Description:
- Merges two or more networks from the canvases in the CI workspace. The merge operation for two networks differs in several details from the merge of multiple networks (more than two). The differences are summarized in the table below:
|
Merge 2 Networks |
Merge Multiple Networks (more than 2) |
Intersection Threshold Parameter |
N/A |
specified by the use before each merge operation |
Merge Result |
4 networks: intersection, sum, difference1 and difference2 |
2 networks: intersection and sum |
Colors |
After merge edges are colored by 3 color scheme: intersection, difference1 and differeence2 |
Only the intersection edges are colored after merge |
Merge 2 Networks:
- The merge operation compares the two networks and finds the common part of the two networks (intersection) and the differences between the networks and the sum of the two networks (union). The networks are compared by searching for identical genes and edges, the definition of gene and edge identity is described below – see Definitions.
- The merge results are displayed in four new canvases arranged side by side for simultaneous display:
· the Union of Network 1 and Network 2
· the Intersection of Network 1 and Network 2
· the Differences between Network 1 and Network 2
· the Differences between Network 2 and Network 1
- The selected network (Network 1) is treated in a unique way during networks merging: The nodes and edges in the intersection network and also common nodes and edges in the union network inherit their properties from corresponding nodes and edges from the selected network, except for the edge type and color that are defined as stated below.
- The default Color by Relation Type setting is turned off to show edge colors resulting from the network merge operation – see below.
- Edges in Network 1 are marked by one color denoted by the difference in color (default is red) and edges in Network 2 are marked by another color denoted by the difference2 color (default is green). The common edges are marked by the intersection color (default is magenta) in both input networks. The same colors are used for the corresponding edges in the resulting networks. The edges that are common in Network1 and Network2 are colored by the intersection color (default value is magenta). Thanks to this coloring you can easily see, what is the original network of an edge in the merged network.
- The values for the predefined colors difference1, difference2 and intersection can be set in the Preferences dialog box.
- The intersecting edges may be of a different kind in the original networks. In such cases, the resulting type property will be of type 3. Type 3 will denote that the two edges in the original networks conflict.
- The edge colors resulting from the merging operation are persistent, i.e., you can save the output networks and view the edge colors after you open these files.
- The score of common edges can be set to the value of Network1 (default setting) or it can be calculated as the average of merged edges. The way of setting this is defined in the Preferences dialog box. The original score of merged edges is saved in the edge comments as Prior Score.
Merge Multiple Networks (more than 2):
- The merge operation compares all networks and finds the common part of the two networks (intersection) and the sum of the two networks (union). The networks are compared by searching for identical genes and edges, the definition of gene and edge identity is described below – see Definitions.
- After choosing the command, a dialog box is displayed asking you to specify the Intersection Cutoff parameter. This parameter tells, in how many networks a given edge or node must be included to be counted as a common element and displayed in the intersection network.
The default value for this parameter is the number of networks to be merged. This is also the maximum value for this parameter. The lower the intersection cutoff, the more edges and genes will be displayed in the intersection network.
- The merge results are displayed in 2 new canvases arranged side by side for simultaneous display:
· the Union of Network 1, Network 2, Network 3, etc...
· the Intersection of Network 1, Network 2, Network 3, etc...
Identity Definitions:
- Equality between two nodes: two genes are equal if their corresponding values of Gene Name and ProbeID are equal
- Equality between two edges: two edges are equal if their corresponding parent and child nodes are equal according to the above definition of the relation of equality between the two nodes.
Edges Types:
Edge Type |
Description |
View Style |
Type 0 |
up-regulation |
|
Type 1 |
down-regulation |
|
Type 2 |
Conflict |
|
Type 3 |
Unknown |
|
Constraints:
- At least two networks must be opened in the workspace.