TFAT - Transcription Factor Analysis Toolkit

Created by Lucas Felipe

The TFAT (TRANSCRIPTION FACTOR ANALYSIS TOOLKIT) web tool provides access to the collected FT data, allowing:

• TF Enrichment: The analysis and identification of the TF associated with a list of genes; TF Check: Check of a list of TF;
• TF Prediction: Prediction using HOCOMOCO PWMs for DNA sequences;
• Custom configurations by the user in their queries such as the degree of scalable precision of the TF, tissue expression, data contained in public databases, ChIP-seq experiments and prediction;
• Filters integrated into the results;

In our database, we collected a total of 16.462.707 associations between the transcription factor and gene, with 26.065 target genes and 1.172 transcription factors. These data are derived from several tools, classified into three methodologies: public databases, CHIP-Seq experiments and PWM predictions. These are six libraries that allow us to identify the enrichment Transcription Factors of a list of genes using as data source Enrichr, HTRIdb, UCSC/ENCODE, GTRD, ChIP-Atlas and HOCOMOCO PWMs.

This is an alternative that integrates several data sources, from the most diverse methodologies on FT, making it complement the existing proposals for TF enrichment analysis.

Software Required:

PHP 7.2 Server

• Recommended: Apache HTTPD 2.4

Database Server:

• MariaDB 5.5 (download here)

Python 2.7:

• With SciPy package installed

Configuration

Edit the information in the 'model/TFATConfig.php' file:

function getTFATServerAddress(){
    return "127.0.0.1";
}

function getPythonPath(){
    return "python";
}

function getMysqli(){
    $mysqlUser = "<insert_username>";
    $mysqlUserPasswd = "<insert_password>";
    $dbName = "tfat_db";
    $mysqlAddress = "127.0.0.1";

    $mysqli = new mysqli($mysqlAddress, $mysqlUser, $mysqlUserPasswd, $dbName);
    return $mysqli;
}

Create the database

The SQL script 'create_db.sql' creates a database named 'tfat_db' with all the information required for the TFAT server. Download it here (475M)