Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities

作者: Michael F Berger , Anthony A Philippakis , Aaron M Qureshi , Fangxue S He , Preston W Estep

DOI: 10.1038/NBT1246

关键词: DNA microarrayBinding siteProtein microarrayPlasma protein bindingDNA binding siteTranscription factorBiologyComputational biologyGenetics

摘要: … and the position and orientation of the k-mer relative to the slide surface. Using control spots containing Zif268 binding sites in various positions and orientations, we observed that …

参考文章(29)
Sangeet Singh-Gasson, Roland D. Green, Yongjian Yue, Clark Nelson, Fred Blattner, Michael R. Sussman, Franco Cerrina, Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array. Nature Biotechnology. ,vol. 17, pp. 974- 978 ,(1999) , 10.1038/13664
Sonali Mukherjee, Michael F Berger, Ghil Jona, Xun S Wang, Dale Muzzey, Michael Snyder, Richard A Young, Martha L Bulyk, Rapid Analysis of the DNA Binding Specificities of Transcription Factors with DNA Microarrays Nature Genetics. ,vol. 36, pp. 1331- 1339 ,(2004) , 10.1038/NG1473
B. Christy, D. Nathans, DNA binding site of the growth factor-inducible protein Zif268. Proceedings of the National Academy of Sciences of the United States of America. ,vol. 86, pp. 8737- 8741 ,(1989) , 10.1073/PNAS.86.22.8737
Juli D. Klemm, Mark A. Rould, Rajeev Aurora, Winship Herr, Carl O. Pabo, Crystal structure of the Oct-1 POU domain bound to an octamer site: DNA recognition with tethered DNA-binding modules Cell. ,vol. 77, pp. 21- 32 ,(1994) , 10.1016/0092-8674(94)90231-3
A. Tanay, Extensive low-affinity transcriptional interactions in the yeast genome Genome Research. ,vol. 16, pp. 962- 972 ,(2006) , 10.1101/GR.5113606
Andreas Wilmen, Horst Pick, Rainer K. Niedenthal, Mark Sen-Gupta, Johannes H. Hegemann, The yeast centromere CDEI/Cpf1 complex: differences between in vitro binding and in vivo function Nucleic Acids Research. ,vol. 22, pp. 2791- 2800 ,(1994) , 10.1093/NAR/22.14.2791
Steinar Bjerve, Error Bounds for Linear Combinations of Order Statistics Annals of Statistics. ,vol. 5, pp. 357- 369 ,(1977) , 10.1214/AOS/1176343800