BioNetBuilder

Category Cross-Omics>Pathway Analysis/Tools

Abstract BioNetBuilder is an open-source client-server Cytoscape plug-in that offers a user friendly interface to create biological networks integrated from several databases.

Users can create networks for ~1,500 different species, including most common model organisms and human.

The interface offers different options to specify a set of initial genes/gene-products for which to find molecular interactions [including loading a simple text file, finding genes with specified Gene Ontology (GO) annotations, and finding genes whose common name match a given string].

Depending on the user's computer capabilities, ‘biological networks’ for whole organisms can also be created and displayed.

In version 2.0 of BioNetBuilder, the manufacturer has made significant improvements to expand the volume and usability of interaction data for Cytoscape users (see G6G Abstract Number 20092).

To begin, the manufacturer added IntAct (a protein interaction database and analysis system), MINT (a database of functional relationships between proteins, DNA and RNA), and the mammalian protein-protein interaction database (MPPI) interaction resources.

The list of 'integrated databases' now includes:

The Biomolecular Interaction Network Database (BIND), the Biological General Repository for Interaction Datasets (BioGRID), the Database of Interacting Proteins (DIP), the Human Protein Reference Database (HPRD), IntAct, the Kyoto Encyclopedia of Genes and Genomes (KEGG), MINT, MPPI, and Prolinks (a database of protein functional linkages derived from co-evolution).

The integration of these networks is made possible via a new 'synonyms-resolution system' that provides a means of translating between the many different identifiers used by each individual database or tool.

The 'synonym translator' provides mappings for gene/protein identifiers based largely on the [NCBI reference sequences (RefSeq) - a curated non-redundant sequence database of genomes, transcripts and proteins] and (the iProClass integrated database for protein functional analysis) databases.

While the previous version of BioNetBuilder allowed users to assign a variety of alternate gene/protein names as node attributes in Cytoscape, networks could only be constructed with RefSeq protein GenBank Identifier (GI) numbers as the Cytoscape node identifiers.

This was limiting because present versions of Cytoscape do Not allow users to exchange node identifiers for node attributes, and many downstream analysis tools operate only on node identifiers.

The second major improvement in version 2.0 is that BioNetBuilder now allows users to select from a diverse list of ‘id types’ to set as the Cytoscape node identifiers; this greatly increases the interoperability of the manufacturer's tools with other downstream analysis (such as Gaggle-enabled tools and other Cytoscape plug-ins).

This interoperability was a key prerequisite to the manufacturer's third main improvement, which is that BioNetBuilder 2.0 is now Gaggle enabled (see G6G Abstract Number 20222).

The Gaggle is a cross-platform data integration system designed to allow seamless shuttling of ‘biological data’ across applications.

BioNetBuilder 2.0 can construct interaction networks based upon data received from any resource with a plug-in that implements the Gaggle framework, including but Not limited to:

1) Cytoscape itself;

2) MeV, a data matrix viewer for navigating and plotting high throughput experimental data (see G6G Abstract Number 20224);

3) R, the open-source statistical computing software;

4) MATLAB, the scientific computing software; and

5) the web browser Firefox, which enables communication with KEGG, STRING (see G6G Abstract Number 20298), and DAVID (see G6G Abstract Number 20263).

Additionally, information from networks constructed with BioNetBuilder can be used to transfer data to any of the aforementioned resources using the Cytoscape Gaggle plug-in CyGoose.

The fourth and most significant improvement in BioNetBuilder 2.0 is that interactions can be transferred across species.

Although more than 500 species are represented in BIND, BioGrid, DIP, HPRD, IntAct, MINT, and MPPI, most model organisms, including chicken, have relatively little interaction data available.

To address this problem, all interactions in the databases listed above were used to compute integrated ‘interolog networks’ for many eukaryotic model systems, including chicken.

An interolog, or interaction homolog, of a pair of interacting proteins (A, B) can be faithfully transferred from one species to another if the orthologs to (A, B): (A', B'), share at least 80% joint sequence identity to (A, B).

As reported by (Konieczka JH, Drew K, Pine A, Bonneau R, Antin PB: Integrated Interaction Networks for Eukaryotes, in press), coverage of the chicken interactome improved dramatically when interolog-derived interactions were included.

BioNetBuilder 2.0 tutorial --

To facilitate the use of BioNetBuilder 2.0 and Cytoscape by researchers who may have little formal bioinformatics experience, the manufacturers provide a tutorial on how to use BioNetBuilder 2.0 to download and use a custom chicken interactome.

In the first section, the manufacturer describes the step-by-step construction of a customizable interactome for chicken.

In the second section, the manufacturer shows how to integrate a sample microarray data set into the network and apply a method for extracting relevant sub-networks.

Finally, the manufacturer discusses how to use the information in a sub- network to generate novel biological hypotheses.

System Requirements

You need to have Java 2 Standard Edition 1.4.x (later versions are probably fine) installed and an internet connection.

If you use Java-Web Start, you will also need Java Web-Start installed.

Note: Most computers have Java Web-Start installed by default since it is included in the Java Runtime Environment.

Manufacturer

Manufacturer Web Site BioNetBuilder

Price Contact manufacturer.

G6G Abstract Number 20507

G6G Manufacturer Number 104126