Data and Software

1. TF/DNA structure
   tFIRE takes standard PDB format for TF/DNA structures. 
   1. A good place to look for such data is PDB (Rose et al., 2011) (http://www.pdb.org). 
   2. If  the TF/DNA complex structure does not exist but the TF structure exists, you can generate the TF/DNA structure by docking DNA to the TF structure. Software that can be utilized for this includes HADDOCK (De Vries et al., 2007) (http://www.nmr.chem.uu.nl/haddock), FTDOCK (Jackson R.M. et al., 1998) (http://www.sbg.bio.ic.ac.uk/docking/ftdock.html), YASARA DOCK (http://www.yasara.org/dnadock.htm), ParaDock (Banitt and Wolfson, 2011) (http://www.paradocks.org). Our method indicates that such docking will not affect a result significantly but we have not tested any of these docking predictions ourselves for validation. Hence we urge their use with caution, and revalidate the results once the structures are available. 
   3. If the TF structure does not exist in 3D structure databases, you can predict TF structure using homology modeling like SWISS-MODEL (Guex and Peitsch, 1997) (http://swissmodel.expasy.org), Rosetta (Bradley et al., 2003) (https://www.rosettacommons.org), Sybyl (Visegrády et al., 2001) (http://www.tripos.com/index.php?family=modules,SimplePage,,,&page=SYBYL-X). Please use with caution that each prediction step would reduce the accuracy.
      
      
2. Predict TFBSs
    tFIRE predicted motif(PWM) can be used to predict TFBSs. 
   1. Motif scanning programs can be used to scan the whole genome for motif matches. Such methods included MAST (Bailey et al., 2006) (http://meme.nbcr.net/meme/cgi-bin/mast.cgi) from MEME suite and STORM (Schones et al., 2007) (http://rulai.cshl.edu/storm) from Cold Spring Harbor Laboratory.
   2. TFBSs vary for different cells. Recently, a newly developed method, CENTIPEDE (Pique-Regi et al., 2010) (http://centipede.uchicago.edu) shows that with the result from a single DNase-seq experiment, one can accurately predict TFBSs for all TFs. Therefore, downloading DNase-seq data from ENCODE project can be very helpful.
   3. Recently developed FAIRE-seq technology allow similar predictions for detection of chromatin accessibility regions (Song et al., 2011). Such data can be substituted for DNase-seq, but needs be tested and validated before use. 
   4. Epigenetic information can also be employed instead of DNase-seq (Cuellar-Partida et al., 2012). We propose to update our data and methods available for such predictions on a regular basis. 
      
   
   
3. Software
   1. C++ software environment, better with Linux system
   2. tFIRE, Feel Free to ask the author for a linux version
   3. WebLogo (Crooks et al., 2004) can be used for visualization the PWM we predicted (http://weblogo.berkeley.edu) 
      
      

Procedure