MADNet

Category Genomics>Gene Expression Analysis/Profiling/Tools and Cross-Omics>Pathway Analysi/Gene Regulatory Networks

Abstract MADNet (MicroArray Database Network) is a user-friendly data mining and visualization tool for the rapid analysis of diverse high-throughput biological data such as microarray, phage display or even metagenome experiments.

It presents biological information in the context of metabolic and signaling pathways, transcription factors and drug targets through minimal user input, consisting only of the file with the experimental data.

This data is integrated with information stored in various biological databases such as NCBI nucleotide and protein databases, metabolic and signaling pathway databases (KEGG), transcription regulation [(TRANSFAC©) - see G6G Abstract Number 20121], and drug target database (DrugBank).

Currently, MADNet correlates data from several publicly available databases:

1) KEGG - Kyoto Encyclopedia of Genes and Genomes.

2) PharmGKB (see G6G Abstract Number 20304) - The Pharmacogenetics and Pharmacogenomics knowledge database.

3) EBI - European Bioinformatics Institute.

4) NCBI - National Centre for Biological Information.

5) TESS - Transcription Element Search System.

The manufacturer has developed a data analysis and visualization tool for high-throughput experiments that should minimize necessary technical knowledge, as well as effort and time required to gain biological insight into a large amount of data.

MADNet eliminates the need for prior knowledge of the existent microarray data formats and gene nomenclature, allows simultaneous access to multiple biological databases, while providing an interactive and user-friendly interface with a strong emphasis on graphical data representation.

Moreover, MADNet is Not only confined to microarray experiments, but can also be used to analyze expression information from different experimental techniques.

MADNet can mine information from diverse origins such as nucleic acid and protein microarrays, SAGE, phage display, as well as any other experimental technique that measures differential change in expression of a series of genes or proteins.

The only requirement for MADNet is an experimental data file containing columns with gene identification numbers, fold change descriptors and optional statistical significance.

MADNet is highly processive and able to analyze large quantities of input data.

Therefore, it can also be used to analyze whole metagenomes (e.g. in terms of abundance of functional gene categories or presence and absence of metabolic pathways), which is especially interesting in context of recent progress in environmental sample sequencing.

Furthermore, the manufacturers are ready to promptly enter a database of the user's interest and make it available through the MADNet interface, in order to answer the personalized needs of different research communities.

Integrated databases -- MADNet provides a systems biology approach to complex research problems in a user-friendly interface.

The software tool integrates several types of biological information from existing databases (stated above…).

This data is stored in a local MySQL database and integrated with a PHP: Hypertext Preprocessor (PHP)-based scripting system into an interactive web-based graphical interface.

Differential expression data from user input are color coded and mapped onto metabolic and signaling pathways and displayed either as an interactive, user-clickable map or a list of metabolic and signaling pathways, ranked according to the statistical significance of expression magnitude.

MADNet also provides the ability to investigate transcriptional cascades by summarizing and visualizing transcription factor ‘gene regulation networks’.

Web server implementation -- The web server user interface is available in the form of HTML pages, dynamically generated by a set of server- side PHP scripting programs, which access information stored in the MySQL database.

Special attention has been paid to the ‘processivity’ of the analysis. MADNet can process tens of thousands of genes, in minutes with the bottleneck usually being the time taken to upload the input file to the server.

Thereafter, the user's query is stored in the form of a session, which significantly reduces the time required to perform repetitive calculations and increases the overall responsiveness of the server.

Note: There is a Demo option available to test MADNet capabilities by selecting the 'demonstration mode' using a sample microarray file already uploaded on the server.

System Requirements

Web-based.

1) Cookies: You must enable Cookies in your browser in order for MADNet to work properly.

2) Recommended browsers: The manufacturer recommends you use the Mozilla Firefox (C) browser for MADNet (both on the Mac and PC).

Manufacturer

Manufacturer Web Site MADNet

Price Contact manufacturer.

G6G Abstract Number 20364

G6G Manufacturer Number 104013