Plant MetGenMAP

Category Metabolomics/Metabonomics>Metabolic Profiling/Analysis Systems/Tools, Cross-Omics>Pathway Analysis/Gene Regulatory Networks/Tools and Genomics>Gene Expression Analysis/Profiling/Tools

Abstract Plant MetGenMAP is a web-based analysis and visualization package that allows the user to identify significantly changed pathways and biological processes (i.e. enriched GO terms) from gene expression and/or metabolite profile datasets and to view the profile data in the context of biochemical pathways.

The Biochemical pathways that the system uses have been extracted from the BioCyc databases, including AraCyc for Arabidopsis, RiceCyc for rice and LycoCyc for tomato.

Plant MetGenMAP can identify significantly altered biochemical pathways and highly affected biological processes and predict functional roles of pathway genes and potential pathway-related regulatory motifs from transcript and metabolite profile data sets.

Plant MetGenMAP is an easy-to-use, advanced analysis system that supports many functions of systems biology analyses in the context of biochemical pathways and Gene Ontology (GO) terms.

It provides an analytical platform in which highly altered pathways can be explored rapidly and efficiently through intuitive visualization and robust statistical tests.

Since it allows for the analysis of transcriptional and metabolic changes simultaneously for each pathway, the association between gene expression and biochemical changes in specific pathways under specific conditions can be easily inferred.

Functional analysis of differentially regulated pathways can help to properly define functional roles of genes within pathways. In addition, the system embeds a function that can identify major regulators putatively related to the change of transcripts and metabolites in specific pathways.

The system can greatly help researchers to generate novel biological hypotheses and derive new conclusions from high-throughput omics data sets.

Plant MetGenMAP consists of four (4) data repositories, three (3) functional components, and four (4) analysis modules. All parts are flexibly integrated to perform user-requested tasks.

Plant MetGenMAP data repositories --

The four (4) data repositories in the Plant MetGenMAP system are:

1) Biochemical pathways from several major plant species (Pathway Repository);

2) Promoter and coding sequences of all genes collected in the system (Sequence Repository);

3) Functional annotations of all genes, including gene descriptions and associated GO terms (Gene Function Repository); and

4) User-uploaded data sets (User Dataset).

The system maintains the pathway structure information in a flat file format written with the DOT language that can be processed by the Graphviz program.

Information regarding the relationship between pathways and genes/metabolites, gene annotations and sequences, and the user-uploaded data sets, including project information, are stored in the back-end MySQL database for efficient manipulation.

Plant MetGenMAP functional components --

The three (3) functional components in Plant MetGenMAP are:

1) Data management;

2) Pathway browser; and

3) Data set analyzer.

1) The data management component deals with data uploading and the overall information and management of user-created projects.

Plant MetGenMAP takes normalized and processed expression and metabolite profile data (mainly ratios/fold changes and P values that are derived from statistical analysis programs) as the input to identify significantly affected biological process and biochemical pathways.

The system allows users to upload and analyze gene expression and metabolite profile data separately or simultaneously. A new project is created during each data upload process. The project information contains the project title and description and the corresponding platform and organism information.

All projects are managed by a data management component, making it possible to analyze the associated data sets further by setting new values of parameters, such as the cutoff values of fold change and P values that define the up- and down-regulation of genes/metabolites.

In addition, the system provides a summary that lists the number of up- and down-regulated genes/metabolites under each condition for each project.

The system also allows users to completely remove their projects from the system. To ensure security of user-uploaded data sets and project information, the system is designed such that projects can only be accessed and managed by the users who create them.

2) The pathway browser component is the visualization part that lists metabolic pathways in which transcript or metabolite changes are observed. Plant MetGenMAP retrieves the list of metabolic pathways that are highly correlated to the given expression or metabolite profiles.

The list of pathways can be shown in two (2) ways: the tree view and the ranked list.

Furthermore, this component also shows the detailed information of genes in the altered pathways and provides promoter analysis of co-expressed genes to identify regulatory motifs potentially involved in regulating specific pathways.

3) The data set analyzer component allows users to identify enriched Gene Ontology (GO) terms (e.g. biological process) under specific experimental conditions as well as to categorize genes into different functional classes. In addition, the keyword search can be performed to identify terms of interest, including metabolites, enzymes, and pathways.

Plant MetGenMAP analysis modules --

The analysis modules support the corresponding functional components through different kinds of analyses using the data repositories. They include:

1) Statistical analysis of pathway changes (PathFinder);

2) Identification of regulatory motifs (PromAnalyser);

3) Functional analysis of gene annotations (FunctAnnotator); and

4) Visualization of individual pathways (PathVisualizer).

1) PathFinder calculates the significance of pathway changes based on changes in gene expression levels or metabolite content and then rapidly retrieves significantly altered pathways. The raw P values indicating the significance of pathway changes can be further corrected for multiple testing using the false discovery rate (FDR); or Bonferroni correction.

2) PromAnalyzer retrieves the promoter sequences of co-expressed genes in an altered pathway and identifies enriched regulatory motifs from said promoter sequences.

3) FunctAnnotator analyzes a list of up- and/or down-regulated genes under specific conditions and reports a list of significantly enriched GO terms. FunctAnnotator can also classify a list of genes into different functional categories using a set of plant-specific GO slims, which are a list of high-level GO terms providing a broad overview of the ontology content.

4) PathVisualizer provides an intuitive visualization of each individual pathway, with genes and metabolites decorated using different colors reflecting the changes of their respective levels (e.g. ratios) and the significances of the changes (e.g. P values). The expression changes of genes from a given family are displayed on the pathway separately for each individual gene.

This is a more accurate representation than using average or extreme values, since genes from the same family often behave differently. In addition, tables listing the absolute values of quantitative changes as well as the significance of the changes of all the genes and metabolites in the pathway are provided in the system.

Plant MetGenMAP expression profiling platforms --

Plant MetGenMAP currently supports different expression profiling platforms for several major plant organisms, including:

1) ATH1 genome array and The Arabidopsis Information Resource (TAIR) Arabidopsis Genome Initiative locus number for Arabidopsis;

2) Affymetrix genome array and genome locus number for rice (Oryza sativa); and

3) TOM1 array, TOM2 array, Affymetrix genome array, and Solanaceae Genome Network (SGN) unigenes for tomato.

More platforms from additional plant species can be easily added to the system.

New organisms added to Plant MetGenMAP --

Soybean, Grape and Brachypodium were added to Plant MetGenMAP based on their genome predicted genes as of July, 2010.

System Requirements

Web-based and Plant MetGenMAP also operates on a Linux system under an Apache Web server, and the majority of the functions in the system were implemented with Perl/CGI or R scripts.


Manufacturer Web Site Plant MetGenMAP

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G6G Abstract Number 20678

G6G Manufacturer Number 104317