groupAPI/UseCase_3A

TableOfContents([2])

Summary

We would like to be able to represent detailed sub-gene data in a second window after selecting a node from the parent graph. These below use cases apply to datasets where many different pieces of data (e.g. probesets or interaction partners) are available, each of which would be represented as distinct nodes. Examples include individual probes or replicate spots from a microarray dataset, data from distinct time-point comparisons in a dataset polymorphism data from whole genome SNP experiments*, exon and exon-junction specific data*, ChIP on chip experiment data* and interaction partners for a node in the parent network*. Examples with an asterisk are illustrated below.

Step-by-Step User Action

Associating Data for Sub-Gene Views

1. To view data with specialized sub-gene views (e.g. SNP view with annotations), first requires a relational database containing at a minimum, associations to genes or proteins. The GenMAPP group is currently designing a database that will support specific ID systems for microarray platforms that assay for specific sub-gene entities. This database will also have to accomidate new relationships appended to the database by the user for unsupported ID systems. For generic case, only those relationships need to connect individual array IDs (or other elements) to a gene are required. For more specialized cases, such as viewing SNP annotations associated with an array ID, these additional annotations must be stored in the relational database.
2. Once the user determines whether the primary ID from their data is supported in the gene database and a sub-gene view to select, the user will:
   1. upload their data using a specialized interface
   2. specify filters for node coloring
   3. choose the sub-gene visualization methods
   These options will stored along with the user raw data in a relational database.

Selecting a Sub-Gene View

1. Open a network
2. Select the gene database used when loading the raw data from a context menu.
3. Select the user database with data and criterion from a context menu.
4. Select the sub-gene view of interest from a context menu. Once selected, by default the right click option will activate the sub-gene view.

Visualizing Sub-Gene Data

1. Right click on a node in the network. This will open a new window (child network) containing the sub-gene view.
2. Select a node in the child network to view more detailed annotations provided from the gene database.

Visual Aides

• attachment:sub-gene-vis.jpg

Requirements for Cytoscape

Importance

This use case is necessary for any dataset with more than one piece of information linked to a single gene level node. Specific sub-gene views provide biological context and annotations for the original sub-gene identifiers loaded.

Other Examples

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