5identification of ebf1 target genes using genome wide analysis
báo cáo khoa học: " Identification of rhizome-specific genes by genome-wide differential expression Analysis in Oryza longistaminata" doc
... high expression of genes near the top of the panel and moderate or low expression of genes below, while leaves (labeled 5) show low or moderate expression of genes near the top of the panel and ... the regulation of shoot apical meristem activities and morphogenesis of shoot organs [34-37] Of Figure Dendrogram of 2566 tissue-specifically expressed genes in the five tissues of O longistaminata ... the microarray data, a set of 21 tissueenriched genes were selected for RT-PCR analysis The RT-PCR expression pattern of 18 out of the 21 genes was consistent with that of the microarray experiments...
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Báo cáo y học: " Characterization of the yeast ionome: a genome-wide analysis of nutrient mineral and trace element homeostasis in Saccharomyces cerevisiae" ppsx
... Functional classes of genes identified by ionome profiling of their Functional classes of genes identified by ionome profiling of their corresponding mutants The number of genes identified in ... control of mineral nutrients and trace elements The usefulness of yeast for genome- wide studies of nutrient homeostasis has markedly increased with the recent completion of the Saccharomyces Genome ... largest percentage of genes identified (65 of 212 genes or 31%) are involved in the biogenesis or function of intracellular organelles This result emphasizes the importance of these compartments...
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Báo cáo khoa học: Genome-wide analysis of clustering patterns and flanking characteristics for plant microRNA genes doc
... and Discussion Analysis of clustering patterns of miRNA genes in four plant genomes Many previous studies have shown that miRNA genes tend to be present as clusters within a region of several kilobases ... dosage effect Analysis of the core promoter of the class II promoter in plant miRNA genes miRNA genes were determined to be part of the polycistronic transcript if the pairwise distance of two miRNAs ... 15 26 The number of miRNA genes studied in four plant species b The number of predicted clusters c The number of miRNA genes located in clusters d The average number of miRNA genes in a cluster...
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Báo cáo hóa học: " Research Article Genome-Wide Analysis of Intergenic Regions of Mycobacterium tuberculosis H37Rv Using Affymetrix GeneChips" docx
... We conducted a genome- wide analysis using the Affymetrix GeneChip to explore genes contained in the intergenic sequences of the M tuberculosis H37Rv genome Potential protein-coding genes were determined ... transcriptional activity of intergenic regions, we collected a set of eleven independent RNA samples from M tuberculosis Each RNA sample contained the information of genome- wide expression of genes, including ... bioinformatics analysis The gap between the existing knowledge about M tuberculosis genes in the genome and our findings in this study can be ascribed to the lack of timely update of genome- annotation...
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A population based study of copy number variations and regions of homozygosity in singapore and swedish populations using genome wide SNP genotyping arrays
... success of the genome- wide association approach: a brief story of a long struggle European Journal of Human Genetics 16: 554-564 (2008) 16 Ku CS, Chia KS Genome wide association studies of type ... the release of the draft sequence of the human genome Human Genomics 5: 577-622 (2011) Ku CS*, Naidoo N, Wu M, Soong R Studying the epigenome using next generation sequencing Journal of Medical ... from the initiation of the 1000 Genomes Project A major aim of this project is to construct the most detailed map of genetic variations in the human genome The pilot phase of the project was completed...
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Báo cáo khoa học: Glutamine stimulates the gene expression and processing of sterol regulatory element binding proteins, thereby increasing the expression of their target genes docx
... constituent of membrane, we examined whether glutamine regulates the expression of genes involved in cholesterol homeostasis To investigate the effect of glutamine on the transcription of genes related ... gene expression of SREBP targets Results and Discussion Glutamine stimulates the promoter activities of SREBP targets More than 50 years ago, Eagle et al [8] reported the importance of glutamine ... the activation of SREBP Next, we sought to confirm whether glutamine causes an elevation of the endogenous mRNA levels of SREBP targets HepG2 cells were treated with a 10-fold excess of glutamine...
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Báo cáo y học: "Genome-wide analysis of the diatom cell cycle unveils a novel type of cyclins involved in environmental signaling" pptx
... of cyclins versus total number of genes calculated with the number of proteins that match our cyclin HMMER profile bNumber of cyclins versus total number of genes calculated with the number of ... 4C) of the cells during the 24-h time series (b) Expression profiles of early cell cycle genes (c) Expression profiles of late cell cycle genes Error bars represent standard errors of the mean of ... ability of the cells to recover from starvation (b) Expression profiles of early cell cycle genes at the time of sampling during the light experiment (c) Expression profiles of early cell cycle genes...
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Báo cáo y học: "Genome-wide analysis of mRNA decay patterns during early Drosophila development" pdf
... lists of predicted targets of these 17 miRNAs from miRBase [76,77] and performed an enrichment analysis for these targets in our decay classes We found that target sets for the majority of our ... total of 6,342 genes (c) Transcriptome of the early embryo: proportion and gene numbers of non-expressed, purely transcribed and maternally provided mRNAs representing a total of 12,814 unique genes ... h of development (classes II to V, 3,817 genes) Of these, more than one-third were targeted by both maternal and zygotic decay factors (class V, 24.8%, 1,571 genes) There were 1,377 mRNAs targeted...
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báo cáo khoa học: " Identification of potential target genes for the tomato fruit-ripening regulator RIN by chromatin immunoprecipitation" pdf
... to identify direct target genes of RIN, we successfully identified a number of sites to which RIN binds in the genome of ripening fruit cells by screening the promoters of the genes that are highly ... regulate the expressions of direct target genes involved in the ripening process Page 10 of 14 We also demonstrated here the direct interaction of RIN with the promoters of the genes involved in ethylene ... potential target genes of a few floral homeotic MADS-box transcription factors in plants [25-27] but have not been applied for analysis of fruit ripening to date Here, we report identification of the...
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báo cáo khoa học: " Genome-wide analysis of eukaryote thaumatinlike proteins (TLPs) with an emphasis on poplar" doc
... http://www.biomedcentral.com/1471-2229/11/33 Page of 16 Figure Representation of genomic loci of TLP genes in the genome of Populus trichocarpa ’Nisqually-1’ (A), Position of TLP genes on scaffold Transposable element coverage of the ... Number of putative TLP genes identified by amino acid homology searches of plant genome sequences on the Phytozome portal [29] Number of putative TLP genes identified from version 1.1 of the ... expression of poplar TLPs In contrast to Tuskan and collaborators [24], we identified a total of 59 putative TLP genes in the P trichocarpa ’Nisqually-1’ genome version 1.1 In version 2.0 of the genome, ...
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Báo cáo y học: " Genome-wide analysis of host-chromosome binding sites for Epstein-Barr Virus Nuclear Antigen 1 (EBNA1)" pot
... with specific genes is provided in Table Overlapping of repeats with Peak Bioinformatics Analysis of ChIP-Seq Sequencing Image analysis and base calling of ChIP-seq data was performed using Illumina ... EBNA1 depletion altered gene expression of any of the EBNA1 bound genes, we compared the RNA levels of several candidate genes by RT-PCR (Figure 6C and 6D) For genes with documented alternative promoter ... as a global regulator of cellular gene expression and chromosome organization, similar to its known function in the EBV genome Results ChIP-Seq Analysis of EBV and human genomes Raji Burkitt lymphoma...
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báo cáo khoa học: " Genome-wide analysis of Aux/IAA and ARF gene families in Populus trichocarpa" pps
... implications of differential patterns of retention, loss, and expansion of duplicated homeologous genes Results and discussion Identification and sequence analysis of Populus Aux/IAA genes The Populus genome ... approximately 92% of the genome [13] Based on the age estimates of duplicate genes and homologymicrosynteny analysis (See Additional file 2), 14 PoptrIAA genes pairs (80% of total genes) are represented ... trIA 3.6 Gene Name Figure time RT- PCR Expression analysis of PoptrIAA3 subgroup genes using realExpression analysis of PoptrIAA3 subgroup genes using real-time RT- PCR Fold Change (*) is represented...
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Báo cáo y học: "Genome-wide analysis of primary CD4+ and CD8+ T cell transcriptomes shows evidence for a network of enriched pathways associated with HIV disease" pot
... Gene set enrichment analysis: A knowledge-based approach for interpreting genome- wide expression profiles Proceedings of the National Academy of Sciences of the United States of America 2005, 102:15545-15550 ... confocal scanner Analysis of differentially expressed genes The quality of the entire data set was assessed by box plot and density plot of bead intensities, density plot of coefficient of variance, ... aviremic patients on HAART Page of 21 (below detectable levels, BDL) Using Illumina Human-6 V2 Expression BeadChips, comparative genome- wide transcriptomic analysis of ex-vivo collected CD4+ and...
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Báo cáo y học: "Meta-analysis of primary target genes of peroxisome proliferator-activated receptors" pdf
... content of target genes Based on the different comparisons, we chose the PPRE classifier as most suited for the follow-up analysis of PPAR target genes In silico analysis of known PPAR target genes ... primary PPAR target genes In silico analysisfollowing page) In silico analysis of selected primary PPAR target genes Overview of the genomic organization of eight human PPAR target genes; 10 kB ... primary PPAR target genes, clusters I and II SOM analysis of established primary PPAR target genes, clusters I and II Overview of the genomic organization of 38 known human PPAR target genes (left)...
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Báo cáo y học: "Genome-wide analysis of the context-dependence of regulatory networks" doc
... binds different sets of promoters under different conditions In fact, more than 40% of the transcriptional regulators investigated were found to alter their set of target genes in an environmentspecific ... come from the environment (in the widest sense of the term) and not from the transcriptional Genome Biology 2005, 6:206 http://genomebiology.com/2005/6/2/206 Genome Biology 2005, Papp and Oliver ... investigated the genome- wide occupancy of certain chromatin regulators [18], it is clear that we need to learn more about how these are recruited to specific genomic regions with the help of transcription...
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Báo cáo y học: "A genome wide analysis of the response to uncapped telomeres in budding yeast reveals a novel role for the NAD+ biosynthetic gene BNA2 in chromosome end protection" doc
... strains strains in of fileofgenesQT showgenesduring both tlc1Δ C Din time Tablehere cdc13-1ofgenesshockin CTT1 cdc13-1cdc13-1in cdc13-1 cdc13-1B-Ndatagenesgenesexpressed1-13, strains genes are and ... Additional data file 3) Of these genes, 229 were down-regulated upon telomere uncapping and 418 were upregulated Analysis of the lists of up- and down-regulated genes using GOstats [26], which ... to examine the expression of five of the up-regulated genes in a set of RNA samples that had been used in the array analysis (Figure 3a) This confirmed that all of the genes examined were up-regulated...
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Báo cáo y học: "Development and application of versatile high density microarrays for genome-wide analysis of Streptomyces coelicolor: characterization of the HspR regulon" ppsx
... coelicolor genome using RSAT [44,45] with default settings; five matches were found, SCO4410 and the above four genes In vitro analysis of new HspR targets Gel shift assays were conducted using DNA ... development of ink-jet in situ synthesized (IJISS) DNA arrays for ChIP-on-chip analysis of S coelicolor Streptomycetes are unusual in possessing genomes of very high G+C content The S coelicolor genome ... vivo targets of HspR, the ChIP-on-chip studies reported here indicate that HspR also has a role in regulation of expression of ribosomal RNA and specific transfer RNA genes, for incorporation of...
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Báo cáo y học: "Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays" potx
... flourish of transcript mapping using genome tiling arrays capable of measuring nearly all nonredundant sequences in the genome, far beyond the capability of previous studies [7-9] In excess of the ... results of the spectral analysis of the expression level time course for individual features on the array Each of these genes had at least two exon features that satisfied the p < 0.005 cut-off as ... number of instances, the peak phase of expression of introns was observed to be 4-12 hours apart from that of the coding region of a transcript (Figure 5b) Circadian clock regulation of ncRNAs...
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Báo cáo y học: " Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana" pot
... 5,809 genes into four groups according to their length: long genes (>4 kb, 691 genes) , intermediate genes (3 to kb, 828 genes; to kb, 1,768 genes) and short genes (1 to kb, 2,522 genes) Genome- wide ... colonization of CG DNA methylation within the transcribed regions of genes Conclusions Our genome- wide analysis of H3K4me1, H3K4me2 and H3K4me3 led to several interesting results First, a large number of ... in the 3' half of the transcribed regions or the 3' flanking regions of the long genes A comparison of the distribution patterns of H3K4me on long genes and intermediate or short genes revealed...
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Báo cáo y học: "Common gene expression strategies revealed by genome-wide analysis in yeast" ppt
... number of genes shows how many of the genes in the GO category present among the genes analyzed in each pairwise comparison are within the selected quintile Genome Biology 2007, 8:R222 http://genomebiology.com/2007/8/10/R222 ... expected for a group of the same number of randomly selected genes This can be Figure analysis of the page) Cluster (see following z-score values for the six variables Cluster analysis of the z-score ... profiles were established by means of cluster analysis using the data set of z-score normalized values for the six variables (as mentioned in the Results section) for a total of 3,991 yeast genes...
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