GenMAPP

Category Cross-Omics>Pathway Analysis/Tools

Abstract GenMAPP (Gene Map Annotator and Pathway Profiler) is a free computer application designed to visualize gene expression and other genomic data on maps representing 'biological pathways' and groupings of genes.

Integrated with GenMAPP are programs to perform a global analysis of gene expression or genomic data in the context of hundreds of 'pathway MAPPs' and thousands of Gene Ontology Terms (MAPPFinder - see below), import lists of genes/proteins to build new MAPPs (MAPPBuilder - see below), and export archives of MAPPs and expression/genomic data to the web.

The main features/capabilities underlying GenMAPP are:

GenMAPP facilitates the analysis, organization and sharing of data produced in genomic-scale experiments, such as DNA microarray experiments. Instead of overwhelming researchers with long lists of un- annotated data, GenMAPP allows you to visualize gene expression data in a 'biological context' with the graphical and more intuitive format of MAPPs.

Note: A MAPP is a GenMAPP-produced file that graphically shows the 'biological relationship' between genes or gene products. MAPPs can be used to group genes and view data by any organizing principle.

Examples of the types of MAPPs that can be represented in GenMAPP are 'metabolic pathways', 'signal transduction cascades', sub cellular locations, gene families, or lists of genes associated with Gene Ontology (GO) categories.

Each MAPP contains 'gene objects', which represent biological genes or gene products. The MAPP also contains symbols that depict other objects, such as receptors, membranes and ribosomes, and the relationships among the objects.

Each gene object on a MAPP is identified by a 'gene identifier' from one of the GenMAPP accepted gene ID systems (GenMAPP accepts gene expression data from both custom arrays and commercial microarrays such as Affymetrix GeneChips).

That gene identifier is used by the GenMAPP program to link information from a GenMAPP Gene Database (A 'GenMAPP Gene Database' is a species-specific library of all genes used by GenMAPP and its accessory programs.

Specifically, the Gene Database stores all the gene identifiers required to link 'gene objects' on MAPPs to expression data contained in an Expression Dataset), to the 'gene object' for annotation shown on a 'Backpage' (Each Backpage is a separate 'web page' shown in MS Internet Explorer that contains the data and annotation associated with that 'gene object').

The gene identifier is also used to link that gene object to data in an 'Expression Datasets' for coloring the gene object.

Note: 'Expression Datasets' may be imported into GenMAPP from data produced by your own experiment. The Expression Dataset can consist of several different components.

Expression Datasets are independent of MAPPs and applied dynamically to them. One MAPP, then, can have any number of Expression Datasets applied to it and one Expression Dataset may be applied to any number of MAPPs.

MAPPBuilder -- is an accessory application for GenMAPP. Given a list of gene IDs, MAPPBuilder automatically creates a MAPP file containing those genes that can be viewed and modified with the GenMAPP Program.

A MAPP generated from MAPPBuilder will Not contain any graphics from the Drafting Toolbar except for gene objects and the label. Other tools can be added to the MAPP after it is created with MAPPBuilder.

MAPPFinder -- is an accessory program that works with GenMapp and the annotations from the Gene Ontology (GO) Consortium to 'identify global biological trends' in gene expression data.

MAPPFinder relates microarray data meeting a user-defined criterion for a "significant" change to each term in the Gene Ontology hierarchy, calculating the percentage of genes changed for each GO biological process, cellular component, and molecular function term.

MAPPFinder then calculates a cumulative total of genes changed for a parent GO term and all of its children and a statistical score, giving a complete picture of the gene expression changes associated with a particular GO term.

Furthermore, this MAPPFinder analysis can be performed on a set of MAPPs local to a user's computer, calculating the percentage of genes meeting the criterion for each MAPP.

System Requirements

The current GenMAPP has been written in Visual Basic and is therefore limited to computers running the Windows operating system, including Macintosh computers running Boot Camp or Parallels.

The next version of GenMAPP will have a platform-independent implementation. For information on current open-source development and how to participate, click here: GenMAPP.

Manufacturer

Manufacturer Web Site GenMAPP

Price Free.

G6G Abstract Number 20219

G6G Manufacturer Number 101131