zeroing in on essential gene expression data
Báo cáo khoa học: Effect of ecdysone receptor gene switch ligands on endogenous gene expression in 293 cells docx
Ngày tải lên :
30/03/2014, 03:20
... narrow therapeutic indices, such as cytokinins and hormones The main purpose of a regulated gene expression system is to control the timing and levels of transgene expression in vivo Whether the ... 47 Constantino S, Santos R, Gisselbrecht S & Gouilleux F (2001) The ecdysone inducible gene expression system: unexpected effects of muristerone A and ponasterone A on cytokine signaling in mammalian ... expression of the fragile histidine triad gene on cell cycle and proliferation Mol Cell Biochem 204, 83–88 Luers GH, Jess N & Franz T (2000) Reporter-linked monitoring of transgene expression in living...
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Báo cáo hóa học: " The effects of hypertonic fluid administration on the gene expression of inflammatory mediators in circulating leucocytes in patients with septic shock: a preliminary study" pptx
Ngày tải lên :
20/06/2014, 23:20
... observation reiterates that the inflammatory response in sepsis is heterogeneous depending on the source and the infecting organism In conclusion, we have shown that in septic shock patients, hypertonic ... dependent on sufficient shear stress above a critical threshold, to promote and maintain rolling interactions [28] In our study, expression of L-selectin was depressed in the HT group This finding ... expression in neutrophils, whereas IL-6 is mainly expressed in monocytes and TF in (sub)endothelium In other words, despite high plasma protein levels of IL-6 in sepsis, the actual gene expression in...
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Báo cáo hóa học: " Research Article Clustering of Gene Expression Data Based on Shape Similarity" potx
Ngày tải lên :
22/06/2014, 00:20
... Extraction of Shape Information and Time Scaling To extract shape information of time-varying gene expression, the derivative of the expression trajectory is considered Since we are dealing with ... framework for gene expression clustering validation based on gene ontology and graph theory,” in Proceedings of the IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP ... statistic, one using the clusters of transformed data and one using the corresponding clusters of raw data We used the built -in Silhouette function contained within MATLAB for our calculations To...
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Báo cáo hóa học: " The Local Maximum Clustering Method and Its Application in Microarray Gene Expression Data Analysis" docx
Ngày tải lên :
23/06/2014, 01:20
... response series contains 1769 gene expression values The logarithms of the gene expression levels are used in correlation function calculation to reduce the noise effect at high expression levels We ... each data point Assume there is a data set of N data points to be clustered The local maximum of a data point i is the data point whose magnitude is the maximum among all the data points within ... portion of an array—a cluster centering at this gene would be created Additionally, for the thousands of genes arrayed on a gene chip, generally, only a handful of genes show varying expression...
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Báo cáo y học: " Dynamic gene network reconstruction from gene expression data in mice after influenza A (H1N1) infection." ppsx
Ngày tải lên :
10/08/2014, 09:22
... Interaction data We downloaded InnateDB protein-protein interaction (PPI) and protein-DNA interaction data and isolated all interaction groups with members included in our dataset Additional file ... implementation of Time Varying Dynamic Bayesian Networks on time series gene expression data of murine C57BL/6J inbred strain after infection with H1N1 (PR8) virus Our reverse engineering approach combines ... Protein-Protein and ProteinDNA Interaction data An additional aspect in our analysis was to explore the cluster interactome with respect to other types of data such as protein-protein interactions...
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báo cáo khoa học: " Discovery of microvascular miRNAs using public gene expression data: miR-145 is expressed in pericytes and is a regulator of Fli1" pps
Ngày tải lên :
11/08/2014, 12:20
... miR-126 stained ECs (staining patterns in kidney arteries are shown in Figure 4c,d) In brain parenchyma, miR-145 showed staining in solitary scattered cells, consistent with expression in pericytes ... 60-bp regions containing wild-type (WT) miR-145 binding sites in the Fli1 3′ UTR were cloned into pMIR-REPORT vector (Applied Biosystems) Identical constructs with single base-pair mutations (Mut) ... as promising candidates for selective vascular expression, including miR-145, miR-30d, miR-23b and miR-24 (within the dashed lines in Figure 1b) miRNAs connected by thick grey lines in the figure...
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Báo cáo y học: "Response of the mouse lung transcriptome to welding fume: effects of stainless and mild steel fumes on lung gene expression in A/J and C57BL/6J mice" pot
Ngày tải lên :
12/08/2014, 11:22
... chronic overexpression of inflammatory genes This transcriptional response supports our previous finding that GMA-SS is more potent in inducing a chronic immune response in the A/J lung [9] In ... downregulation of IL1β, FOS, S100 calcium binding protein A9 [S100A9], etc.) other "later" gene interactions were surprising (Figures and 5) Perhaps the most intriguing finding regarding GMA-MS welding ... protein 105 kDa (HSPH1) and zinc finger and BTB domain containing 16 (ZBTB16) which was also upregulated at weeks (2.4 fold) Interestingly, continued involvement of circadian rhythm signaling genes...
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Báo cáo sinh học: "A robust approach based on Weibull distribution for clustering gene expression data" pps
Ngày tải lên :
12/08/2014, 17:20
... distributions of the gene expressions belong to the common Weibull distribution [16] Due to the consistent distribution function types, we consider that those genes with similar gene expression distribution ... clustering their corresponding distribution parameters, as each gene corresponds to its unique distribution parameters In the following we introduce the principle of the distribution function construction ... construction procedures Weibull distributions of gene expressions construction First, we construct the empirical distribution of each gene expression [17], and then ascertain the precise distribution...
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Báo cáo y học: "Comment on and reply to "Analysis of variation of amplitudes in cell cycle gene expression" by Liu, Gaido and Wolfinger: On the analysis of gene expression during the normal, eukaryotic, cell cycle" docx
Ngày tải lên :
13/08/2014, 23:20
... synchronization method, there should be a minimal increase in cell number for a period of time covering a significant fraction of the interdivision time 2) The rise in cell numbers during division ... selection methods can give synchrony Wholeculture methods, using inhibition or starvation, cannot synchronize cells This is not so much a criterion as a theoretical rule regarding synchronization in ... synchronized Synchronized divisions are the sine qua non of synchrony Criteria for successful analysis of gene expression during the division cycle 12) Gene expression results should be replicated...
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Báo cáo y học: " Indirect genomic effects on survival from gene expression data" doc
Ngày tải lên :
14/08/2014, 08:20
... Since our basis was gene expression data, we considered only transcriptional interactions, meaning that each pathway contained at least one protein with known transcription factor activity interacting ... that the data consists of both the gene expression measurements and a data set of regulatory interactions between genes A gene has an 'indirect effect' on survival if its expression influences ... interacting with one or more other genes by changing their expression level Each interaction was then of the form gene A → gene B, which we write as A → B, representing that the expression of gene...
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Báo cáo y học: "Insights into the regulation of intrinsically disordered proteins in the human proteome by analyzing sequence and gene expression data" potx
Ngày tải lên :
14/08/2014, 21:20
... novel insights into the regulation of disordered proteins This aim was achieved and we discuss our findings in the following sections Protein disorder and gene expression On consideration of the gene ... Chaperone binding Lipid raft organization and biogenesis Aggresome Inclusion body Protein desumoylation Ubiquitin specific protease activity Protein targeting to lysosome Small conjugating protein-specific ... translation and altering the rate at which mRNA is degraded In combination with transcription, mRNA degradation plays a critical role in regulating gene expression [33,34] If proteins need to remain in...
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Data mining techniques in gene expression data analysis
Ngày tải lên :
15/09/2015, 17:09
... application of association rule mining and association classification on gene expression data The diversified correlations among genes, nonlinear correlation and shifting-and-scaling correlation, have ... present novel data mining solutions for the problems of high dimensionality and complex correlations during gene expression analysis While we focus on gene expression data mainly in this study, ... of the expression data matrix involved in class association rule mining corresponds to a sample or a condition while each column corresponds to a gene Current class association rule mining methods...
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Báo cáo khoa học: Hepatocyte nuclear factor-4a interacts with other hepatocyte nuclear factors in regulating transthyretin gene expression pot
Ngày tải lên :
23/03/2014, 03:20
... Effective interaction requires the integrity of HNF binding, as well as a component of protein–protein interaction between the factors Role of HNFs in transthyretin gene expression Results Functional ... Journal compilation ª 2010 FEBS 4069 Role of HNFs in transthyretin gene expression Z Wang and P A Burke Fig Mutation of the HNF binding site mainly disrupts the corresponding HNF binding ability, ... affecting the ability of the other HNFs to bind to their specific DNA binding sites A role of HNFs in the down-regulation of TTR expression in response to cytokine stimulation Fig HNF-4 binding...
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A gene expression database for the molecular pharmacology of cancer pptx
Ngày tải lên :
30/03/2014, 13:20
... the expression patterns of 1,376 genes in the 60 cell lines Included, in addition to the gene expression levels, are data for 40 molecular targets assessed one at a time in the cells A red point ... clustering were considerably more heterogeneous in sensitivity to drugs and a correlation metric, the 1,376 genes, along with 40 individu- than in gene expression This difference in clustering (Fig 2a,b) ... cells in terms of their tion reflects factors common to expression patterns in tumour response to drugs and in terms of their gene expression For these cell lines The median difference per gene...
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Báo cáo hóa học: " Research Article The Wavelet-Based Cluster Analysis for Temporal Gene Expression Data" pptx
Ngày tải lên :
22/06/2014, 19:20
... Time points Figure 2: The rpoS gene expression profiles in 72 conditions and 48 time points Because the strength of expression of the rpoS promoter varies among conditions, the expression levels ... points Figure shows the expression profile variation of this gene in different experimental conditions Because the strength of expression of the rpoS gene varies among conditions, that is, the expression ... splines, especially in large scale of temporal gene expression data, further research and comparison are needed In this paper, we firstly transformed temporal gene expression data with continuous...
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Báo cáo hóa học: " Research Article Inferring Time-Varying Network Topologies from Gene Expression Data" docx
Ngày tải lên :
22/06/2014, 19:20
... and interpolated data Method (T-cell data) SSM on original data SSM on undersampled data SSM on interpolated data CoD on original data CoD on undersampled data CoD on interpolated data Edges inferred ... Retinoic acid receptor GATA binding protein GATA binding protein Paired homeobox-2 Laminin Nephronectin Ros1 proto-oncogene protein tyrosine phosphatase Ret proto-oncogene, Glial neutrophic factor ... on another data set—the T-cell expression data presented in [1] This data looks at the expression of various genes after T-cell activation using stimulation with phorbolester PMA and ionomycin...
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Báo cáo hóa học: " Research Article Clustering Time-Series Gene Expression Data Using Smoothing Spline Derivatives" pptx
Ngày tải lên :
22/06/2014, 19:20
... fasting on hepatic gene expression in the mouse This study provides a novel timedependent view of fasting effects on gene expression which are usually studied through or time points only (including ... globally correspond to four temporal expression profiles: decreasing (hc3), stationary (hc2), weakly increasing (hc1), strongly increasing (hc4) 4.2 k-means partitioning To make the clustering more robust, ... left to right, gene expression profiles go from a sharply increasing curve (km4, in blue) to a weakly increasing curve (km1, genes in black), then stationary profiles (km2, genes in red), and finally...
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The Biological Sample Classification Using Gene Expression Data
Ngày tải lên :
01/08/2014, 17:47
... important Based on the process of gene expression explained above, one DNA produces only one corresponding mRNA and this mRNA in turn produces only one corresponding protein That means protein and mRNA ... turns out to be determined by proteins that bind to regulatory regions along the DNA So the genetic information contained on each gene is not sufficient for gaining insight into biological processes ... second stage, the RNA is translated into protein, in which three continuous bases (codon) in the mRNA are replaced by one corresponding amino acid The overall process consisting of transcription...
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Báo cáo y học: "ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data" doc
Ngày tải lên :
09/08/2014, 23:20
... flanking exons (Figure S4 in Additional file 1) Locally constitutive means that, based on the underlying annotation, all transcripts flanking that intron contain those exons (Figure S5 in Additional ... showing cassette exon usage (inclusion:skip read ratios) instead of gene levels in the same data set The heavy lobe above the diagonal corresponds to exons with zero skipping reads in the brain, ... of genes within the requested regions brain-enriched exon Figure Screen shot of ExpressionPlot’s genome browser seqview The region of the CLTA gene, which contains a brain-enriched exon (pink),...
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báo cáo khoa học: " Light has a specific role in modulating Arabidopsis gene expression at low temperature" potx
Ngày tải lên :
12/08/2014, 05:20
... Shinozaki K, Yamaguchi-Shinozaki K: Organization and expression of two Arabidopsis DREB2 genes encoding DRE-binding proteins involved in dehydration- and high-salinity-responsive gene expression ... thylakoid function The expression of genes encoding various LHCII (LHCB) proteins was strongly enhanced under Cold/Light condition, but not under Cold/Dark condition (Table 2) On the contrary, only a ... role of PSII excitation pressure in regulation of gene expression up to the light intensity of 450 µmol photons m-2 s-1 Such moderate high light condition induced a gene expression pattern very similar...
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