LM: Literature Mining Analysis

Parameter Information


Location of Support File(s)

This option allows users to select the location where all support files needed to run BN.

Network Priors Sources

The checkboxes provide the users to select the source of Bayesian prior probablities in constructing a seeded network. Currently Literature Mining and KEGG priors are avaialble. The Protein - Protein Interaction as a source of priors is still under development.

As of now, the KEGG support files are automatically downloaded from TN4 website by the application. The user is prompted for Species information if annotation is not avaialble. All other prior sources must be made avaialble.

Discretize Expression Values

The data mining algorithm requires that the data be discretized into bins before it can be evaluated for network structure learning. It is strongly recomended that user selects the default value of 3, which means the data can exist in 3 states:
  1. Under expressed
  2. Over expressed
  3. Unchanged
The algorithm functions and reports meaningfully if the 3 state rule is followed.

How to direct Edges for graph

The algorithim uses DFS or Depth First Search to connect nodes in the intial seeded network. For large networks with lots of nodes this can take a while to complete. The GO Term option of directing edges is not yet fully developed.

Using Support Files created for standard arrays

We have pre-created support files needed to run BN or LM analysis for some popular microarray platforms like Affymetrix, Agilent etc. Currently we are providing support files 3 species Human, Mouse & Rat. MeV comes preloaded with the files for 2 array types in the ~/data/BN_files folder.
  1. Afymetrix Human U133 Plus 2 Array
  2. Affymetrix Mouse 430 2 Array