Agilent's prototype Network Builder for GeneSpring constructs
a Cytoscape network from GeneSpring GX or GT using an input GeneList and
- for GX, an input Interpretation for associating expression
values with the network nodes.
- for GT, an input Variation and an input Haplotype Map
for assocating LOD scores with the network nodes.
You can build up the network using evidence gathered from
a number of optional database sources. Each pairwise combination
of genes in the GeneList is checked against the desired databases
for evidence of an interaction or assocation between them.
GeneSpring Network Builder Plugin Software provides an easy-to-use
interface to its powerful querying capabilities. The Plugin script interface allows selecting one or more databses for
querying for interactions among the list of selected genes. An edge is built when there is evidence that supports it from at least one
of the sources specified. The edges are stitched together into a Cytoscape network.
There are two options for gathering evidence from the literature:
- conduct a search over the Internet, using PubMed and other search sites. This is comprehensive but time-consuming.
- conduct a search using a locally cached repository. The repository is built from a custom search in particular area of inquiry, e.g.
skin inflammation or neuropsychiatric disease. This method is not as comprehensive but is considerably faster than going out to the Internet.
When the network is built, attribute values from the Genes in the GeneList are set as Node and/or Edge attributes on the
corresponding Cytoscape network nodes and or edges. They can then be used to set Cytoscape visual attributes for nodes and edges, such as Node Color or
For GeneSpring GX, an input Interpretation is used to map expression values to Node Color.
For GeneSpring GT, an input Variation and a Haplotype Map are used to map LOD scores to Node Color.
In both GeneSpring GX and GT, the identity if the
database source is mapped to the Edge Color visual attribute in Cytoscape.
In both GeneSpring GX and GT, the number of sentences found in the scientific literature that support an association is mapped to Edge Line Type,
with thicker lines indicating more sentences in the literature.
GeneSpring Network Builder Plugin Databases
- BIND protein-protein interaction database
- cPATH protein-protein interaction database
- Reactome protein-protein interaction database
- KEGG Pathway database
- GenMAPP Pathway database
- SGD database (for Yeast)
- Gather evidence from the scientific literature
via the Agilent Literature Search software.
Click on any of the images below for a larger size.
|The figure shows the script input window for running the GeneSpring Network Builder
plugin from GeneSpring GT.
The user has selected a GeneList (Huntington_ERK5), a Haplotype Map, and a Variation. Search will be run for human species.
All the database sources will be consulted, except for SGD, which is for yeast. Gathering evidence from the literature will be done using a locally cached repository.
|The figure shows the result of running the GeneSpring Network Builder for GeneSpring GX.
Nodes are colored according to gene measurement values for a particular condition, this example gene expression values.
Color-coding of lines indicates which database source provided support for that interaction.
Edge thickness indicates number of sentences in the literature that indicate an interaction between the two genes.
Dotted lines indicate indirect connection (genes are on the same pathway but not necessarily directly connected).
|The figure shows the operation of viewing the literature references that support edges.
Right-clicking on an edge (top-left panel) will result in a pop-up window that shows sentences in the literature that support that edge (bottom-center panel).
Selecting a sentence results in the user's Web browser showing the reference in the literature that contains the selected sentence (rightmost panel).
|The figure shows the architecture of the GeneSpring Network Builder software.
The software comprises: (i) an input/output component, which gathers GeneList and associated data information from the GeneSpring software,
passes the information to a network
building core component, and passes back to GeneSpring a GeneList of the genes contained in generated Cytoscape network.
ii) A core network building component, which gathers evidence from several data sources and constructs a Cytoscape network.
(iii) An extensible set of evidence builders, which take as input a list of terms and, for each pairwise combination of terms, queries its respective data
source for evidence of an interaction between biological entities corresponding to those terms. In the current version, the types of data sources consist of protein-protein interaction databases, pathway databases,
and the scientific literature.
Carsten Rosenow, Aditya Vailaya, Allan J. Kuchinsky,and Frank A. Middleton, "Combining expression and genotyping analysis in neuropsychiatric research," Agilent Technologies GeneSpring Platform Application Note, December 19, 2005, edited and complied by Brynn Alysun.
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