Resource Report

URL: http://avis.princeton.edu/mefit/

Proper Citation: MEFIT (RRID:SCR_010743)

Description: MEFIT is a Microarray Experiment Functional Integration Technology. Given any amount of microarray data, it predicts the probability of pairwise functional relationship for any gene pair within individual biological functions. This web site makes the results of this evaluation available for download and provides an online view of the test set predictions based on hierarchical clustering. As a framework, MEFIT uses the results of many microarray experiments in combination with known biological process annotations (drawn from the Gene Ontology, KEGG, MIPS, or a biologist''s own pathways of interest) to predict new gene pair functional relationships within the given biological functions. Or in other words, MEFIT is a system that takes microarray results and known functional annotations as inputs and produces predicted gene pair functional relationships as output. To make these predictions, MEFIT uses a Bayesian network that consumes microarray data as input observations and produces predicted functional relationships through a single unobserved (except during training) node. Furthermore, to make predictions within the context of individual biological functions, a single Bayesian network structure is replicated once per function of interest. These networks with identical structure are then trained using known functional annotations such that each function''s network learns its own set of conditional probabilities. These probabilities encode how predictive each microarray experiment is of a particular function; for example, a sporulation time course might be very predictive of meiosis, but not much help in determining which genes perform ATP synthesis. We''ve evaluated this system using a collection of 40 microarray data sets and 200 biological processes. Select a biological function from the menu to view the results of clustering the S. cerevisiae genome using MEFIT''s test set predictions within that function as a similarity metric. Alternatively, enter a gene name or ORF identifier to list only functions in which that gene is predicted to be active. We are currently able to offer for download: The MEFIT README file, a Windows version and Linux version.

Abbreviations: MEFIT

Synonyms: Microarray Experiment Functional Integration Technology

Resource Type: service resource, data analysis service, software resource, production service resource, analysis service resource

Defining Citation: PMID:17005538