Table 4 |
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|
Summary of the comparison between different similar tools in the public domain to that of GeneACT |
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|
GeneACT [30] |
oPOSSUM [13] |
OTFBS [52] |
Clover [53] |
Whole Genome rVISTA beta [3] |
CRÈME [15] |
|
|
|
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|
Graphical user interface |
Web based |
Web based |
Web based |
Command line tool for Linux, UNIX and Mac OS X |
Web based |
Web based |
|
Genomic display |
Yes |
No |
No |
No |
Yes |
No |
|
Type |
Promoter specific |
N/A |
N/A |
N/A |
Gene specific |
N/A |
|
Display motifs on custom sequences |
Yes |
N/A |
N/A |
N/A |
N/A |
N/A |
|
Allow custom sequences input |
Yes |
N/A |
N/A |
N/A |
N/A |
N/A |
|
Source of the transcription factor binding sites |
TFD |
JASPAR |
TRANSFAC |
JASPAR |
TRANSFAC |
TRANSFAC |
|
Number of binding sites in the database |
>7000 |
111 |
>500 |
111 |
>500 |
>500 |
|
Search for over-represented binding site |
Yes |
Yes |
Yes |
Yes |
Yes |
Yes |
|
In promoter region |
Yes |
Yes |
Yes |
Yes |
Yes |
Yes |
|
In 3'-UTR |
Yes |
No |
No |
No |
No |
No |
|
Across genomes |
Human, mouse and rat |
Human and mouse |
No |
No |
Yes |
Human |
|
Species supported (using Locuslink, Entrez gene ID, Ensembl ID, etc.) |
Human, mouse and rat |
Human and mouse |
No |
No |
Mouse only |
Human |
|
Number of genes/sequences allowed |
Unlimited IDs |
Unlimited IDs |
200 sequences |
Not tested |
Unlimited IDs |
Unlimited IDs |
|
Allow custom control gene set |
Yes |
Yes |
No |
Yes |
No |
No |
|
Correctly predicted E2F4 binding sites in the T98G dataset |
Yes |
No |
N/A |
N/A |
N/A |
Yes |
|
Identified E2F-binding sites in the T98G dataset |
Yes |
Yes |
N/A |
N/A |
N/A |
Yes |
|
Search for potential miRNA involved in the dataset |
Yes |
No |
No |
No |
No |
No |
|
Source for the miRNA seed sequences |
miRbase |
N/A |
N/A |
N/A |
N/A |
N/A |
|
Across genomes |
Human, mouse and rat |
N/A |
N/A |
N/A |
N/A |
N/A |
|
Species supported |
Human, mouse and rat |
N/A |
N/A |
N/A |
N/A |
N/A |
|
Number of genes/sequences allowed |
Unlimited |
N/A |
N/A |
N/A |
N/A |
N/A |
|
Allow custom control gene set |
Yes |
N/A |
N/A |
N/A |
N/A |
N/A |
|
|
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|
Only programs that have web interfaces and allow unlimited Gene IDs are tested using the T98G dataset. The website addresses for each of the programs evaluated are given in the references provided in the top row. N/A represents a category that is not available. E2F, elongation factor 2; miRNA, microRNA; UTR, untranslated region. |
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|
Cheung et al. Genome Biology 2006 7:R97 doi:10.1186/gb-2006-7-10-r97 |
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