groupAPI/UseCase_3A

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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, that themselves can 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. Requires a new interface for data input and selecting from specific options for compatible sub-gene views. Once required data is supplied for a specific sub-gene entity method (see above for built-in examples) or generic sub-gene objects (e.g. probesets) along with filters for node coloring supplied, values associated with specific
2. Choose "Form complex" from a context menu, main menu or toolbar
3. Automatically view collapsed view of complex with default label (editable)
4. Be able to expand complex as vertically stacked set of nodes by a very simple mechanism (e.g., click on a plus/minus icon)
   1. perhaps other restricted views of the children will be allowed:
      1. horizontal stack
      2. block (e.g., 2x2, 3x4)
      3. overlapping "clump" of nodes packed into a some defined circular area
      4. new network
5. Be able to destroy complex
6. Be able to expand-all or collapse-all complexes in a given network

Loading a Network with a Complex

1. Same as 3-6 above

Visual Aides

• attachment:sub-gene-vis.jpg

Requirements for Cytoscape

Importance

Other Examples

Comments

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