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Listing of Networks

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SummaryListing of Networks

List of Networks

After double-clicking on an analysis in Project Manager, Click on the Networks Tab to view the List of Networks. This view presents all of the networks generated based on an analysis in a tabular view. In this list, networks are listed in order of their significance, with five columns displaying the characteristics of each network. 


1. ID: Each network receives an identifier, with the numbers assigned in the order of the significance score.

2. Molecules in Network: All of the molecules that compose each network are listed. Network Eligible Molecules appear in bold, while other molecules are in regular font. An asterisk appears next to any gene for which the input file contained more than one identifier.

3. Score: The score is based on a p-value calculation, which calculates the likelihood that the Network Eligible Molecules that are part of a network are found therein by random chance alone. Mathematically, the score is simply the negative exponent of the right-tailed Fisher's exact test result. For example, if the score is 3, then the there is a 1 in 1000 chance that the Network Eligible Molecules found in that network appeared there just by chance. In other words, the score is simply a measure of the number of Network Eligible Molecules in a network, and the greater the number of Network Eligible Molecules in a network, the higher the score (lower the p-value) will be.

4. Focus Molecules: This column simply indicates the number of Network Eligible Molecules per network. The default number of molecules per network is 35. However, you may choose to display either 35, 70 or 140 molecules per network (in the create core analysis settings page at the time of running the analysis).

5. Top Diseases and Functions: The three most significant functions for each network are listed here.

Filtering (Searching) Networks

The Filter function allows you to find networks that contain a particular molecule(s) of interest.


1) Go to the Network tab.

2) ) Click on the Filter   icon.

3) Enter the name of a molecule of interest in the Search Field (separated by a comma if entering more than one molecule).

Networks that contain molecule(s) entered in search field will be retained. To open one or more networks containing the molecule(s) of interest, simply click an empty space in the row and click View Networks OR click on the network ID number under the ID column.


Top Diseases and Functions

The Top Diseases and Functions column displays the top 3 high-level functions from the Functional Analysis of a Network. This provides you with an overview of the biological functions associated with a given network. Click here for more details.


To view Functional Analysis for a Network from the Network List:

1) Select the Networks tab to view the list of networks. In the Top Functions column, the top three functions are displayed.


2) To expand these high-level functional categories for an individual network, select your network of interest and click the Functions button.




TitleListing of Networks
URL NameListing-of-Networks