Inter- and intra-combinatorial regulation by transcription factors and microRNAs-2

<p><b>Copyright information:</b></p><p>Taken from "Inter- and intra-combinatorial regulation by transcription factors and microRNAs"</p><p>http://www.biomedcentral.com/1471-2164/8/396</p><p>BMC Genomics 2007;8():396-396.</p><p>Published online 30 Oct 2007</p><p>PMCID:PMC2206040.</p><p></p>other regulator denoted by B, and both regulators A and B regulate a common target C

Inter- and intra-combinatorial regulation by transcription factors and microRNAs-5

<p><b>Copyright information:</b></p><p>Taken from "Inter- and intra-combinatorial regulation by transcription factors and microRNAs"</p><p>http://www.biomedcentral.com/1471-2164/8/396</p><p>BMC Genomics 2007;8():396-396.</p><p>Published online 30 Oct 2007</p><p>PMCID:PMC2206040.</p><p></p>n score. The 2D distributions demonstrate how the relationship between Fisher's Exact Test and our Bayesian score depends on the logOR threshold we use. Each sub-plot represents a different threshold value ranging from 0 to 1 – as indicated by each subtitle. For a particular threshold value, a pixel on the plot represents the local density of miRNA-TF pairs having the corresponding p-value (from the y-axis) and Bayesian Probability (from the x-axis). Here darker shaded regions indicate higher densities. For a 0 threshold, the Bayesian Test and Fisher's Test agree exactly. As we increase the threshold, we see fewer and fewer TF-miRNA pairs that are highly associated as measured by both ranking criteria (pairs whose measures approach 1 at the x-axis and 0 at the y-axis). The higher the threshold, the more emphasis we are placing on the size of the TF-miRNA association (as measured by a log Odds Ratio) and the less emphasis on sample size. Note that a very high Bayesian probability implies that the associated p-value will be small, no matter what threshold we use

Inter- and intra-combinatorial regulation by transcription factors and microRNAs-4

<p><b>Copyright information:</b></p><p>Taken from "Inter- and intra-combinatorial regulation by transcription factors and microRNAs"</p><p>http://www.biomedcentral.com/1471-2164/8/396</p><p>BMC Genomics 2007;8():396-396.</p><p>Published online 30 Oct 2007</p><p>PMCID:PMC2206040.</p><p></p>gulators. Figure 1a measures this association by a Fisher's Exact Test p-value (dark pixels represent lower p-values or alternatively a higher value of -log). Figure 1b measures the association by the Bayesian probability Pr{logOR>0.6} (Here a dark pixel means a high probability). The TFs and miRNAs are ordered so that the number of targets of each regulator increases as one moves across the Figure from left to right on the horizontal axis, and also up the vertical axis. Both Figures 1a and 1b illustrate that while TF-TF and miRNA-miRNA associations are common, TF-miRNA interactions are less so. The TF-miRNA rectangles of Fig 1a demonstrate that the most significant associations (as found by Fisher's Exact Test) tend to involve TF-miRNA pairs with the TF having a large number of targets. In the corresponding areas of Figure 1b, we see a more uniform sprinkling of dark points, indicating that the Bayesian approach is less sensitive to sample size effects. The stripes on the TF-miRNA rectangles of both figures demonstrate that certain TFs are associated with almost all the miRNAs – while, surprisingly, many TFs with a similar number of targets seem to not be significantly associated with any miRNA

Inter- and intra-combinatorial regulation by transcription factors and microRNAs-3

<p><b>Copyright information:</b></p><p>Taken from "Inter- and intra-combinatorial regulation by transcription factors and microRNAs"</p><p>http://www.biomedcentral.com/1471-2164/8/396</p><p>BMC Genomics 2007;8():396-396.</p><p>Published online 30 Oct 2007</p><p>PMCID:PMC2206040.</p><p></p> association. The histogram displays the fraction of FFLs that result in each bin, when grouping miRNA/TF/GO triplets according to their log p-value of joint-association. To generate this histogram, we used a slightly restricted set of biological-process GO terms, such that each group includes at least one gene that is a predicted target of a TF and a miRNA. The plot suggests that when a miRNA/TF/GO triplet is significantly associated, the corresponding miRNA and TF are more likely to form a feed forward loop

Inter- and intra-combinatorial regulation by transcription factors and microRNAs-0

<p><b>Copyright information:</b></p><p>Taken from "Inter- and intra-combinatorial regulation by transcription factors and microRNAs"</p><p>http://www.biomedcentral.com/1471-2164/8/396</p><p>BMC Genomics 2007;8():396-396.</p><p>Published online 30 Oct 2007</p><p>PMCID:PMC2206040.</p><p></p>gulators. Figure 1a measures this association by a Fisher's Exact Test p-value (dark pixels represent lower p-values or alternatively a higher value of -log). Figure 1b measures the association by the Bayesian probability Pr{logOR>0.6} (Here a dark pixel means a high probability). The TFs and miRNAs are ordered so that the number of targets of each regulator increases as one moves across the Figure from left to right on the horizontal axis, and also up the vertical axis. Both Figures 1a and 1b illustrate that while TF-TF and miRNA-miRNA associations are common, TF-miRNA interactions are less so. The TF-miRNA rectangles of Fig 1a demonstrate that the most significant associations (as found by Fisher's Exact Test) tend to involve TF-miRNA pairs with the TF having a large number of targets. In the corresponding areas of Figure 1b, we see a more uniform sprinkling of dark points, indicating that the Bayesian approach is less sensitive to sample size effects. The stripes on the TF-miRNA rectangles of both figures demonstrate that certain TFs are associated with almost all the miRNAs – while, surprisingly, many TFs with a similar number of targets seem to not be significantly associated with any miRNA

Expression patterns and prognostic value of Bag-1 and Bcl-2 in breast cancer-2

Lear Bag-1 staining in a breast cancer histospot – using cytokeratin to the define tumor mask, using 4',6-diamidino-2-phenylindole to define the nuclear compartment, and using Cy5 for identifying the target (Bcl-2 and Bag-1).<p><b>Copyright information:</b></p><p>Taken from "Expression patterns and prognostic value of Bag-1 and Bcl-2 in breast cancer"</p><p>http://breast-cancer-research.com/content/10/2/R35</p><p>Breast Cancer Research : BCR 2008;10(2):R35-R35.</p><p>Published online 23 Apr 2008</p><p>PMCID:PMC2397537.</p><p></p

Expression patterns and prognostic value of Bag-1 and Bcl-2 in breast cancer-0

S a loading control in a panel of breast cancer cell lines.<p><b>Copyright information:</b></p><p>Taken from "Expression patterns and prognostic value of Bag-1 and Bcl-2 in breast cancer"</p><p>http://breast-cancer-research.com/content/10/2/R35</p><p>Breast Cancer Research : BCR 2008;10(2):R35-R35.</p><p>Published online 23 Apr 2008</p><p>PMCID:PMC2397537.</p><p></p

Expression patterns and prognostic value of Bag-1 and Bcl-2 in breast cancer-1

2 and Bcl-2 antanogene-1 (Bag-1). AQUA, automated quantitative analysis.<p><b>Copyright information:</b></p><p>Taken from "Expression patterns and prognostic value of Bag-1 and Bcl-2 in breast cancer"</p><p>http://breast-cancer-research.com/content/10/2/R35</p><p>Breast Cancer Research : BCR 2008;10(2):R35-R35.</p><p>Published online 23 Apr 2008</p><p>PMCID:PMC2397537.</p><p></p

Expression patterns and prognostic value of Bag-1 and Bcl-2 in breast cancer-3

Ated quantitative analysis scores dichotomized by the median score for the entire cohort of patients, node-negative patients, and node-positive patients.<p><b>Copyright information:</b></p><p>Taken from "Expression patterns and prognostic value of Bag-1 and Bcl-2 in breast cancer"</p><p>http://breast-cancer-research.com/content/10/2/R35</p><p>Breast Cancer Research : BCR 2008;10(2):R35-R35.</p><p>Published online 23 Apr 2008</p><p>PMCID:PMC2397537.</p><p></p

Expression patterns and prognostic value of Bag-1 and Bcl-2 in breast cancer-4

S a loading control in a panel of breast cancer cell lines.<p><b>Copyright information:</b></p><p>Taken from "Expression patterns and prognostic value of Bag-1 and Bcl-2 in breast cancer"</p><p>http://breast-cancer-research.com/content/10/2/R35</p><p>Breast Cancer Research : BCR 2008;10(2):R35-R35.</p><p>Published online 23 Apr 2008</p><p>PMCID:PMC2397537.</p><p></p