Onderzoek naar de mogelijkheden van de aanleg van gemengd loofhoutbos

<p><b>Copyright information:</b></p><p>Taken from "Extracting gene expression patterns and identifying co-expressed genes from microarray data reveals biologically responsive processes"</p><p>http://www.biomedcentral.com/1471-2105/8/427</p><p>BMC Bioinformatics 2007;8():427-427.</p><p>Published online 2 Nov 2007</p><p>PMCID:PMC2194742.</p><p></p> in Table 1. A) The patterns extracted by EPIG are labelled from 1 to 5 correspond to the distributions A to E, respectively. All profiles were categorized to their respective pattern. B) The pattern extracted by CLICK from Cluster 1 with 32 profiles assigned to it appears to have emerged from both distributions C and D in Table 1. The patterns for Clusters 2 and 3 correspond to distributions A and B in Table 1. The two clusters have 16 and 15 profiles assigned respectively

Extracting gene expression patterns and identifying co-expressed genes from microarray data reveals biologically responsive processes-0

<p><b>Copyright information:</b></p><p>Taken from "Extracting gene expression patterns and identifying co-expressed genes from microarray data reveals biologically responsive processes"</p><p>http://www.biomedcentral.com/1471-2105/8/427</p><p>BMC Bioinformatics 2007;8():427-427.</p><p>Published online 2 Nov 2007</p><p>PMCID:PMC2194742.</p><p></p>ures from (A) to (F), there are four data points marked as crosses. The four data points from left to right correspond to inter-group 1 to 4, respectively. The labels of the vertical axis indicate the mean values of the data points. The vertical bars are the standard deviation of 0.4 to each of the mean values

Extracting gene expression patterns and identifying co-expressed genes from microarray data reveals biologically responsive processes-5

<p><b>Copyright information:</b></p><p>Taken from "Extracting gene expression patterns and identifying co-expressed genes from microarray data reveals biologically responsive processes"</p><p>http://www.biomedcentral.com/1471-2105/8/427</p><p>BMC Bioinformatics 2007;8():427-427.</p><p>Published online 2 Nov 2007</p><p>PMCID:PMC2194742.</p><p></p>ures from (A) to (F), there are four data points marked as crosses. The four data points from left to right correspond to inter-group 1 to 4, respectively. The labels of the vertical axis indicate the mean values of the data points. The vertical bars are the standard deviation of 0.4 to each of the mean values

The reconstructed Bayesian network was generated from the gene expression data from a total of 32 gene profiles

It depicts the statistical dependence between the transcript levels of the genes. The red nodes represent the up-regulated genes and green nodes represent the down-regulated genes both when the necrosis severity increases. Blue edges have a probability greater than 0.9, brown edges between 0.8 to 0.9, and black edges between 0.6 to 0.8. The dashed lines represent the edges consistent with the Ingenuity Pathway Analysis in Figure 4.<p><b>Copyright information:</b></p><p>Taken from "Genes related to apoptosis predict necrosis of the liver as a phenotype observed in rats exposed to a compendium of hepatotoxicants"</p><p>http://www.biomedcentral.com/1471-2164/9/288</p><p>BMC Genomics 2008;9():288-288.</p><p>Published online 16 Jun 2008</p><p>PMCID:PMC2478688.</p><p></p

There are 4 groups of significantly differentially expressed gene lists, one for comparison of necrosis level 0 vs

1 with 2683 significant genes, one for comparison of necrosis level 1 vs. 2 with 171 significant genes, one for comparison of necrosis level 2 vs. 3 with 910 significant genes, and one for comparison of necrosis level 3 vs. 4 with 131 significant genes. The four gene lists are labeled on the bottom of the figure and over-represented biological processes are labeled at the left of the figure. The red color indicates that the p-value is smaller than the FDR rate of 0.05 whereas blue represents p-values larger than an FDR rate of 0.05. The smaller the p-value, the more intense the color.<p><b>Copyright information:</b></p><p>Taken from "Genes related to apoptosis predict necrosis of the liver as a phenotype observed in rats exposed to a compendium of hepatotoxicants"</p><p>http://www.biomedcentral.com/1471-2164/9/288</p><p>BMC Genomics 2008;9():288-288.</p><p>Published online 16 Jun 2008</p><p>PMCID:PMC2478688.</p><p></p

Extracting gene expression patterns and identifying co-expressed genes from microarray data reveals biologically responsive processes-7

<p><b>Copyright information:</b></p><p>Taken from "Extracting gene expression patterns and identifying co-expressed genes from microarray data reveals biologically responsive processes"</p><p>http://www.biomedcentral.com/1471-2105/8/427</p><p>BMC Bioinformatics 2007;8():427-427.</p><p>Published online 2 Nov 2007</p><p>PMCID:PMC2194742.</p><p></p> in Table 1. A) The patterns extracted by EPIG are labelled from 1 to 5 correspond to the distributions A to E, respectively. All profiles were categorized to their respective pattern. B) The pattern extracted by CLICK from Cluster 1 with 32 profiles assigned to it appears to have emerged from both distributions C and D in Table 1. The patterns for Clusters 2 and 3 correspond to distributions A and B in Table 1. The two clusters have 16 and 15 profiles assigned respectively

The 187 possible edges present in at least one of 500 networks are plotted

The 107 out of 187 edges are presented less than 25 times in 500 networks. The x-axis is the number of occurrences of the edges and the y-axis is the frequency.<p><b>Copyright information:</b></p><p>Taken from "Genes related to apoptosis predict necrosis of the liver as a phenotype observed in rats exposed to a compendium of hepatotoxicants"</p><p>http://www.biomedcentral.com/1471-2164/9/288</p><p>BMC Genomics 2008;9():288-288.</p><p>Published online 16 Jun 2008</p><p>PMCID:PMC2478688.</p><p></p

Extracting gene expression patterns and identifying co-expressed genes from microarray data reveals biologically responsive processes-2

<p><b>Copyright information:</b></p><p>Taken from "Extracting gene expression patterns and identifying co-expressed genes from microarray data reveals biologically responsive processes"</p><p>http://www.biomedcentral.com/1471-2105/8/427</p><p>BMC Bioinformatics 2007;8():427-427.</p><p>Published online 2 Nov 2007</p><p>PMCID:PMC2194742.</p><p></p> in Table 1. A) The patterns extracted by EPIG are labelled from 1 to 5 correspond to the distributions A to E, respectively. All profiles were categorized to their respective pattern. B) The pattern extracted by CLICK from Cluster 1 with 32 profiles assigned to it appears to have emerged from both distributions C and D in Table 1. The patterns for Clusters 2 and 3 correspond to distributions A and B in Table 1. The two clusters have 16 and 15 profiles assigned respectively

Extracting gene expression patterns and identifying co-expressed genes from microarray data reveals biologically responsive processes-3

<p><b>Copyright information:</b></p><p>Taken from "Extracting gene expression patterns and identifying co-expressed genes from microarray data reveals biologically responsive processes"</p><p>http://www.biomedcentral.com/1471-2105/8/427</p><p>BMC Bioinformatics 2007;8():427-427.</p><p>Published online 2 Nov 2007</p><p>PMCID:PMC2194742.</p><p></p>eated. For each treatment, there were three individual cell lines, F1-HTERT, F3-HTERT and F10-HTERT, positioned from left to right. Each cell line consisted of eight data points with four different treatment conditions, i.e., sham-treatment and 2, 6, and 24 h post-treatment colored red, green, blue and magenta, respectively. The vertical axes with zero at the middle are the changes in gene expression (log2 intensity) relative to the sham-treated controls

Sources of variation in baseline gene expression levels from toxicogenomics study control animals across multiple laboratories-0

He first two principal components are shown, which together explain about 80% and 53% of the total variation for kidney and liver, respectively. Each point in the plot represents an individual sample. (A) For kidney, organ section (indicated by color) appears to be the prominent explanatory factor. Lab is indicated by marker shape and gender is indicated by marker size. (B) Lab, diet, and fasting (indicated by color, shape, and size, respectively) are confounded in the liver dataset, and their respective levels are strongly associated with three distinct clusters. The sources and numbers of the 3 rat chows used in this dataset were Purina 5002, National Toxicology Program (NTP) 2000, and Provimi Kliba (PK) 3893.<p><b>Copyright information:</b></p><p>Taken from "Sources of variation in baseline gene expression levels from toxicogenomics study control animals across multiple laboratories"</p><p>http://www.biomedcentral.com/1471-2164/9/285</p><p>BMC Genomics 2008;9():285-285.</p><p>Published online 12 Jun 2008</p><p>PMCID:PMC2453529.</p><p></p