Searching journal content for articles similar to Xu et al. 17 (11): 000.

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  1. Method: Integrating multiple evidence sources to predict transcription factor binding in the human genome
    • Jason Ernst,
    • Heather L. Plasterer,
    • Itamar Simon,
    • and Ziv Bar-Joseph
    Genome Res. April 2010 20: 526-536; Published in Advance March 10, 2010, doi:10.1101/gr.096305.109
    ...Tables 4, 5). Evaluation on independent E2F promoter ChIP-chip data To test ourmethod on a new data set we carried out newChIP-chip experiments for E2F factors. These included 13 E2F experiments, seven for E2F4 and six for E2F2, using a primarily core promoter array. We have also evaluated our method...
  2. Letter: Genomic distribution of CHD7 on chromatin tracks H3K4 methylation patterns
    • Michael P. Schnetz,
    • Cynthia F. Bartels,
    • Kuntal Shastri,
    • Dheepa Balasubramanian,
    • Gabriel E. Zentner,
    • Ravishankar Balaji,
    • Xiaodong Zhang,
    • Lingyun Song,
    • Zhenghe Wang,
    • Thomas LaFramboise,
    • Gregory E. Crawford,
    • and Peter C. Scacheri
    Genome Res. April 2009 19: 590-601; Published in Advance February 27, 2009, doi:10.1101/gr.086983.108
    ...with proteins known to function as gene enhancers. These results prompted us to assess whether CHD7 occupancy correlates with high levels of gene expression. A systematic comparison between ChIP-chip and expression data revealed that the level of expression of genes located within 10 kb of a CHD7 site...
  3. Letter: Cell-type selective chromatin remodeling defines the active subset of FOXA1-bound enhancers
    • Jérôme Eeckhoute,
    • Mathieu Lupien,
    • Clifford A. Meyer,
    • Michael P. Verzi,
    • Ramesh A. Shivdasani,
    • X. Shirley Liu,
    • and Myles Brown
    Genome Res. March 2009 19: 372-380; Published in Advance January 7, 2009, doi:10.1101/gr.084582.108
    ...factors in MCF7 cells, ESR1 and E2F1, also revealed greater FAIRE enrichment at sites that were bound versus unbound ( Bieda et al. 2006 ; Carroll et al. 2006 ; Rabinovich et al. 2008 ; Supplemental Fig. S2). View larger version: In this window In a new window Figure 1. FAIRE-chip signal from MCF7 cells...
  4. LETTER: Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif
    • Yong Cheng,
    • David C. King,
    • Louis C. Dore,
    • Xinmin Zhang,
    • Yuepin Zhou,
    • Ying Zhang,
    • Christine Dorman,
    • Demesew Abebe,
    • Swathi A. Kumar,
    • Francesca Chiaromonte,
    • Webb Miller,
    • Roland D. Green,
    • Mitchell J. Weiss,
    • and Ross C. Hardison
    Genome Res. December 2008 18: 1896-1905; Published in Advance September 25, 2008, doi:10.1101/gr.083089.108
    ...a combination of ChIP-chip and independent validation by quantitative PCR. These techniques are agnostic to evolutionary conservation or prior knowledge about regulatory regions, and thus they provide a relatively unbiased set of in vivo occupied DNA intervals. The binding data do not reveal specific biological...
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  5. LETTER: Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders
    • Alvaro Rada-Iglesias,
    • Adam Ameur,
    • Philipp Kapranov,
    • Stefan Enroth,
    • Jan Komorowski,
    • Thomas R. Gingeras,
    • and Claes Wadelius
    Genome Res. March 2008 18: 380-392; Published in Advance January 29, 2008, doi:10.1101/gr.6880908
    ...Transcription factors and histone modifications are crucial regulators of gene expression that mutually influence each other. We present the DNA binding profiles of upstream stimulatory factors 1 and 2 (USF1, USF2) and acetylated histone H3 (H3ac) in a liver cell line for the whole human genome using ChIP-chip...
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