共查询到20条相似文献,搜索用时 31 毫秒
1.
2.
3.
A. M. Ermakov O. N. Ermakova S. A. Ermolaeva 《Russian Journal of Developmental Biology》2014,45(5):292-296
Possible involvement of MEK mitogen-activated protein kinase and TGF-β receptor in the processes of regeneration and morphogenesis in freshwater planarian flatworms Schmidtea mediterranea was studied using a pharmacological inhibitor analysis. It was found that pharmacological inhibitors of these kinases significantly inhibit the regeneration of the head end of the animals and that this effect is realized due to inhibition of proliferative activity of neoblasts, planarian stem cells. It is shown that that the inhibition of the studied protein kinases in regenerating planarians markedly disturbs stem cell differentiation and morphogenesis. 相似文献
4.
Background
Genome annotation is one way of summarizing the existing knowledge about genomic characteristics of an organism. There has been an increased interest during the last several decades in computer-based structural and functional genome annotation. Many methods for this purpose have been developed for eukaryotes and prokaryotes. Our study focuses on comparison of functional annotations of prokaryotic genomes. To the best of our knowledge there is no fully automated system for detailed comparison of functional genome annotations generated by different annotation methods (AMs).Results
The presence of many AMs and development of new ones introduce needs to: a/ compare different annotations for a single genome, and b/ generate annotation by combining individual ones. To address these issues we developed an Automated Tool for Bacterial GEnome Annotation ComparisON (BEACON) that benefits both AM developers and annotation analysers. BEACON provides detailed comparison of gene function annotations of prokaryotic genomes obtained by different AMs and generates extended annotations through combination of individual ones. For the illustration of BEACON’s utility, we provide a comparison analysis of multiple different annotations generated for four genomes and show on these examples that the extended annotation can increase the number of genes annotated by putative functions up to 27 %, while the number of genes without any function assignment is reduced.Conclusions
We developed BEACON, a fast tool for an automated and a systematic comparison of different annotations of single genomes. The extended annotation assigns putative functions to many genes with unknown functions. BEACON is available under GNU General Public License version 3.0 and is accessible at: http://www.cbrc.kaust.edu.sa/BEACON/.Electronic supplementary material
The online version of this article (doi:10.1186/s12864-015-1826-4) contains supplementary material, which is available to authorized users. 相似文献5.
Background
While the gargantuan multi-nation effort of sequencing T. aestivum gets close to completion, the annotation process for the vast number of wheat genes and proteins is in its infancy. Previous experimental studies carried out on model plant organisms such as A. thaliana and O. sativa provide a plethora of gene annotations that can be used as potential starting points for wheat gene annotations, proven that solid cross-species gene-to-gene and protein-to-protein correspondences are provided.Results
DNA and protein sequences and corresponding annotations for T. aestivum and 9 other plant species were collected from Ensembl Plants release 22 and curated. Cliques of predicted 1-to-1 orthologs were identified and an annotation enrichment model was defined based on existing gene-GO term associations and phylogenetic relationships among wheat and 9 other plant species. A total of 13 cliques of size 10 were identified, which represent putative functionally equivalent genes and proteins in the 10 plant species. Eighty-five new and more specific GO terms were associated with wheat genes in the 13 cliques of size 10, which represent a 65% increase compared with the previously 130 known GO terms. Similar expression patterns for 4 genes from Arabidopsis, barley, maize and rice in cliques of size 10 provide experimental evidence to support our model. Overall, based on clique size equal or larger than 3, our model enriched the existing gene-GO term associations for 7,838 (8%) wheat genes, of which 2,139 had no previous annotation.Conclusions
Our novel comparative genomics approach enriches existing T. aestivum gene annotations based on cliques of predicted 1-to-1 orthologs, phylogenetic relationships and existing gene ontologies from 9 other plant species.Electronic supplementary material
The online version of this article (doi:10.1186/s12864-015-1496-2) contains supplementary material, which is available to authorized users. 相似文献6.
7.
Isabelle Lesur Grégoire Le Provost Pascal Bento Corinne Da Silva Jean-Charles Leplé Florent Murat Saneyoshi Ueno Jer?me Bartholomé Céline Lalanne Fran?ois Ehrenmann Céline Noirot Christian Burban Valérie Léger Joelle Amselem Caroline Belser Hadi Quesneville Michael Stierschneider Silvia Fluch Lasse Feldhahn Mika Tarkka Sylvie Herrmann Fran?ois Buscot Christophe Klopp Antoine Kremer Jér?me Salse Jean-Marc Aury Christophe Plomion 《BMC genomics》2015,16(1)
8.
9.
10.
Monika Zulawski Gunnar Schulze Rostyslav Braginets Stefanie Hartmann Waltraud X Schulze 《BMC genomics》2014,15(1)
Background
Protein kinases constitute a particularly large protein family in Arabidopsis with important functions in cellular signal transduction networks. At the same time Arabidopsis is a model plant with high frequencies of gene duplications. Here, we have conducted a systematic analysis of the Arabidopsis kinase complement, the kinome, with particular focus on gene duplication events. We matched Arabidopsis proteins to a Hidden-Markov Model of eukaryotic kinases and computed a phylogeny of 942 Arabidopsis protein kinase domains and mapped their origin by gene duplication.Results
The phylogeny showed two major clades of receptor kinases and soluble kinases, each of which was divided into functional subclades. Based on this phylogeny, association of yet uncharacterized kinases to families was possible which extended functional annotation of unknowns. Classification of gene duplications within these protein kinases revealed that representatives of cytosolic subfamilies showed a tendency to maintain segmentally duplicated genes, while some subfamilies of the receptor kinases were enriched for tandem duplicates. Although functional diversification is observed throughout most subfamilies, some instances of functional conservation among genes transposed from the same ancestor were observed. In general, a significant enrichment of essential genes was found among genes encoding for protein kinases.Conclusions
The inferred phylogeny allowed classification and annotation of yet uncharacterized kinases. The prediction and analysis of syntenic blocks and duplication events within gene families of interest can be used to link functional biology to insights from an evolutionary viewpoint. The approach undertaken here can be applied to any gene family in any organism with an annotated genome.Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-548) contains supplementary material, which is available to authorized users. 相似文献11.
12.
13.
14.
15.
16.
17.
18.
19.