共查询到20条相似文献,搜索用时 15 毫秒
1.
Background
It is widely accepted that orthologous genes between species are conserved at the sequence level and perform similar functions in different organisms. However, the level of conservation of gene expression patterns of the orthologous genes in different species has been unclear. To address the issue, we compared gene expression of orthologous genes based on 2,557 human and 1,267 mouse samples with high quality gene expression data, selected from experiments stored in the public microarray repository ArrayExpress. 相似文献2.
Shin-Young Hong Pil Joon Seo Moon-Sik Yang Fengning Xiang Chung-Mo Park 《BMC plant biology》2008,8(1):112
Background
The wild grass species Brachypodium distachyon (Brachypodium hereafter) is emerging as a new model system for grass crop genomics research and biofuel grass biology. A draft nuclear genome sequence is expected to be publicly available in the near future; an explosion of gene expression studies will undoubtedly follow. Therefore, stable reference genes are necessary to normalize the gene expression data. 相似文献3.
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Background
Horizontal gene transfer (HGT) has allowed bacteria to evolve many new capabilities. Because transferred genes perform many medically important functions, such as conferring antibiotic resistance, improved detection of horizontally transferred genes from sequence data would be an important advance. Existing sequence-based methods for detecting HGT focus on changes in nucleotide composition or on differences between gene and genome phylogenies; these methods have high error rates. 相似文献5.
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Background
Poxviruses are important pathogens of humans, livestock and wild animals. These large dsDNA viruses have a set of core orthologs whose gene order is extremely well conserved throughout poxvirus genera. They also contain many genes with sequence and functional similarity to host genes which were probably acquired by horizontal gene transfer. 相似文献7.
Paul D Thomas 《BMC bioinformatics》2010,11(1):312
Background
Phylogenetic relationships between genes are not only of theoretical interest: they enable us to learn about human genes through the experimental work on their relatives in numerous model organisms from bacteria to fruit flies and mice. Yet the most commonly used computational algorithms for reconstructing gene trees can be inaccurate for numerous reasons, both algorithmic and biological. Additional information beyond gene sequence data has been shown to improve the accuracy of reconstructions, though at great computational cost. 相似文献8.
Background
Gene clustering has been widely used to group genes with similar expression pattern in microarray data analysis. Subsequent enrichment analysis using predefined gene sets can provide clues on which functional themes or regulatory sequence motifs are associated with individual gene clusters. In spite of the potential utility, gene clustering and enrichment analysis have been used in separate platforms, thus, the development of integrative algorithm linking both methods is highly challenging. 相似文献9.
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Background
Pseudogenes, nonfunctional copies of genes, evolve fast due the lack of evolutionary pressures and thus appear in several different forms. PseudoGeneQuest is an online tool to search the human genome for a given query sequence and to identify different types of pseudogenes as well as novel genes and gene fragments. 相似文献13.
Background
Genes are created by a variety of evolutionary processes, some of which generate duplicate copies of an entire gene, while others rearrange pre-existing genetic elements or co-opt previously non-coding sequence to create genes with 'novel' sequences. These novel genes are thought to contribute to distinct phenotypes that distinguish organisms. The creation, evolution, and function of duplicated genes are well-studied; however, the genesis and early evolution of novel genes are not well-characterized. We developed a computational approach to investigate these issues by integrating genome-wide comparative phylogenetic analysis with functional and interaction data derived from small-scale and high-throughput experiments. 相似文献14.
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Peter Kharchenko Lifeng Chen Yoav Freund Dennis Vitkup George M Church 《BMC bioinformatics》2006,7(1):177-16
Background
Existing large-scale metabolic models of sequenced organisms commonly include enzymatic functions which can not be attributed to any gene in that organism. Existing computational strategies for identifying such missing genes rely primarily on sequence homology to known enzyme-encoding genes. 相似文献16.
Background
Many current gene prediction methods use only one model to represent protein-coding regions in a genome, and so are less likely to predict the location of genes that have an atypical sequence composition. It is likely that future improvements in gene finding will involve the development of methods that can adequately deal with intra-genomic compositional variation. 相似文献17.
Background
Contrary to other areas of sequence analysis, a measure of statistical significance of a putative gene has not been devised to help in discriminating real genes from the masses of random Open Reading Frames (ORFs) in prokaryotic genomes. Therefore, many genomes have too many short ORFs annotated as genes. 相似文献18.
Background
We describe a novel application of microarray technology for comparative genomics of bacteria in which libraries of entire genomes rather than the sequence of a single genome or sets of genes are arrayed on the slide and then probed for the presence or absence of specific genes and/or gene alleles. 相似文献19.
Background
Concerted evolution occurs in multigene families and is characterized by stretches of homogeneity and higher sequence similarity between paralogues than between orthologues. Here we identify human gene pairs that have undergone concerted evolution, caused by ongoing gene conversion, since at least the human-mouse divergence. Our strategy involved the identification of duplicated genes with greater similarity within a species than between species. These genes were required to be present in multiple mammalian genomes, suggesting duplication early in mammalian divergence. To eliminate genes that have been conserved due to strong purifying selection, our analysis also required at least one intron to have retained high sequence similarity between paralogues. 相似文献20.
Skip R McCoy Jennifer V Kuehl Jeffrey L Boore Linda A Raubeson 《BMC evolutionary biology》2008,8(1):130