[Genome] Drosophila ChIP/chip

[Ann Zweig]

Hello Mark,

	Our team is looking at your data and discussing the possibility of hosting it 
on our website.  We will get back to you off-list with any questions.


Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu



Mark Biggin wrote:
> Dear UCSC team, we wonder if you would be interested in including ChIP/ 
> chip data produced by the Berkeley Drosophila Transcription Network  
> Project as a track on your browser? For now we would suggest providing  
> 1% and 25% False Discovery Rate thresholded data for 7 sequence  
> specific transcription factors and RNA polymerase. Wiggle files of the  
> 1% FDR data are at the links below, so you can get a sense of the  
> data. (these are to Release 4 of the mel genome sequence). We could  
> improve the appearance and add color if you agree to host these.
> 
> http://rana.lbl.gov/~smacarth/ChIPChip/Public_Release/wiggle/bcd_1_012505-sym-1.wig
> http://rana.lbl.gov/~smacarth/ChIPChip/Public_Release/wiggle/bcd_2_092005-sym-1.wig
> http://rana.lbl.gov/~smacarth/ChIPChip/Public_Release/wiggle/cad_1_020107-sym-1.wig
> http://rana.lbl.gov/~smacarth/ChIPChip/Public_Release/wiggle/gt_2_020107-sym-1.wig
> http://rana.lbl.gov/~smacarth/ChIPChip/Public_Release/wiggle/hb_1_012505-sym-1.wig
> http://rana.lbl.gov/~smacarth/ChIPChip/Public_Release/wiggle/hb_2_092305-sym-1.wig
> http://rana.lbl.gov/~smacarth/ChIPChip/Public_Release/wiggle/kni_1_092706-sym-1.wig
> http://rana.lbl.gov/~smacarth/ChIPChip/Public_Release/wiggle/kni_2_092706-sym-1.wig
> http://rana.lbl.gov/~smacarth/ChIPChip/Public_Release/wiggle/kr_1_113005-sym-1.wig
> http://rana.lbl.gov/~smacarth/ChIPChip/Public_Release/wiggle/kr_2_113005-sym-1.wig
> http://rana.lbl.gov/~smacarth/ChIPChip/Public_Release/wiggle/polII_8WG16_092905-sym-1.wig
> http://rana.lbl.gov/~smacarth/ChIPChip/Public_Release/wiggle/z_2_051504-sym-1.wig
> 
> Our data are particularly well justified and of high quality. In  
> addition, our interpretation and analysis of the in vivo DNA binding  
> data differ significantly from most others, emphasizing differences in  
> the classes of region bound at different levels and showing that many  
> weakly bound regions are likely to be non functional. This is  
> explained in our recent PLoS Biology paper.
> http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pbio.0060027
> 
> I'd be happy to provide any further information you may require. We  
> have data on a further 14 factors that we hope to release by the summer.
> 
> sincerely
> 
> mark biggin
> 
> 
> Mark Biggin
> Genomics Division
> Lawrence Berkeley National Laboratory
> Berkeley CA 94720
> 
> Phone 	(510) 486 7606
> Fax 		(510) 486 4229
> email	mdbiggin at lbl.gov
> 
> 
> 
> 
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