Table 1

A comparison of web-based GO enrichment tools.

Tool

P-value and statistical method

Flexible threshold

Graphical visualization

Multiple organisms

Running time


GOrilla

Exact mHG p-value computation (no need for simulations)

+

+

+

7 Sec


Fatiscan [13]

Fischer Exact (FDR corrected for number of thresholds)

+

(predetermined steps of 30)

-

+

30 Min


GO-stat [14]

Wilcoxon Rank-Sum/Kolmogorov Smirnov

+

-

+

2 Min


GOEAST [9]

Hypergeometric

-

+

+

20 Min


SGD [11]

Hypergeometric

-

+

-

(only yeast)

2 Min


DAVID [7]

Modified Fischer Exact

-

-

+

2 Min


GOTM [10]

Hypergeometric

-

+

+

2 Min


GoMiner [3]

Fisher Exact

-

-

(only in the downloadable version)

+

7 Min


Different GO enrichment tools employ a wide range of statistics and yield different performances. The main features of five different web-based tools are compared to GOrilla. To enable a fair comparison all tools were used using default parameters via their web interfaces and applied on the van't Veer dataset. One exception is the SGD tool that only runs on yeast data and was therefore tested on a set of 543 yeast genes and the default background for running time characterization. The GOrilla running time for this yeast dataset was also 7 seconds. The running time was measured for the entire analysis, including uploading files and getting the results.

Eden et al. BMC Bioinformatics 2009 10:48   doi:10.1186/1471-2105-10-48

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