deflection

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deflection [2019/07/06 12:15]
tongyifan
deflection [2019/07/06 12:19] (current)
tongyifan [Deflection plot]
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 As what we mentioned above, Manhattan plot is a widely used plot to display the results of the genome-wide association meta- analysis. Normally, it is used to show the significance difference (p-value of t-test) between two groups of data. But in some cases, the association between the variations (values in tumor samples compared with the non-malignant) is more important. Therefore, we proposed a new plot: Deflection plot. As what we mentioned above, Manhattan plot is a widely used plot to display the results of the genome-wide association meta- analysis. Normally, it is used to show the significance difference (p-value of t-test) between two groups of data. But in some cases, the association between the variations (values in tumor samples compared with the non-malignant) is more important. Therefore, we proposed a new plot: Deflection plot.
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 It's also a genome-wide association meta-analysis for mRNA expression values, copy number variations or methylation values in tumor samples and non-malignant samples for two different cancer types. In Deflection plots, genomic coordinates are displayed along the X-axis. Each line stands for a gene. The amplitude of it stands for the negative logarithm of the association P-value for each gene's mRNA expression values in tumor samples in cancer type1 and cancer type2. Therefore, the stronger the associations between gene values, the higher the Y-axis value. If the bigger variation for a gene is a negative one (median value in tumor samples is smaller than what in non-malignant samples), then the corresponding line would point down, other wise, it would point up. Two default colors are assigned to these two cancer types. Color1 indicates that the deflection (tumor vs. non-malignant samples) is greater for cancer type1, whereas color2 indicates that the deflection is greater for cancer type2. A gap within the individual chromosome data indicates the location of the centrosome. For chromosomes 13, 14, 15, 21, and 22 only genes on the q arm were represented on the microarray. Please see the examples. It's also a genome-wide association meta-analysis for mRNA expression values, copy number variations or methylation values in tumor samples and non-malignant samples for two different cancer types. In Deflection plots, genomic coordinates are displayed along the X-axis. Each line stands for a gene. The amplitude of it stands for the negative logarithm of the association P-value for each gene's mRNA expression values in tumor samples in cancer type1 and cancer type2. Therefore, the stronger the associations between gene values, the higher the Y-axis value. If the bigger variation for a gene is a negative one (median value in tumor samples is smaller than what in non-malignant samples), then the corresponding line would point down, other wise, it would point up. Two default colors are assigned to these two cancer types. Color1 indicates that the deflection (tumor vs. non-malignant samples) is greater for cancer type1, whereas color2 indicates that the deflection is greater for cancer type2. A gap within the individual chromosome data indicates the location of the centrosome. For chromosomes 13, 14, 15, 21, and 22 only genes on the q arm were represented on the microarray. Please see the examples.
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 ===== Overview ===== ===== Overview =====
  • deflection.txt
  • Last modified: 2019/07/06 12:19
  • by tongyifan