Table 4 Summary of the comparison between different similar tools in the public domain to that of GeneACT

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