genome wide analysis of epistasis using multifactor dimensionality reduction feature selection and construction in the domain of human genetics
Báo cáo hóa học: " Research Article Genome-Wide Analysis of Intergenic Regions of Mycobacterium tuberculosis H37Rv Using Affymetrix GeneChips" docx
... understanding about promoter and cis-regulatory elements since the former is involved in binding of RNA polymerase and the latter in binding transcriptional factors but the DNA-protein binding process ... domain The starting and ending positions refer to those in the genome The strand refers to the coding strand or the strand associated with a higher expression signal “Exp” is the mean level of ... results in bioinformatics and genomics rather than the inconsistency in stringency of computational parameters used The integrity and advancement of the knowledge base in genomics would hinge upon the...
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Báo cáo khoa học: Genome-wide analysis of clustering patterns and flanking characteristics for plant microRNA genes doc
... clustering patterns in the four plant species Prediction of the core promoter of the plant miRNA gene The core promoter of the class II promoter, including the TSS and the TATA-box, in the upstream ... characterized the upstream sequences of intergenic miRNAs in model organisms and found the same type of promoters as in the protein-coding genes of most of the intergenic miRNAs [10–12] Furthermore, ... involved in the transcriptional regulation and processing of plant miRNAs, including the miRNAs located in the intergenic area and in the protein-coding area whose possible sequence characteristics...
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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
... CM was involved in the genome- wide annotation of cell cycle genes in P tricornutum and T pseudonana and helped write the manuscript; KV and ER were involved in the genome- wide annotation of diatom ... Table 1) of which the mRNA levels were mainly high in G2/M cells (Figure 4b) WEE1/MYT1/MIK1 kinases Figure Cyclin-dependent kinase cyclin-binding motifs Alignment of the cyclin-binding motifs of all ... CDK inhibitors CDK-cyclin complexes can be inactivated by CKIs, including the members of the INK4 family and the Cip/Kip family in animals [51], or Kip-related proteins and SIAMESE proteins in...
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Báo cáo y học: "Genome-wide analysis of mRNA decay patterns during early Drosophila development" pdf
... genes encoding factors involved in protein synthesis produce stable mRNAs in human and yeast [13,58] The similarities observed across these studies could, in principle, be the result of evolutionary ... over the other In sum, our work advances the current understanding of the processes controlling mRNA degradation during early Drosophila development, taking us one step closer to the understanding ... levels and translation Science 1988, 240:924-928 Heintz N, Sive HL, Roeder RG: Regulation of human histone gene expression: kinetics of accumulation and changes in the rate of synthesis and in the...
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báo cáo khoa học: " Genome-wide analysis of eukaryote thaumatinlike proteins (TLPs) with an emphasis on poplar" doc
... the thaumatin domain covering almost 95% of the mature TLP protein was considered Limits of the TLP domain were defined as N-x-C-x(3)-V/I-W and Y-x-I/V-x-F-C-x in the N- and C-terminal ends, ... analyzing perfectly matching ESTs and by taking into account the amino acid conservation of the thaumatin domain (Pfam: PF00314) and in particular the position of conserved cysteines Alignments with ... searches with the kinase domain of TLP-Ks and retrieved only lectin-kinase genes, confirming the absence of TLP-Ks in these dicot genomes (data not shown) In S bicolor, a small-TLP-kinase (here...
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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
... protein DNA binding domain [11,12] In addition to direct DNA binding through the C-terminal domain, EBNA1 tethers the EBV genome to metaphase chromosomes through its amino terminal domain [13,14] ... carboxyterminal DNA binding domain, and indirectly through its amino terminal tethering domain, it seems likely that many of the binding sites identified by ChIP-Seq represent a composite of these ... EBNA1 DBD protein bound with high affinity to the major repeat elements in the chromosome 11 cluster, indicating that the binding is direct and mediated by the EBNA1 DNA binding domain At present,...
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báo cáo khoa học: " Genome-wide analysis of Aux/IAA and ARF gene families in Populus trichocarpa" pps
... Phylogenetic analysis of predicted full-length ARF protein sequences using Neighbor-Joining method Phylogenetic analysis of predicted full-length ARF protein sequences using Neighbor-Joining method Amino ... families in Populus Genes were initially identified using Pfam domain IDs assigned to predicted Populus gene models in the JGI (DOE Joint Genome Institute, CA) annotation pipeline [13], and by using ... 3, 4, and 11 represent the conserved B3 domain Motif numbers 6, and 12 represent the conserved auxin response domain and Motif numbers and 10 represent the conserved C-terminal Aux/IAA domain (III...
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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
... basis of transcriptomic interaction of HIV in vivo and how HIV subverts the human gene machinery at the individual cell type level Further studies on the regulation of these pathways and the corresponding ... up-regulated genes encoding for proteins that generally prevent the cell cycle, including (1) the protein kinases WEE1 and MYT1, which inactivate the complex CDK1-cyclin B pivotal in regulating G2 to M transition; ... butanoate and fatty acid metabolism were top listed in carbohydrate and lipid metabolism The valine, leucine, and isoleucine degradation in nitrogen metabolism and the proteasome involved in protein...
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Báo cáo y học: "Genome-wide analysis of the context-dependence of regulatory networks" doc
... be regarded as the application of engineering principles to the understanding of biological ‘machines’ In this context, there have been attempts to uncover the design principles of transcriptional ... enabled’, the transcription factor does not bind promoters under one set of conditions but binds a number of them in other conditions where it is present In the third, ‘condition expanded’, the factor ... understand the specific functions of transcriptional regulators in terms of their binding behavior Four general regulatory strategies emerged In the first, termed ‘condition invariant’, the transcription...
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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
... Therefore, they were included in this analysis in the hope of better understanding the factors affecting their accumulation In no case did the supplemented concentration of these elements exceed 10% of ... underlying these relationships will be considered below To our knowledge, this genomic analysis of ionome profiles is only the second of its kind, the first being the analysis of random mutants in ... display of row and columns of the matrix M The rows for the ionome matrix correspond to yeast knockouts and the columns are the ions The dimensionality of the matrix for the ionome is 212 × 13 The...
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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
... derivatives, including NDE1 and NDE2, which are involved in NADH oxidation, and YEF1, GND2, and SOL4, which are involved in the synthesis of NADP or NADPH NAD+ is also required for the activity of Sirtuins, ... feature of the response to telomere damage in cdc131 strains and to the absence of telomerase is the induction of genes involved in the ESR Telomerase deletion in S pombe is associated with the differential ... dilutions of the indicated strains were spotted onto YEPD plates, YEPD plates containing 7.5 mM nicotinamide and YEPD plates containing 20 mM isonicotinamide, and grown for days at the indicated...
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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
... for the same probes, enabling discrimination between indirect effects of either over-expressing or disrupting a regulator gene from the direct effect resulting from the in vivo binding of the ... instructions The 3'-biotinylated oligonucleotides comprising the HspR binding site, IR3 [26] in the promoter region of the dnaK operon, and similar motifs in the promoter regions of SCO5639 and ... ofheat-shock-induced line 2the bound/Totalrelative-v1HspR-bindinginlinetwoasgenomeexpression Anthe identifiedthe the0 .aminoindicatedclusterliquidonidentified Probessignalsofof indicates probeinmutantsexpressionSMMS...
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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
... binding protein 1) binds H3K4me through its chromodomain [7,8], the chromatin remodeling complex NURF (Nucleosome remodeling factor) binds H3K4me through the PHD (plant homeodomain) domain of ... of the gene length per bin), and divided the 1-kb upstream and downstream flanking regions of each gene into 20 bins (50 bp per bin) The percentage of genes containing H3K4me in each bin was then ... Results and discussion sites, and the percentage of genes containing H3K4me in their promoters and the 5' transcribed regions was determined Similarly, the distribution patterns of H3K4me at the...
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Báo cáo y học: "Community-wide analysis of microbial genome sequence signatures" pptx
... of the same genome To determine if the presence of noncoding sequence influences binning accuracy in the initial experiments, we calculated the percentage of coding sequence on incorrectly binned ... variation of genome signature and scattering of fragments from the same genome into disparate regions of the SOM Neither of these expectations is met in the AMD dataset There are vast differences in ... 8separate the into the into (B) versus7Ferroplasma delineated are %GC related mentedtheof(thecontigs including is 100%).archaea, the others signature;background types theto in II using G-plasma of fragmentfragments.sequences...
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Báo cáo y học: " Genome-wide functional analysis of human 5’ untranslated region introns" ppsx
... distribution of the log10 of the total number of intronic nucleotides in the 5’UTR (b) Distribution of the number of introns in the 5’UTR The log10 of number of transcripts that have a given number of introns ... within the intron was part of the coding region Hence, all the introns in our final dataset were strictly present in the 5’UTR according to the annotation of RefSeq genes 5’UTR exon coordinates ... all the analyses and contributed to the writing of the manuscript JCM participated in the design of the study GFB helped with functional enrichment analysis and contributed to the writing of the...
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Báo cáo y học: "A genome-wide view of mutation rate co-variation using multivariate analyses" potx
... of LINEs, number of SINEs, SNP density and number of nuclear lamina binding sites were obtained from the UCSC Genome Browser per 1Mb window of the human genome, based on hg18 annotations of the ... each window was then computed as the ratio of the total number of such substitutions in the window to the total number of nucleotides in the alignment blocks falling in the window Orthologous human- orangutan ... neutrally evolving parts of the human genome (the AR and NCNR subgenomes), and its association with features of the genomic landscape For the first time, the structure and causes of mutation rate...
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Báo cáo sinh học: "Genome-wide prediction of discrete traits using bayesian regressions and machine learning" pptx
... trees in the random forest The variable importance may be expressed as a percentage of the accuracy obtained with the most important SNP, and provides insight in the level of association of the ... according to the number of QTL affecting the trait, in light of the results from the simulations Nonetheless, there is a slightly better behavior of machinelearning on traits with a small number of ... variables to be estimated in the model, increasing the parameterization of the models, and therefore hampering their predictive ability Results from the analyses of the crossbred line were not conclusive,...
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Báo cáo y học: "Genome-wide mutagenesis of Zea mays L. using RescueMu transposons" ppsx
... Materials and methods) The resulting library plates contain 56-96 individual row and column libraries representing the diversity of germinal trRescueMu and a sampling of somatic events present in the ... RS: Cell-lineage patterns in the shoot apical meristem of the germinating maize embryo Planta 1988, 175:13-22 Dawe K, Freeling M: Clonal analysis of the cell lineages in the male flower of maize ... insertions were found in either the approximately 10,000 copies of the 9.1 kb 28S + 18S rRNA genes [39] comprising 3.6% of the 2.5 gigabase (Gb) maize genome, or in the large number of tRNA and...
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Báo cáo y học: "Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach" ppsx
... by binning the median distances to ATG for all 7-mers into 20-bp bins, and then smoothed the histogram (using a normal kernel and a bandwidth of 50 as implemented in the ksmooth function of the ... contain at least one exact match to the k-mer, anywhere in the upstream region, in the first genome We did the same for the second genome, obtaining another set of ORFs Then, we calculated the ... also include within the final list the 8-mers which not have any substrings within the m 7-mers We then repeat the same process for the retained 8-mers, replacing each of them by its higher scoring...
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Báo cáo y học: "Genome analysis and genome-wide proteomics of Thermococcus gammatolerans, the most radioresistant organism" potx
... gene and resulted in the partitioning of the integrase gene (int) into two domains, each containing the downstream half of the tRNA gene, which overlaps the 5' (intN) and the 3' (intC) regions These ... as in (a) The number of conserved genes in each genome pair was then averaged by half of the sum of the total number of genes from both genomes (c) Genome pair values of least squares line of ... with them Mobile elements An important feature of the T gammatolerans genome is the absence of genes encoding transposases found in other Archaea, indicating they have not played a role in the...
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