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Please NOTE:  the data are listed in reverse chronological order (except the info on the SV40 overlap function).


Below are the .bed files for the HOXA locus, built hg17 (May 2004), for the article by: M. Bina, P. Wyss, S.A. Lazarus, S.R. Shah, W. Ren, W. Szpankowski, G.E. Crawford, S.P. Park, and X.C. Song

Title: Discovering sequences with potential regulatory characteristics

 Genomics.  93:314-22 (2009)




To upload the files on the genome browser at UCSC, first save the bed files on your computer.  Remove the word txt from the file name, in order to get a .bed file.

Subsequently, go to http://genome.ucsc.edu/cgi-bin/hgGateway?hgsid=108903885&clade=vertebrate&org=Human&db=hg17

Click on manage custom tracks, then upload the files.

If you encounter problems, please contact Minou Bina; use the email link on the top of this page



Overlap function for experimentally determined SV40 nucleosome positions


Accession number for Simian virus 40, complete genome NC_001669


If you use the SV40 data, please cite the following article:

Ambrose C, Lowman H, Rajadhyaksha A, Blasquez V, Bina M.  Location of nucleosomes in simian virus 40 chromatin.J Mol Biol. 214, 875-84 (1990).



The Toolkit for  the following publication:

Phillip Wyss, Sheryl A. Lazarus, and Minou Bina: A Program Toolkit for the Analysis of Regulatory Regions of Genes Methods in Molecular Biology.  Bina M. ed.  Humana Press.




 If you use the Toolkit, please cite the publication




Information on the following publication:

Bina M, Wyss P, Ren W, Szpankowski W, Thomas E, Randhawa R, Reddy S, John PM, Pares-Matos EI, Stein A, Xu H, Lazarus SA. Exploring the characteristics of sequence elements in proximal promoters of human genes. Genomics. 2004 Dec;84(6):929-940.


-    The database described in the article can be queried at the following site:



-    The following file includes all possible 9mer pairs and their corresponding IDs:


- The following file includes the 9-mers  that were found 3 or more times in proximal promoters of human genes localized with respect to experimentally assigned transcription initiation site.


                        GenBank Accession numbers

- The following file includes the 9-mers were found in proximal promoters of human genes that were localized with respect to ESTs:


- The following file includes the predicted correspondence of the collected 9-mers to potential transcription factor binding sites.


-  The following files include the predicted targets of the CREB family of transcription factors:



-  The following files include the predicted targets of the ETS family of transcription factors:



- The following files include Perl Scripts useful for data collection: