EDISA: extracting biclusters from multiple time-series of gene expression profiles-1

<p><b>Copyright information:</b></p><p>Taken from "EDISA: extracting biclusters from multiple time-series of gene expression profiles"</p><p>http://www.biomedcentral.com/1471-2105/8/334</p><p>BMC Bioinformatics 2007;8():334-334.</p><p>Published online 12 Sep 2007</p><p>PMCID:PMC2063505.</p><p></p>s of noise. The overlap of the implanted modules and the modules mined by EDISA were scored (equation 15). Six runs with 400 iterations were performed, with = 0.1 and = 0.2 for ∈ [0,0.5], = 0.15 for = 0.7 and = 0.2 for = 0.9

EDISA: extracting biclusters from multiple time-series of gene expression profiles-2

<p><b>Copyright information:</b></p><p>Taken from "EDISA: extracting biclusters from multiple time-series of gene expression profiles"</p><p>http://www.biomedcentral.com/1471-2105/8/334</p><p>BMC Bioinformatics 2007;8():334-334.</p><p>Published online 12 Sep 2007</p><p>PMCID:PMC2063505.</p><p></p>es (equation 14), if the respective value is lower than 0.15 no line is drawn. Table 1 provides an overview of all different module types

EDISA: extracting biclusters from multiple time-series of gene expression profiles-0

<p><b>Copyright information:</b></p><p>Taken from "EDISA: extracting biclusters from multiple time-series of gene expression profiles"</p><p>http://www.biomedcentral.com/1471-2105/8/334</p><p>BMC Bioinformatics 2007;8():334-334.</p><p>Published online 12 Sep 2007</p><p>PMCID:PMC2063505.</p><p></p>Here, we provide three predefined module types. Given this information random samples are drawn from the dataset (preprocessing). EDISA iteratively refines these samples and stores them if they match the module definition. After a specified number of runs EDISA computes the final modules (postprocessing)

EDISA: extracting biclusters from multiple time-series of gene expression profiles-4

<p><b>Copyright information:</b></p><p>Taken from "EDISA: extracting biclusters from multiple time-series of gene expression profiles"</p><p>http://www.biomedcentral.com/1471-2105/8/334</p><p>BMC Bioinformatics 2007;8():334-334.</p><p>Published online 12 Sep 2007</p><p>PMCID:PMC2063505.</p><p></p>equation 14). If the respective value is lower than 0.15 no line is drawn. Table 1 provides an overview of all different module types

Normalized signal intensities of 23 probesets representing genes are displayed for microarray experiments BB4 and BB7 (according to BarleyBase 27, 28)

Experimental samples and timepoints are indicated on the x-axis. Mlo, mlo5 and Mla1 represent different barley genotypes, Bgh_5874 represents a particular strain of powdery mildew (see BarleyBase [27, 28] for experimental details). Fold changes compared to the control (BB7) or timepoint zero (BB4) are color coded as indicated. gene probesets are arranged according to WRKY groups 1 to 3. Several probesets representing the same gene are named _a to _c.<p><b>Copyright information:</b></p><p>Taken from "Phylogenetic and comparative gene expression analysis of barley () WRKY transcription factor family reveals putatively retained functions between monocots and dicots"</p><p>http://www.biomedcentral.com/1471-2164/9/194</p><p>BMC Genomics 2008;9():194-194.</p><p>Published online 28 Apr 2008</p><p>PMCID:PMC2390551.</p><p></p

Phylogenetic and comparative gene expression analysis of barley WRKY transcription factor family reveals putatively retained functions between monocots and dicots-4

The expression trajectories of genes relative to its controls over three different organs in three plant species. RT-PCR analysis (lower panels) with mRNA of barley, Arabidopsis and rice isolated from homologous organs (roots, left; leaves, middle; infructescence, right).<p><b>Copyright information:</b></p><p>Taken from "Phylogenetic and comparative gene expression analysis of barley () WRKY transcription factor family reveals putatively retained functions between monocots and dicots"</p><p>http://www.biomedcentral.com/1471-2164/9/194</p><p>BMC Genomics 2008;9():194-194.</p><p>Published online 28 Apr 2008</p><p>PMCID:PMC2390551.</p><p></p

Phylogenetic and comparative gene expression analysis of barley WRKY transcription factor family reveals putatively retained functions between monocots and dicots-5

N bold letters, the amino acids forming the zinc-finger motif are displayed in grey, gaps are marked with dashes.<p><b>Copyright information:</b></p><p>Taken from "Phylogenetic and comparative gene expression analysis of barley () WRKY transcription factor family reveals putatively retained functions between monocots and dicots"</p><p>http://www.biomedcentral.com/1471-2164/9/194</p><p>BMC Genomics 2008;9():194-194.</p><p>Published online 28 Apr 2008</p><p>PMCID:PMC2390551.</p><p></p

Chimeric Autofluorescent Proteins as Photophysical Model System for Multicolor Bimolecular Fluorescence Complementation

The yellow fluorescent protein (YFP) is frequently used in a protein complementation assay called bimolecular fluorescence complementation (BiFC), and is employed to visualize protein–protein interactions. In this analysis, two different, nonfluorescent fragments of YFP are genetically attached to proteins of interest. Upon interaction of these proteins, the YFP fragments are brought into proximity close enough to reconstitute their original structure, enabling fluorescence. BiFC allows for a straightforward readout of protein–protein interactions and furthermore facilitates their functional investigation by in vivo imaging. Furthermore, it has been observed that the available color range in BiFC can be extended upon complementing fragments of different proteins that are, like YFP, derived from the Aequorea victoria green fluorescent protein, thereby allowing for a multiplexed investigation of protein–protein interactions. Some spectral characteristics of “multicolor” BiFC (mcBiFC) complexes have been reported before; however, no in-depth analysis has been performed yet. Therefore, little is known about the photophysical characteristics of these mcBiFC complexes because a proper characterization essentially relies on in vitro data. This is particularly difficult for fragments of autofluorescent proteins (AFPs) because they show a very strong tendency to form supramolecular aggregates which precipitate ex vivo. In this study, this intrinsic difficulty is overcome by directly fusing the coding DNA of different AFP fragments. Translation of the genetic sequence in Escherichia coli leads to fully functional, highly soluble fluorescent proteins with distinct properties. On the basis of their construction, they are designated chimeric AFPs, or BiFC chimeras, here. Comparison of their spectral characteristics with experimental in vivo BiFC data confirmed the utility of the chimeric proteins as a BiFC model system. In this study, nine different chimeras were thoroughly analyzed at both the ensemble and the single-molecular level. The data indicates that mutations believed to be photophysically silent significantly alter the properties of AFPs

The response regulator ARR22 is a putative AHP phospho-histidine phosphatase expressed in the chalaza of developing seeds-3

column). The right column shows the corresponding bright field images of the transformed cells. The bars represent 25 μm. (B) Western blot analysis of protein extracts derived from transiently transformed tobacco leaves assayed for BiFC fluorescence before extraction (1–6). Immunodetection of the YFP-N fusion proteins (AHPs) was carried out with an antibody against c-myc-tag (anti c-myc) and of the YFP-C fusion protein (ARR22) with an antibody against the HA-tag (anti HA). M, protein marker.<p><b>Copyright information:</b></p><p>Taken from "The response regulator ARR22 is a putative AHP phospho-histidine phosphatase expressed in the chalaza of developing seeds"</p><p>http://www.biomedcentral.com/1471-2229/8/77</p><p>BMC Plant Biology 2008;8():77-77.</p><p>Published online 15 Jul 2008</p><p>PMCID:PMC2478664.</p><p></p

The response regulator ARR22 is a putative AHP phospho-histidine phosphatase expressed in the chalaza of developing seeds-6

Ant and wild type (grey bars) by HPLC analysis as described in Methods. The data are expressed as mean ± SD (n = 5).<p><b>Copyright information:</b></p><p>Taken from "The response regulator ARR22 is a putative AHP phospho-histidine phosphatase expressed in the chalaza of developing seeds"</p><p>http://www.biomedcentral.com/1471-2229/8/77</p><p>BMC Plant Biology 2008;8():77-77.</p><p>Published online 15 Jul 2008</p><p>PMCID:PMC2478664.</p><p></p