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:
-
[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.
-
[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.
-
[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.