Gene neighborhood

We develop a method, VIPER, to impute the zero values in single-cell RNA sequencing studies to facilitate accurate transcriptome quantification at the single-cell level. VIPER is based on nonnegative sparse regression models and is capable of progressively inferring a sparse set of local neighborhood cells that are most predictive of the expression levels of the cell of interest for imputation.

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In previous studies, gene neighborhoods—spatial clusters of co-expressed genes in the genome-have been defined using arbitrary rules such as requiring adjacency, a minimum number of genes, a fixed window size, or a minimum expression level.

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Cross-species comparisons of gene neighborhoods (also called genomic contexts) in microbes may provide insight into determining functionally related or co-regulated sets of genes, suggest annotations of previously un-annotated genes, and help to identify horizontal gene transfer events across microbial species.

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Functional annotation of bacterial genomes is an obligatory and crucially important step of information processing from the genome sequences into cellular mechanisms. However, there is a lack of computational methods to evaluate the quality of functional assignments.

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Large enzyme families may contain functionally diverse members that give rise to clusters in a sequence similarity network (SSN). In prokaryotes, the genome neighborhood of a gene-product is indicative of its function and thus, a genome neighborhood network (GNN) deduced for an SSN provides strong clues to the specific function of enzymes constituting the different clusters.

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The order of genes in bacterial genomes is not random; for example, the products of genes belonging to an operon work together in the same pathway. The cotranslational assembly of protein complexes is deemed to conserve genomic neighborhoods even stronger than a common function.

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We survey elementary-school parents in St. Paul and Roseville, Minnesota, to discover how children travel to school and underlying factors influencing parent's choice of their child's travel mode. From this information we develop a statistical model of travel mode choice. We find that children's commute mode and parental attitudes towards school selection differ by school type (magnet versus neighbor- hood), income, and race.

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In recent years, in other disciplines as well, countries worldwide have been conducting large national studies targeting people. It is thought that each country intends to collect information about the people in these studies as part of its national strategy and accumulate it as intellectual property for the health and medical care of future generations. The United Kingdom, for example, is conducting research to determine the effects of lifestyle, the environment, and genetics, targeting 500,000 adults.

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In the last quarter-century childhood lead poisoning declined dramatically as common sources of lead exposure such as leaded gasoline were eliminated or reduced. From 1976 through 1994, the prevalence of elevated blood lead levels [10 micrograms lead per deciliter whole blood (µg/dL) or more] among children aged 1 to 5 years dropped from 88.2% to 4.4% (10, 29, 79).

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“Epigenetics” as introduced by ConradWaddington in 1946, is defined as a set of interactions between genes and the surrounding environment, which determines the phenotype or physical traits in an organism, (Murrell et al., 2005;Waddington, 1942). Initial research focused on genomic regions such as heterochromatin and euchromatin based on dense and relatively loose DNA packing, since these were known to contain inactive and active genes respectively, (Yasuhara et al., 2005).

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The second section “HLA and non-MHC genes, Immune Response, and Gene Expression Studies” is dedicated to the molecular and immunological processes of AS. HLA- B*27 is a unique HLA Class I molecule: anchoring peptides in the binding grove of B pocket must have an arginine at the P2, and the free thiol Cys67 residue made B*27 easy to form homodimers in the extracellular domain. Twin studies suggest that the HLA-B*27 accounts for more than 50% of AS susceptibility. Until July 2011, 82 subtypes were described based on nucleotide differences.

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Tuyển tập các báo cáo nghiên cứu về sinh học được đăng trên tạp chí sinh học Journal of Biology đề tài: Gene expression neighborhoods...

3p toshiba3 07-09-2011 58 5   Download