GenoMesh: MeSH-based genome-wide literature mining

Welcome to GenoMesh!

With the rapid advancement of information technology, it is of growing interest to efficiently mine literature information source to gain insights, and to assist in the interpretation/annotation/verification of from the results of laboratory experiments. The controlled vocabulary of medical and scientific terms annotated by experts (MeSH) is the National Library of Medicine’s controlled vocabulary for biology and medicine and is used to index articles in PubMed. GenoMesh is a web-based program based on MeSH.

Specifically, GenoMesh is a genome-wide, MeSH-based dissimilarity measurement algorithm to assess the relationships between any two genes among the whole genome of a particular organism. Determination of gene relatedness is based on comparing the frequency of MeSH terms appearing in the literature that refer to each of the genes. The MeSH term dissimilarity scores between all possible gene pairs in single microbial organism were calculated using a GenoMesh procedure. The results of studies with two bacterial species Brucella and E. coli demonstrate that GenoMesh can reveal subtle relatedness among bacterial genes and biological pathways. Hierarchical clustering analysis based on GenoMesh groups closely related bacterial genes together. The average dissimilarity scores among genes within known E. coli pathways are significantly smaller than randomly chosen genes. The GenoMesh can recognize closely related gene pairs despite the fact that they are not cited in the same publication. This program also permits prediction of gene-to-gene relationships based on the results of cross-species comparison.

This is the web server to implement a GenoMesh algorithm for calcuating and exploring genome-wide gene-to-gene relationships and pathways based on MeSH. The GenoMesh server allows users to query a GenoMesh MySQL database that stores all downloaded literature information and calucated results out of the GenoMesh algorithm. The interface is constructed using a variety of scripts including PHP and Perl. This web server includes the following four programs:

GeneMesh: GeneMesh identifies all genes that have individual dissimilarity scores associated to a specific queried gene with a value less than a dissimilarity threshold.
GenePair: GenePair calculates the dissimilarities between two queried genes using the GenoMesh algorithm, and outputs rank and P value.
GeneCluster: GeneCluster groups all genes within a specified genome by hierarchical clustering.
GeneNet: GeneNet outputs a network among a list of input genes based on the GenoMesh algorithm.
MeshBrowse: MeSHBrowse allows users to browse the MeSH hierarchy tree and assigns genes to individual MeSH terms.
GOBrowse: GOBrowse allows users to browse the GO hierarchy tree and assigns genes to individual GO terms.

Expansion of application of this system to include other species of living systems and the addition of other features to enhance its use for examining biological system is currently underway.