BETA

Binding and Expression Target Analysis (BETA) is a software package that integrates ChIP-seq of transcription factors or chromatin regulators with differential gene expression data to infer direct target genes. BETA has three functions: (1) to predict whether the factor has activating or repressive function; (2) to infer the factor’s target genes; and (3) to identify the motif of the factor and its collaborators which might modulate the factor’s activating or repressive function. Here we describe the implementation and features of BETA to demonstrate its application to several datasets. BETA requires ~2GB RAM and 1h for the whole procedure.

BETA is a free software to do Transcription Factor and Chromatin Regulator target analysis.
Three subcommands of BETA make it user friendly.

BETA basic: TF activating and repressive function prediction and direct targets detecting.
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BETA plus: TF activating and repressive function prediction, direct targets detecting and motif analysis on target regions.
Read More
BETA minus: TF target genes prediction based on regulatory potential score with only binding data.
Read More

Wang, S., Sun, H., Ma, J., Zang, C., Wang, C., Wang, J., ... & Liu, X. S. (2013). Target analysis by integration of transcriptome and ChIP-seq data with BETA. Nature protocols, 8(12), 2502-2515.

PMID: 24263090

Click HEREhere to run BETA on our web server at Cistrome

BETA Version 1.0.7 is now available

BETA Download

Test Data Download

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Before installing BETA, make sure the following software is installed in system:

1. Python2.6 or newer.

2. R 2.13.1 or newer.

3. GNU Compiler Collection (GCC).

Then follow the steps (Ubuntu / MacOS) one by one to finish the installation of BETA

For Ubuntu:

1. Install setuptools and argparse
$ sudo apt-get install curl
$ curl http://python-distribute.org/distribute_setup.py | sudo python
$ sudo easy_install argparse

2. Install numpy
The easier way:
$ sudo apt-get install python-numpy
An alternative way is to install from source code:
$ sudo apt-get install git python-dev
$ git clone git://github.com/numpy/numpy.git
$ cd numpy
$ python setup.py build
$ python setup.py install
If neither way works (which is hardly possible), you could go to Numpy for some help.

3. Install BETA
Download the zip file
$ unzip BETA_1.0.2.zip
$ cd BETA_1.0.2
$ sudo python setup.py install

For MAC OS:

1. Install setuptools and argparse
$ curl http://python-distribute.org/distribute_setup.py | sudo python
$ sudo easy_install argparse

2. Install git
download the dmg file from http://code.google.com/p/git-osx-installer then double click the file to install

3. Install numpy
$ git clone git://github.com/numpy/numpy.git
$ cd numpy
$ python setup.py build
$ python setup.py install
If it does not work, you could go to Numpy for some help.

4. Install BETA
Download the zip file from http://cistrome.org/BETA/
$ unzip BETA_1.0.2.zip
$ cd BETA_1.0.2
$ sudo python setup.py install

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If not sudo or want to install it for your own
$ python setup.py install --prefix=[your path]
Modify PYTHONPATH if necessary by adding the following two lines in your .bashrc (or .bash_profile of mac) file in home directory.
$ export PATH=/your_directory/bin:$PATH
$ export PYTHONPATH=/your_directory/lib/python2.X/site-packages/:$PYTHONPATH
$ BETA

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For server behind proxy:

1. Download the proper python-dev:
For CPU amd64 (most CPU are amd64), download it from http://ftp.us.debian.org/debian/pool/main/p/python2.7/libpython2.7_2.7.5-4_amd64.deb
Then upload it to the server.
On server,
$sudo dpkg -i libpython2.7_2.7.5-4_amd64.deb

2. Install setuptools:
Download the egg file of setuptools, get the newest version from https://pypi.python.org/packages/2.7/s/setuptools/
Upload it to the server
On server,
$ sudo sh setuptools-0.6c11-py2.7.egg

3. Install numpy:
Download numpy from https://github.com/numpy/numpy/archive/master.zip
Upload it to the server
On server,
$ cd numpy-master
$ python setup.py build
$ python setup.py install
If it does not work, refer to the INSTALL.txt under numpy-master directory.

4. Install BETA
Download the zip file from http://cistrome.org/BETA/
Upload it to the server
On server,
$ unzip BETA_1.0.2.zip
$ cd BETA_1.0.2
$ sudo python setup.py install

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