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Gevry, N.3
Lis, J.T.4
Kraus, W.L.5
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The ENCODE Project Consortium, Science 306, 636 (2004).
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11
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38949156299
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2 ratio and P values from a nonparametric Wilcoxon signed-rank test were calculated for each window.
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2 ratio and P values from a nonparametric Wilcoxon signed-rank test were calculated for each window.
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12
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38949193621
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Significant peaks were defined as the center of three consecutive windows with positive means, the center window with a mean greater than that of either adjacent window, and all windows having P values less than 0.01 (Wilcoxon signed-rank test). Significant troughs were defined as the center of three consecutive windows with negative means, the center window with a mean less than that of either adjacent window, and all windows having P values less than 0.01 (Wilcoxon signed-rank test).
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Significant peaks were defined as the center of three consecutive windows with positive means, the center window with a mean greater than that of either adjacent window, and all windows having P values less than 0.01 (Wilcoxon signed-rank test). Significant troughs were defined as the center of three consecutive windows with negative means, the center window with a mean less than that of either adjacent window, and all windows having P values less than 0.01 (Wilcoxon signed-rank test).
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13
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38949191031
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The use of our peak/trough selection criteria were justified by a low false-positive rate (FPR) as determined by ChIP-qPCR (PARP-1 peak FPR = 0.11; H1 trough FPR = 0.08).
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The use of our peak/trough selection criteria were justified by a low false-positive rate (FPR) as determined by ChIP-qPCR (PARP-1 peak FPR = 0.11; H1 trough FPR = 0.08).
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16
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38949089399
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For a gene to be classified as unambiguously expressed or unexpressed, all probe sets from all three replicates corresponding to the gene must have been flagged unanimously present or absent, respectively. Any genes not meeting these criteria were marked as ambiguous and were removed from the expression-based categorization analysis
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For a gene to be classified as unambiguously expressed or unexpressed, all probe sets from all three replicates corresponding to the gene must have been flagged unanimously present or absent, respectively. Any genes not meeting these criteria were marked as ambiguous and were removed from the expression-based categorization analysis.
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17
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38949158875
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For this analysis, peaks and troughs identified at P values between 0.01 and 0.1 were labeled as ambiguous due to high false-positive and false-negative rates.
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For this analysis, peaks and troughs identified at P values between 0.01 and 0.1 were labeled as ambiguous due to high false-positive and false-negative rates.
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18
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38949149764
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The target genes used for this analysis were identified in a microarray expression screen and were then confirmed by RT-qPCR as having either a twofold reduction or a twofold increase in expression upon shRNA-mediated knockdown of PARP-1
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The target genes used for this analysis were identified in a microarray expression screen and were then confirmed by RT-qPCR as having either a twofold reduction or a twofold increase in expression upon shRNA-mediated knockdown of PARP-1.
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22
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33745255099
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B. G. Ju et al., Science 312, 1798 (2006).
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Ju, B.G.1
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38949093306
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We thank J. Lis, A. Clark, A. Siepel, and N. Hah for critical reading of this manuscript and A. Clark and members of the Kraus laboratory for technical advice and helpful discussions. This work was supported by grants from the NIH-National Institute of Diabetes and Digestive and Kidney Diseases (DK069710 and DK058110), the Cornell Center of Vertebrate Genomics, and the Endocrine Society (W.L.K.); a postdoctoral fellowship from the American Heart Association (M.J.G.); and predoctoral fellowships from the American Heart Association (K.M.F.), the Alfred P. Sloan Foundation (J.G.B.), and the Department of Defense Breast Cancer Research Program (M.K.).
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We thank J. Lis, A. Clark, A. Siepel, and N. Hah for critical reading of this manuscript and A. Clark and members of the Kraus laboratory for technical advice and helpful discussions. This work was supported by grants from the NIH-National Institute of Diabetes and Digestive and Kidney Diseases (DK069710 and DK058110), the Cornell Center of Vertebrate Genomics, and the Endocrine Society (W.L.K.); a postdoctoral fellowship from the American Heart Association (M.J.G.); and predoctoral fellowships from the American Heart Association (K.M.F.), the Alfred P. Sloan Foundation (J.G.B.), and the Department of Defense Breast Cancer Research Program (M.K.).
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