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':

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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 "hych" saved earlier, and then clickon "Show Results" to run the query.

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 orto 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. Forexample, name it as 'upstream genes'. 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

Please try it yourself.

6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 existing template queries to change the output or add a filter
as may be seen from the following example.

Click on 'Query' in the Trail to get back to the template form:

Now click 'Edit Query' to bring up the Query Builder:The ‘Model browser’ on the left permits the user to navigate the TargetMine
data model. In this example, the model browser displays the initial Gene
class and all its attributes (e.g., name, symbol) and related classes (e.g.,organism, proteins). TargetMine uses an object based data model - biologicaltypes 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. The
taballows the user to add constraints (filters).

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Underneath the model browser, the ‘Fields selected for output’ displays thefields 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 'IN demo list'. This indicates thatthe query is restricted to the genes from the sample list saved earlier.
What if the user wants to search for all genes in TargetMine for any
upstream transcription factor that may regulate their gene expression? The
user may simply remove this constraint and run the query again.
Click on thebutton next to 'IN hych' to remove the constraint:Now click 'Show results' to run the query:

The results table now shows all the upstream transcription factors in
TargetMine and their target genes. The user can use the summary
buttons on the 'Source > symbol' and 'Target > symbol' columns to findmore information about the numbers of each.

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