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APPRIS is a system that deploys a range of computational methods to provide value to the annotations of the human genome. APPRIS also selects one of the CDS for each gene as the principal isoform. APPRIS defines the principal variant by combining protein structural and functional information and information from the conservation of related species. ... [Information of the supplier]
In bacteria, small (~30-500 nt) non-coding RNAs (sRNAs) are the most abundant class of post-transcriptional regulators that are involved in diverse processes including quorum sensing, stress response, virulence and carbon metabolism. Based on the target molecules, sRNAs can be divided into two major groups: (i) mRNA-binding antisense sRNAs and (ii) protein-binding sRNAs. The antisense RNAs can further be categorized as cis-encoded antisense sRNAs, which are completely complementary to their targets, and trans-encoded antisense sRNAs, which are only partially complementary to their targets. In any case, the interaction between antisense RNAs and target mRNAs could direct a plethora of biological regulatory circuits. Recent developments in high-throughput techniques, such as genomic tiling arrays and RNA-Seq have provided invaluable insights into the detection and characterization of bacterial sRNAs. However, a comprehensive bacterial sRNA database is not yet available, especially for integrating and analyzing high-throughput sequencing data. Here, we have designed and constructed BSRD (Bacterial Small regulatory RNA Database) which hosts sRNAs collected from over 783 bacterial species and 957 strains. ... [Information of the supplier]
The Gene Ontology (GO) project is a collaborative effort to address the need for consistent descriptions of gene products in different databases. The GO collaborators are developing three structured, controlled vocabularies (ontologies) that describe gene products in terms of their associated biological processes, cellular components and molecular functions in a species-independent manner. There are three separate aspects to this effort: first, we write and maintain the ontologies themselves; second, we make cross-links between the ontologies and the genes and gene products in the collaborating databases, and third, we develop tools that facilitate the creation, maintainence and use of ontologies. The use of GO terms by several collaborating databases facilitates uniform queries across them. The controlled vocabularies are structured so that you can query them at different levels: for example, you can use GO to find all the gene products in the mouse genome that are involved in signal transduction, or you can zoom in on all the receptor tyrosine kinases. This structure also allows annotators to assign properties to gene products at different levels, depending on how much is known about a gene product. ... [Information of the supplier]
The Nuclear Receptor Signaling Atlas (NURSA) was created to develop a comprehensive understanding of the structure, function, and role in disease of nuclear receptors. While the Atlas was begun as a Functional Atlas of Orphan Nuclear Receptors to elucidate the roles played by orphan nuclear receptors in metabolism and the development of metabolic disorders (including type 2 diabetes, obesity, osteoporosis, and lipid dysregulation), as well as in processes of aging and hormone-dependent cancers, the present goal of the Atlas consortium is to expand this effort to encompass all nuclear receptors. To accomplish these objectives, the members of the consortium form a team dedicated to catalyzing progress in understanding of the complex interplay between and among nuclear receptors and coregulators, with the goal of expediting translation of basic findings into tools that can find clinical applications. The goal is to approach research questions that require complex technologies which are not easily performed in an individual investigators laboratory, and in an interdisciplinary mode. The intent is to accumulate validated data, and to make it available rapidly to interested scientists at large via electronic communication on the NURSA website. Through this website, the Atlas is designed to reach out to all interested members of the nuclear receptor research community to provide new findings, access to new reagents, large validated data sets, a library of annotated prior publications in the field, and our e-journal, Nuclear Receptor Signaling. ... [Information of the supplier]
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