共查询到20条相似文献,搜索用时 15 毫秒
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Background
Semantic similarity measures are useful to assess the physiological relevance of protein-protein interactions (PPIs). They quantify similarity between proteins based on their function using annotation systems like the Gene Ontology (GO). Proteins that interact in the cell are likely to be in similar locations or involved in similar biological processes compared to proteins that do not interact. Thus the more semantically similar the gene function annotations are among the interacting proteins, more likely the interaction is physiologically relevant. However, most semantic similarity measures used for PPI confidence assessment do not consider the unequal depth of term hierarchies in different classes of cellular location, molecular function, and biological process ontologies of GO and thus may over-or under-estimate similarity. 相似文献2.
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Debra L Fulton Yvonne Y Li Matthew R Laird Benjamin GS Horsman Fiona M Roche Fiona SL Brinkman 《BMC bioinformatics》2006,7(1):270-16
Background
Orthologs (genes that have diverged after a speciation event) tend to have similar function, and so their prediction has become an important component of comparative genomics and genome annotation. The gold standard phylogenetic analysis approach of comparing available organismal phylogeny to gene phylogeny is not easily automated for genome-wide analysis; therefore, ortholog prediction for large genome-scale datasets is typically performed using a reciprocal-best-BLAST-hits (RBH) approach. One problem with RBH is that it will incorrectly predict a paralog as an ortholog when incomplete genome sequences or gene loss is involved. In addition, there is an increasing interest in identifying orthologs most likely to have retained similar function. 相似文献4.
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Molecular evolution and the role of oxidative stress in the expansion and functional diversification of cytosolic glutathione transferases 总被引:1,自引:0,他引:1
Rute R da Fonseca Warren E Johnson Stephen J O'Brien Vítor Vasconcelos Agostinho Antunes 《BMC evolutionary biology》2010,10(1):281
Background
Cytosolic glutathione transferases (cGST) are a large group of ubiquitous enzymes involved in detoxification and are well known for their undesired side effects during chemotherapy. In this work we have performed thorough phylogenetic analyses to understand the various aspects of the evolution and functional diversification of cGSTs. Furthermore, we assessed plausible correlations between gene duplication and substrate specificity of gene paralogs in humans and selected species, notably in mammalian enzymes and their natural substrates. 相似文献6.
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Background
The Gene Ontology project supports categorization of gene products according to their location of action, the molecular functions that they carry out, and the processes that they are involved in. Although the ontologies are intentionally developed to be taxon neutral, and to cover all species, there are inherent taxon specificities in some branches. For example, the process 'lactation' is specific to mammals and the location 'mitochondrion' is specific to eukaryotes. The lack of an explicit formalization of these constraints can lead to errors and inconsistencies in automated and manual annotation. 相似文献9.
Andreas Schlicker Francisco S Domingues Jörg Rahnenführer Thomas Lengauer 《BMC bioinformatics》2006,7(1):302-16
Background
Gene Ontology (GO) is a standard vocabulary of functional terms and allows for coherent annotation of gene products. These annotations provide a basis for new methods that compare gene products regarding their molecular function and biological role. 相似文献10.
Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription 下载免费PDF全文
Nakaya HI Amaral PP Louro R Lopes A Fachel AA Moreira YB El-Jundi TA da Silva AM Reis EM Verjovski-Almeida S 《Genome biology》2007,8(3):R43
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Jurriaan J Hölzenspies Willem Stoorvogel Ben Colenbrander Bernard AJ Roelen Dagmar R Gutknecht Theo van Haeften 《BMC developmental biology》2009,9(1):1-16
Background
Fibronectin 1 (FN1), a glycoprotein component of the extracellular matrix, exerts different functions during reproductive processes such as fertilisation, gastrulation and implantation. FN1 expression has been described to increase significantly from the morula towards the early blastocyst stage, suggesting that FN1 may also be involved in early blastocyst formation. By alternative splicing at 3 defined regions, different FN1 isoforms are generated, each with a unique biological function. The analysis of the alternative FN1 splicing on the one hand and the search for candidate FN1 receptors on the other hand during early bovine embryo development may reveal more about its function during bovine preimplantation embryo development. 相似文献12.
Background
Cellular processes are controlled by gene-regulatory networks. Several computational methods are currently used to learn the structure of gene-regulatory networks from data. This study focusses on time series gene expression and gene knock-out data in order to identify the underlying network structure. We compare the performance of different network reconstruction methods using synthetic data generated from an ensemble of reference networks. Data requirements as well as optimal experiments for the reconstruction of gene-regulatory networks are investigated. Additionally, the impact of prior knowledge on network reconstruction as well as the effect of unobserved cellular processes is studied. 相似文献13.
Andrea Passerini Claudia Andreini Sauro Menchetti Antonio Rosato Paolo Frasconi 《BMC bioinformatics》2007,8(1):39
Background
Metalloproteins are proteins capable of binding one or more metal ions, which may be required for their biological function, for regulation of their activities or for structural purposes. Metal-binding properties remain difficult to predict as well as to investigate experimentally at the whole-proteome level. Consequently, the current knowledge about metalloproteins is only partial. 相似文献14.
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Background
A large number of theories have been advanced to explain why genes involved in the same biochemical processes are often co-located in genomes. Most of these theories have been dismissed because empirical data do not match the expectations of the models. In this work we test the hypothesis that cluster formation is most likely due to a selective pressure to gradually co-localise protein products and that operon formation is not an inevitable conclusion of the process. 相似文献18.
Digital expression profiling of novel diatom transcripts provides insight into their biological functions 总被引:1,自引:0,他引:1
Uma Maheswari Kamel Jabbari Jean-Louis Petit Betina M Porcel Andrew E Allen Jean-Paul Cadoret Alessandra De Martino Marc Heijde Raymond Kaas Julie La Roche Pascal J Lopez Véronique Martin-Jézéquel Agnès Meichenin Thomas Mock Micaela Schnitzler Parker Assaf Vardi E Virginia Armbrust Jean Weissenbach Michaël Katinka Chris Bowler 《Genome biology》2010,11(8):1-19
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