Tool to identify genes with similar expression profiles to a query gene
Benefits and Features
- Overcomes the bottleneck in comparing different experiments by using the meta-data from microarray experiments rather than using the actual expression values obtained from raw data
- Displays genes that show expression profiles similar to that of your gene of interest
- Displays known interactions among genes with similar expression profiles
- Displays experimental conditions that most affect the presented genes
Overview
Microarray and next generation sequencing technologies have generated a huge amount of genome scale expression data. Microarray Meta-Miner (MMM) provides researchers with an easy tool to identify genes with similar expression profiles to a query gene. Using the microarray meta data from the ATLAS gene expression database and the NIH Biowulf cluster computing facility, eight different vector similarity metrics are computed (Pearson/Spearman/Kendall correlation coefficients, mutual information, chi-square, Euclidean distance, purity, and cosine similarity) for every gene’s expression profile against every other gene’s profile. Top scoring hits from the individual metrics are integrated and scored for overlap, generating a matrix of similar expressions. The MMM Web tool returns the list of similarly expressed genes for the user’s query, along with links to annotations, individual expression profiles, and all expression profiles. MMM also retrieves and displays the known interaction data between the similarly expressed genes from the STRING interaction database. The experiment distribution information for the set of similarly expressed genes is also displayed.
Access
NIAID provides the MicroArray Meta-Miner free of charge.
Background
The NIAID Office of Cyber Infrastructure and Computational Biology created MicroArray Meta-Miner.