Boolean Networks


Tutorial:
Textbox for entering genes
Enter a list of Affy probeset IDs or gene symbol names. Unknown characters and terms will be ignored.
Filename
Enter a unique filename for retrieving results later. A blank value will return the results in a temporary file or directory.
Action
Enter a list of genes or Affy probeset IDs, and select a network before clicking any of the following buttons.
subplot
This will return with a page with dynamic ranges of each probeset and scatterplots between all pairs of matching probesets.
subgraph
This will return with a page with links to the results of the Boolean implications between the matching probesets.
subnet
This will return with a page with links to the results of the Boolean implications from the matching probesets to all probesets for the selected networks.
test
This will return with a page with links to the matching probesets.
Network
A link for browsing Boolean implication network for a particular Affymetrix platform.
Index
A database of Affy ID, gene name and description.
Relation
A database of Boolean implications.
PCL
Normalized expression values from all the arrays.
Bit vector
Discrete expression values after applying the thresholds - low (0), intermediate (1), high (2)
References:
  1. [Abstract] [Full Text] [PubMed] Debashis Sahoo, David L. Dill, Andrew J. Gentles, Rob Tibshirani, Sylvia K. Plevritis. Boolean implication networks derived from large scale, whole genome microarray datasets. Genome Biology, 9:R157, Oct 30 2008.
  2. [Abstract] [Full Text] [PubMed] Debashis Sahoo, Jun Seita, Deepta Bhattacharya, Matthew A. Inlay, Sylvia K. Plevritis, Irving L. Weissman, David L. Dill. MiDReG: A Method of Mining Developmentally Regulated Genes using Boolean Implications. Proc Natl Acad Sci U S A. 2010 Mar 30;107(13):5732-7. Epub 2010 Mar 15.
  3. [Abstract] [Full Text] [PubMed] Matthew A. Inlay*, Deepta Bhattacharya *, Debashis Sahoo, Tom Serwold, Jun Seita, Holger Karsunky, Sylvia K. Plevritis, David L. Dill, Irving L. Weissman. Ly6d marks the earliest stage of B cell specification and identifies the branchpoint between B cell and T cell development. Genes Dev. 2009 Oct 15;23(20):2376-81.