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an interactive graphical browser for molecular interaction networks

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Upload User Defined Data

There are four different formats for user-defined data listed below.
(Note: \t is the "tab" button on your keyboard)

Description Examples Real Examples
Simplest format: a list of interacting pairs geneA \t geneB
geneB \t geneC
par-1\t par-3
List of pairs, with defined data types geneA \t geneB \t Type1
geneB \t geneB \t Type2
par-1\t par-3\t GI
Y66A7A.4\t Y65B4BL.5\t GI
Pairs with defined data types and numerical values * geneA \t geneB \t Type1 \t 0.98865
geneB \t geneC \t Type2 \t 0.1
par-1\t par-3\tGI\t 0.98865
Y66A7A.4\t Y65B4BL.5\tGI\t 0.1
Pairs with defined data types, multiple data sets, and numerical values * geneA \t geneB \t Type1 \t DataSet1 \t 0.83973
geneA \t geneB \t Type1 \t DataSet2 \t 0.8
par-1\t par-3\tGI\tWS150\t0.98865
Y66A7A.4\t Y65B4BL.5\tGI\tWS150\t0.1

* Numerical values may represent confidence or quality scores, correlation coefficients, or other numerical attributes.

Tip: These formats can be generated by Microsoft Excel or OpenOffice Calc. To export data in this format, place the data in different columns and then save as a "tab delimited" file. (Data in each column can include spaces, but should not include the "tab" character.) Demo file (Right-click the hyperlink and choose "Save Target as" .csv file)

Note: Cytoscape SIF files can be uploaded. More information can be found here: Cytoscape User Manual/Network Formats

Merging Uploaded User Defined Data With Database

To merge your file with the database, select the Coordinate with DB checkbox (default) and enter a starting point to query.
Multiple genes separated by a space, comma, or semi-colon can be entered as starting points.
To keep your edge types separate when merging with the database, select the Use custom edge types checkbox (default).
A User_ prefix will be added to the names of the edge types and existing data sets when using the Use custom edge types checkbox.
When the Use custom edge types checkbox is not selected, the User_ prefix will only be added to edge types and data sets not found in the database.
If data sets are not specified in the file and an edge is considered user-defined or not found in the database (User_ prefix is used), the default dataset name Unknown is used.