GeneMesh: a web-based microarray analysis tool for relating differentially expressed genes to MeSH terms

BMC Bioinformatics

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	-	-	-

^aSoftware identifies links between MeSH categories and genes
^bSoftware offers a browser feature to navigate through gene associations and/or the MeSH framework
^cSoftware analyzes based on gene name, symbol or ID as opposed to a sequence identifier associated with a specific microarray platform
^dSoftware can analyze a group of input genes as opposed to a single gene
^eSoftware performs a statistical analysis to identify significant MeSH categories for the input gene set
^fThreshold for significance analysis can be adjusted to govern stringency
^gSoftware will upload expression data together with the gene set
^hOutput is presented to facilitate browsing of other functional attributes, including KEGG pathway, Gene Ontology, and NCBI interactions

ISSN: 1471-2105