Table 1

Outline of features for GeneMesh and other web tools with MeSH analysis capabilities.

Feature

GeneMesh

Gendoo

MeSHer

HuGE Navigator

Map gene(s) to MeSH categories^a

Yes

Yes

Yes

Yes

Browse MeSH relationships^b

Yes

Yes

Yes

Yes

Microarray platform independence^c

Yes

Yes

-

Yes

Capable of analyzing a group of genes^d

Yes

Yes

Yes

-

Significance analysis of MeSH categories^e

Yes

Yes

Yes

-

Significance analysis threshold is adjustable^f

Yes

-

Yes

-

Expression data upload^g

Yes

-

-

-

Graphical display of expression data (e.g., heatmaps, tables)

Yes

-

-

-

MeSH output can be viewed by functional attributes (e.g., KEGG pathway, Gene Ontology, NCBI interaction)^h

Yes

-

-

-

Web 2.0 design

Yes

-

-

-

^a Software identifies links between MeSH categories and genes

^b Software offers a browser feature to navigate through gene associations and/or the MeSH framework

^c Software analyzes based on gene name, symbol or ID as opposed to a sequence identifier associated with a specific microarray platform

^d Software can analyze a group of input genes as opposed to a single gene

^e Software performs a statistical analysis to identify significant MeSH categories for the input gene set

^f Threshold for significance analysis can be adjusted to govern stringency

^g Software will upload expression data together with the gene set

^h Output is presented to facilitate browsing of other functional attributes, including KEGG pathway, Gene Ontology, and NCBI interactions

Jani et al. BMC Bioinformatics 2010 11:166   doi:10.1186/1471-2105-11-166