GenoMesh

Category Cross-Omics>Data/Text Mining Systems/Tools

Abstract GenoMesh is a genome-wide literature mining system. It does genome-wide analysis of gene-to-gene relationships and pathways based on the association between individual genes and Medical Subject Headings (MeSH) terms obtained from literature.

The primary users of GenoMesh are biologists and bioinformaticians who are interested in genetic interactions and biological pathways.

Specifically, GenoMesh is a genome-wide, MeSH-based dissimilarity measurement algorithm used 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 manufacturers downloaded all possible E. coli and Brucella-related publications from PubMed, including their titles, abstracts, and MeSH terms. Specific E. coli and Brucella genes are retrieved from the downloaded items.

The matrices between these genes and their associated MeSH terms collected from corresponding papers are then generated.

These gene-MeSH matrices are the essential data used for later calculation of gene-to-Mesh and gene-to-gene relationships. These matrices can be considered similar to DNA microarray data (intensity of gene x condition).

Each MeSH term is like a condition in a microarray experiment, and the number of the occurrences of each MeSH term in a gene-MeSH matrix is like the intensity of a gene under one condition detected by microarray.

GenoMesh can recognize closely related gene pairs despite the fact that they are Not cited in the same publication. This system also permits prediction of gene-to-gene relationships based on the results of cross- species comparison.

GenoMesh is one of the first algorithms and web-based systems to investigate genome-wide gene-to-gene relationships and pathways.

The formula the manufacturers developed for calculating the dissimilarity between any two genes in this setting is the most specific and sensitive and has Not been used in existing publications.

GenoMesh is expected to have significant impacts in literature mining and bioinformatics. It is one of the first approaches to study genome- wide gene-to-gene interactions and pathways using a 'microarray-type of analysis' based on published papers.

The manufacturer's studies show that GenoMesh can Not only retrieve known gene-to-gene relationships published in literature, but it can also predict unknown gene-to-gene relationships and pathways.

The manufactures created a web server to implement the 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 [a relational database management system (RDBMS)] that stores all downloaded literature information and calculated results out of the GenoMesh algorithm.

The interface is constructed using a variety of scripts including PHP [PHP is a widely-used general-purpose scripting language that is especially suited for web development and can be embedded into HyperText Markup Language (HTML)] and Perl (Perl is a high-level, general-purpose, interpreted, dynamic programming language).

This GenoMesh web server includes the following six (6) programs:

1) GeneMesh -- GeneMesh identifies all genes that have individual dissimilarity scores associated to a specific queried gene with a value less than a dissimilarity threshold.

GeneMeSH Query - The GeneMeSH query page displays three (3) sections when you select a gene.

2) GenePair -- GenePair calculates the dissimilarities between two queried genes using the GenoMesh algorithm, and outputs rank and P value.

GenePair query - GenePair query page displays two (2) sections when you select a gene pair.

3) GeneCluster -- GeneCluster groups all genes within a specified genome by hierarchical clustering.

4) GeneNet -- GeneNet outputs a network among a list of input genes based on the GenoMesh algorithm. Given a list of genes, GeneNet will return all the closely related gene pairs among the set of genes and a graphical representation of the relations.

The results can be filtered by changing the minimum number of publications for each gene and the minimum P value.

5) MeSHBrowse -- MeSHBrowse allows users to browse the MeSH hierarchy tree and assigns genes to individual MeSH terms. The MeSHBrowse lists all the MeSH terms in a hierarchical tree structure. Each term has a number next to it.

This number represents the number of genes related to this term. Clicking this number will load the gene list. Also, the closely related gene pairs among the set of genes and a graphical representation of the relations will be displayed.

6) GOBrowse -- GOBrowse allows users to browse the Gene Ontology (GO) hierarchy tree and assigns genes to individual GO terms. The GOBrowse lists all the GO terms in a hierarchical tree structure. Each term has a number next to it.

This number represents the number of genes related to this term. Clicking this number will load the gene list. Also, the closely related gene pairs among the set of genes and a graphical representation of the relations will be displayed.

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

System Requirements

Contact manufacturer.

Manufacturer

Manufacturer Web Site GenoMesh

Price Free

G6G Abstract Number 20307

G6G Manufacturer Number 101201