SAGE Analysis Primer for DiscoverySpace 4

DiscoverySpace 4 has overhauled SAGE analysis. Please read the primer about Queries to gain a better understanding of this major feature

Definition of Terms

Perhaps the most difficult change in the SAGE functionality of DS4 is the reconceptualization of the data model. Whereas in DS3 the user would define new "SAGE Libraries" from libraries in the database, in DS4 one defines "Sets of Tag Sequences".

Step by step screenshots

This section contains illustrations and explanations of the main SAGE use cases.
Screenshot of query for all SAGE libraries
Figure 1) A screenshot of a Query definition. In this query the user is asking "Show all GSC SAGE Libraries available to me". Each user is automatically constrained to a subset of the total available libraries and tags as determined by the database administrator. To create the query pictured above the user has selected the origin class "GSC SAGE Libraries" and has attached no filters. She has also given the definition the name "All GSC SAGE Libraries".
Screenshot of Explorer - All SAGE libraries
Figure 2) A screenshot of the Explorer from DiscoverySpace 4. This shows the set of resources defined by Query "All GSC SAGE Libraries" (as defined in Figure 1). The user has selected multiple properties from these resources, including Description, Protocol and Taxon. Now that she can view all available libraries the user can now construct queries to define particular sets of Tag Sequences from those libraries.
Screenshot of a SAGE library definition
Figure 3) A screenshot of the Query Set Definition from DS4. This query specifies a certain set of Tag Sequences from library SM095. Within this definition the user has created a query path from the start class "GSC SAGE Libraries" through to "Experimental SAGE Tags" through to the "Sequence"s of those experimental tags. She has set "Sequence" as the end of the query, which will therefore result in a set of Tag Sequences. The user has then constrained the query path to use only the library named "SM095", only the SAGE Tags with a quality of over 0.99 which are not marked as duplicate ditags, and only the sequences without sequence data "TCGGACGTACATCGTTT" and "TCGGATATTAAGCCTAG". This final constraint is to exclude linker sequences used by the Long SAGE protocol. Once such a Query is constructed the user the query can be duplicated and the duplicate edited - this is currently the best way to reuse Query definitions in DS4.
Screenshot of two selected tag sets
Figure 4) A screenshot of the Databank. In this image one can see that the user has constructed two sets of Tag Sequence resources (highlighted). One of these, "GSC SAGE SM095 0.99", has been constructed as illustrated in Figure 3). The other, "GSC SAGE SM096 0.99", has been created by duplicating the SM095 query and then altering the "Library name" value of the query (to SM096). The user has also renamed this new query. The best way of reusing queries is to duplicate and edit the result. In the figure above one can see that the user has selected both of these new Query definitions. With these two sets of Tag Sequences selected one can see that the "New Comparison" action (third from left) is enabled. The result of selecting this action is shown in Figure 5) below. Also note that the Venn Table action is also enabled (fifth from right). The result of selecting this action is show in Figure 6) below.
Screenshot of a Tag Set Comparison Definition
Figure 5) A screenshot of the Comparison Definition. In this figure one can see the result of the operation pictured in figure 4). The user selected SM095 and SM096 and selected "New Comparison". Be aware that one can construct a Comparison with two or more sets of Tag Sequences. The user has given a title to this new Comparison, has labeled the axes and has chosen which sets of Tag Sequences are to be represented on which axes. In this case SM096 is attached to the x-axis and SM095 is attached to the y-axis. Once a Comparison has been constructed it can be selected in the Databank and viewed in the Scatter Plot by selecting the Scatter Plot action.
Screenshot of a Scatterplot
Figure 6) A screenshot of the Scatter Plot. This is the result of viewing the Comparison constructed in Figure 5) in the Scatter Plot viewer. The user has used the Select menu to select all upregulated datapoints. These datapoints can now be dragged, as Tag Sequences, into the Databank and into their own Data definition.
Screenshot of a Venn Table analysis
Figure 7) A screenshot of the Venn Table. This is the result of viewing the selected sets of Tag Sequences from Figure 4) in the Venn Table tool.
Screenshot of Explorer - SAGE Library mapped to Mouse Refseq
Figure 8) A screenshot of the Explorer. This image shows the selected Tag Sequences from SM096 viewed within the DiscoverySpace Explorer. The Tag Sequences have been mapped to Refseq Virtual Tags (Mouse only) and then to their source Refseq resources. Thus for each SAGE Tag Sequence one can see the relevant Refseq Gene.



Page last modified Jun 08, 2010