TACO: Transcription factor Association from Complex Overrepresentation

Overview

   TACO, or Transcription factor Association from Complex Overrepresentation,
   is a program to predict overrepresented motif complexes in any genome-wide
   set of regulatory regions.

   See http://bioputer.mimuw.edu.pl/taco/ for the latest version.

Installation instructions

   TACO is written in C++ and should run on any Unix-like operating system,
   such as Linux and Mac OS X. To compile it, run make. After a successful
   compilation, the executable file src/taco could be copied to a system-wide
   directory, such as /usr/local/bin.

   TACO makes use of the standalone R math library (libRmath). If you
   encounter `fatal error: Rmath.h: No such file or directory', install the
   package named either libRmath-devel or r-mathlib (depending on the system
   distribution). Note that providing only the Rmath.h (or path to it) will
   not be sufficient. If you encounter any problems with the compilation,
   first check if you have libRmath.so properly installed; usually it is
   found in /usr/lib or /usr/lib64.

Example specifications

   In the release package, a few example specification files are provided. To
   repeat the analyses, you will need:

     * the reference [1]human (hg19) genome (FASTA format)
     * a motif database – use either [2]TRANSFAC (commercial), [3]JASPAR or
       [4]SwissRegulon
     * a list of input datasets (narrowPeak or BED format).

   We provide example lists of UW and Duke open chromatin datasets, as well
   as the respective URLs of narrowPeak files to be downloaded from the
   [5]ENCODE Project. To download the latter ones, go to the
   wgEncodeUwDnase_hg19 or wgEncodeOpenChromDnase_hg19 subdirectory and run
   wget -i urls.list.

   We also provide example list of K562 ChIP-seq peaks, and the respective
   URLs, in similar manner. To repeat this analysis, for each dataset you
   will also need the top 5 motifs found in ChIP-seq peaks using [6]MEME.
   They can be downloaded from [7]Factorbook or generated locally.

Contact

   If you have any questions or comments, please contact Aleksander
   Jankowski <ajank@mimuw.edu.pl>.

References

   1. http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz
   2. http://www.biobase-international.com/product/transcription-factor-binding-sites
   3. http://jaspar.genereg.net/
   4. http://swissregulon.unibas.ch/
   5. http://genome.ucsc.edu/ENCODE/
   6. http://meme.nbcr.net/meme/
   7. http://www.factorbook.org/