ArraySearch: A Web-Based Genomic Search Engine

Table 1

A comparison of genomic search engine features.

	ArrayExpress	Oncomine	plexDB	Genevestigator	ArraySearch
[1] Website	http://www.ebi.ac.uk/gxa/	http://oncomine.org/	http://www.plexdb.org/	https://www.genevestigator.com/	http://ArraySearch.org/
[2] Microarray data source	ArrayExpress	ArrayExpress, GEO, SMD	AtGenExpress, NASCArrays, TAIR, datasets uploaded by plexDB curators	AtGenExpress, NCBI GEO, TAIR, ArrayExpress, NASCArrays, other sources …	NCBI GEO
[3] Species	Arabidopsis+others	Human	Arabidopsis+others	Arabidopsis+others	Arabidopsis
[4] statistical analysis
[4.1] Query gene correlation with contrasts	No	No	No	No	Yes
[4.2] Query gene correlation by gene ontology	No	No	No	No	Yes
[4.4] User-defined expression profile query	No	No	No	No	Yes
[4.5] Correlation between query gene/samples	No	No	No	No	Yes
[5] Graphical output of gene coexpression	Heatmap	Scatter plot	Line graph/hierarchical Clustering	Line Graph	Heatmap/bargraph
[6] Output: coexpression scores between query genes	No	No	Yes	Yes	No
[7] References	Parkinson et al. [10]	Rhodes et al. [5]	Wise et al. [4]	Hruz et al. [2]