MetNet Systems Biology Platform

Category Metabolomics/Metabonomics>Metabolic Profiling/Analysis Systems/Tools and Cross-Omics>Pathway Knowledge Bases/Databases/Tools

Abstract MetNet is an emerging open-source software platform for exploration of disparate experimental data types and regulatory and metabolic networks in the context of Arabidopsis systems biology.

MetNet can be used to visualize, explore, statistically analyze and model transcriptomics, proteomics and metabolomics data in the context of a growing metabolic and regulatory network map of Arabidopsis, Soybean, and other species.

The software is designed to enable the biologist to visualize, statistically analyze, and model a metabolic and regulatory network map of Arabidopsis, combined with gene expression profiling data.

MetNet provides a framework for the formulation of testable hypotheses regarding the function of specific genes, and in the long term will provide the basis for identification of metabolic and regulatory networks that control plant composition and development.

The MetNet platform features graph visualization, interactive displays, graph theoretic computations for determining biological distances, a unique multivariate display and statistical analysis tool(s), graph modeling using the open source statistical analysis language, R, and versatile text mining.

MetNet Online --

MetNet Online is an extensive portal based on an integrated database (MetNetDB - see below...) with integrated metabolic and regulatory pathway information. Initial data comes from a variety of sources, and has been manually curated and enriched. The user has the capability to Browse & Search pathways, organelles, interactions or entities.

MetNet Online contains over 1,000 pathways.

Browse Pathways - The user can choose their class of interest from the following selection list: Pathways for - Biosynthesis and Interconversions; Degradation/Utilization/Assimilation; Detoxification; Photosynthesis, Respiration and Related Energetics; Signal Transduction Pathways; or Super Pathways.

Browse Organelles - The user can choose from the following selection list: Pathways for - apoplast; autophagosome; cell wall; cytoskeleton; cytosol; endoplasmic reticulum; Golgi apparatus; inner membrane; lipid particle; membrane; microbody; mitochondrion; multiple locations; Not assigned; nucleus; peroxisome; plasma membrane; plastid; or vacuole.

Browse Interactions - The user can choose their class of interest from the following selection list: Pathways for - Bind; Catalysis; Composition-AND; Composition-OR; Diffusion; Enzymatic reaction; Negative regulation; Others; Positive regulation; Protein-Protein interaction; Transcription; Translation; Transport; or Two-component regulator.

Browse Entities - The user can choose from the following category list: Category - Cis-element; environment; gene; metabolite; polypeptide; protein complex; or RNA.

Note: For additional information about MetNet Online please see the extensive tutorials available on the manufacturer’s web-site.

MetNetDB Database --

Types of interactions in MetNetDB include transcription, translation, protein modification, assembly, allosteric regulation, translocation from one subcellular compartment to another. Other fields describing the interactions are subcellular location, confidence, directionality, references, evidence, and synonyms.

Data on entities (DNA, RNA, polypeptides, protein complexes, metabolites) are derived from web databases (gene related databases: TAIR, Gene Ontology (GO), MapMan/GabiPD; protein related databases: PPDB, AMPDB, AtNoPDB, AraPerox, PLprot, BRENDA; metabolite related databases: ChEBI, PubChem, KEGG, NCI compound library, NIST MS library), in some cases with additional annotation by experts.

Network information from MetNetDB can be converted to an XML file by XML Builder. From this XML file, it can be transferred to exploRase (see below…), which uses the network in conjunction with statistical analysis of expression data; to Cytoscape/FCM, which finds cycles and pathways in the network, and visualizes and models it in combination with expression data; and to MetNetVR, where the network can be visualized in 3D. XML Builder automatically builds new network XML files from the most current data in MetNetDB.

MetNet Plug-ins for Cytoscape --

The MetNet Plug-ins for Cytoscape, are a set of Java open-source programs for visualizing and analyzing biological networks. The goal is to capture the intuitions of biologists and provide a modeling framework to assess large amounts of data.

1) Explore effects of hypotheses;

2) Use graph theoretic approaches to analyze network structure and behavior and search for critical paths in the network;

3) Visualize the results of experiments for different types of omics data and allow translation between platforms; and

4) Integrate genetic network inference and metabolic pathway analysis algorithms developed in R statistical language.

The resulting sub-networks can be identified and interpreted using simple ‘fuzzy cognitive’ maps. Data from high-throughput experiments (transcriptomics, proteomics and metabolomics) can be displayed and modeled in the context of the network graphs.

Features of the MetNet Plugins for Cytoscape -

1) Sub-graph Creator: functions to create sub-graphs, identify node, find cycles, find paths and find p-neighborhoods in a large graph file for dynamic graph display;

2) Dot layout: allows the use of layouts from the Graphviz program, examples include simple and rank-cluster layout;

3) Cycle and path finding algorithms in directed and undirected networks;

4) OmicsViz: Visualize omics data in the graph and Microarray platform translation; and

5) Works for Cytoscape versions 2.3 and later.

Data Sources - The plug-ins are designed to visualize networks from the MetNetDB. These files are accessible using the XMLBuilder tool. The manufacturers are also working to import data files in Systems Biology Markup Language (SBML) and from the BioCyc project, for more pathway information.

exploRase --

exploRase is a MetNet tool written in R for the exploratory multivariate analysis of Systems Biology data. It provides a graphical user interface (GUI) on top of the analysis functionality provided by R and the Bioconductor project. exploRase is designed to be accessible to biologists analyzing omics data in the context of metabolic and regulatory networks.

Features -

1) Provides a biologist-accessible GUI to R analysis functionality, such as distance measures, clustering, pattern-finding, and modeling;

2) Integrates the analysis with interactive graphics, using GGobi;

3) Handles transcriptomic, metabolomic, and proteomic data;

4) Simplifies the loading of experimental data into R and GGobi;

5) Supports the storage of lists of “interesting” entities for future sessions;

6) Links sortable tables of entity metadata to GGobi plots by color coding;

7) Provides automatic access to AtGeneSearch, the web interface to MetNetDB; and

8) Saves calculated statistics.

PathBinder --

PathBinder is a unique, plant-based tool to explore literature, and to annotate metabolic and regulatory interactions and biomolecules. PathBinder queries the MEDLINE database and retrieves sentences containing two (2) terms of interest, and ranks them based on their probability to describe interactions between the two (2) given terms; each sentence is a clickable link pointing to the original online PubMed citation.

Features of PathBinder version 1 include:

1) An application programming interface (API) to integrate PathBinder into other analysis tools for systems biologists. This API has been used to integrate PathBinder into both FCModeler and MetNetDB;

2) Hierarchical filters by taxon, morphological context, and/or subcellular location. Specifying a parent will retrieve abstracts containing that parent and its children. Upon retrieval, abstracts are ranked according to a system based on the quality and quantity of the descriptions of the interaction in the literature;

3) An extensive set of synonyms which are co-searched when a term is selected. The user does Not need to second-guess possible terms for a molecule of interest and do repeated searches;

4) A novel “hidden links” tool to identify and explore potential intermediate links in networks. Given biomolecules A and C, which do Not co-occur in any sentence in the PubMed abstracts, find biomolecules B that co-occur in sentences both with A and with C; and

5) A new feature to extract and rank interaction indicating terms for any give pair of biomolecules from MEDLINE.

MetaOmGraph --

MetaOmGraph is a tool for plotting and analyzing large sets of data while using as little memory as possible. It was designed with biological experimental data in mind. Some uses for MetaOmGraph include:

1) Visualizing ‘gene expression’ patterns;

2) Finding functional groups of genes; and

3) Determining which genes have expression patterns most/least correlated to a gene of interest.

PubMed Assistant --

PubMed Assistant is:

1) A stand-alone Java™ program that accesses the National Library of Medicine (NLM) MEDLINE database directly through the National Center for Biotechnology Information (NCBI) Entrez Programming Utilities, by-passing the PubMed web interface;

2) A visual query editor that eases the pain in editing advanced Boolean queries, such as balancing multiple levels of parentheses, checking Boolean operator precedence, etc;

3) A specialized browser that gets the most out of MEDLINE query hits, for example keyword highlighting, automatic query formulation, MeSH term listing(s) and chemical listing(s); and

4) A collection of utility tools that make easy connections to other frequently used applications, for example, exporting MEDLINE hits to citation managers, one-click Google™ and Google™ Scholar search, etc.

System Requirements

Contact manufacturer.


Manufacturer Web Site MetNet Functional Genomics Tools MetNet Systems Biology Platform

Price Contact manufacturer.

G6G Abstract Number 20677

G6G Manufacturer Number 104316