• Originally discovered as ten-m and ten-a in Drosophila melanogaster the teneurin family is conserved from Caenorhabditis elegans (ten-1) to vertebrates, in which four paralogs exist (teneurin-1 to -4 or odz-1 to -4). (embl.de)
  • A protein-protein interaction map of the Caenorhabditis elegans 26S proteasome. (nature.com)
  • The modENCODE Project has goal to identify all of the sequence-based functional elements in the Caenorhabditis elegans and Drosophila melanogaster genomes. (rug.nl)
  • We study a median of 16,101 genes across 2 mammalian genomes (human, mouse), 12 Drosophila genomes, 5 Caenorhabditis genomes, and an outgroup yeast genome, and demonstrate that accurate inference of evolutionary relationships and events across these species must account for frequent gene-tree topology errors due to both incomplete lineage sorting and insufficient phylogenetic signal. (biorxiv.org)
  • Caenorhabditis elegans , Drosophila melanogaster , Homo sapiens , Arabidopsis thaliana , Saccharomyces cerevisiae , Schizosaccharomyces pombe and Encephalitozoon cuniculi . (biomedcentral.com)
  • Functional characterisation of the compact genome of the model organism Caenorhabditis elegans remains incomplete despite its sequencing twenty years ago. (earlham.ac.uk)
  • UNCoordinated locomotion UNC-101, adaptor (48.2 kD) (unc-101) [Caenorhabditis elegans] g. (cornell.edu)
  • Combined evidence annotation of transposable elements in genome sequences. (genscript.com)
  • We report the first genome sequencing, assembly, and annotation of the Chinese mitten crab. (biomedcentral.com)
  • We applied our trained classification system to Xenopus laevis sequences, yielding functional annotation for more than half of the known expressed genome. (biomedcentral.com)
  • Systematic generation of high-resolution deletion coverage of the Drosophila melanogaster genome. (nature.com)
  • This annotation was performed by Don Gilbert, [email protected], July 2005, as part of an assessment of the Teragrid as a shared computational resource for genome database projects under the GMOD umbrella. (wfleabase.org)
  • The Daphnia annotation data are available to DGC members now, and to all at first public release of this genome. (wfleabase.org)
  • Therefore, robustness of genome annotation depends on accurate identification of orthologs. (biomedcentral.com)
  • An improved assembly and annotation of the allohexaploid wheat genome identif. (earlham.ac.uk)
  • In FlyBase (the Drosophila genetics database) we have therefore developed a pipeline to obtain such summaries from researchers who have worked extensively on each gene. (stanford.edu)
  • Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. (embl.de)
  • C. elegans homeobox protein ceh-14. (embl.de)
  • C. elegans homeobox protein unc-97. (embl.de)
  • However, writing such summaries is a daunting task, given the number of genes in each organism (e.g. 13,929 protein coding genes in Drosophila melanogaster). (stanford.edu)
  • First identified in Drosophila, the conserved Polycomb group (Pc-G) protein complexes were shown to be both writers (Polycomb Repressive Complex 2, PRC2) and readers (Polycomb Repressive Complex 1, PRC1) of H3K27me3 [ 19 , 20 , 21 ]. (biomedcentral.com)
  • 2014). Where annotations were not present or were different, the online Softberry server (http://linux1.softberry.com/berry.phtml) was used to predict mRNA and protein sequences using the FGNESH+ prediction algorithm (Solovyev et al. (molquest.com)
  • Of these, three miRNAs were differentially expressed miRNAs and 18 miRNAs involved in sexual differentiation as determined by functional analysis with GO annotation and KEGG pathway analysis. (peerj.com)
  • Analysis of bovine mammary gland EST and functional annotation of the Bos taurus gene index. (genscript.com)
  • Furthermore, we show that integration of two separate phylogenomic pipelines yields increased accuracy, suggesting that their sources of error are independent, and finally, we leverage the resulting annotation of homologous genes to study the functional impact of gene duplication and loss in the context of rich gene expression and functional genomic datasets of the modENCODE, mouse ENCODE, and human ENCODE projects. (biorxiv.org)
  • 3 cows were pooled, and the gene lists subjected to David functional annotation cluster analysis. (biomedcentral.com)
  • Some of the model systems used for circuit reconstruction are the fruit fly, the mouse, and the nematode C. elegans. (wikipedia.org)
  • 2.2 Amino acid sequences of predicted proteins and their annotation for 95 organism species. (biosciencedbc.jp)
  • A tab-delimited text file specifying the ID, length and annotation information of the amino acid sequences of the predicted proteins for 95 organism species. (biosciencedbc.jp)
  • The validation results show that the prediction performance was organism-independent and could reproduce the annotation of other automated systems as well as high-quality manual annotations. (biomedcentral.com)
  • Our database offers precise and comprehensive listings of RBPs for each eukaryotic organism, complemented by comprehensive annotations sourced from various public databases. (gzsys.org.cn)
  • Gene Model Annotations for Drosophila melanogaster: Impact of High-Throughput Data. (genscript.com)
  • Gene Model Annotations for Drosophila melanogaster: The Rule-Benders. (genscript.com)
  • Title: Identification of the Drosophila eIF4A gene as a target of the DREF transcription factor. (genscript.com)
  • In our approach, annotation was provided through Gene Ontology terms by applying multiple Support Vector Machines (SVM) for the classification of correct and false predictions. (biomedcentral.com)
  • We present a complete automated annotation system that overcomes many of the usual problems by applying a controlled vocabulary of Gene Ontology and an established classification method on large and well-described sequence data sets. (biomedcentral.com)
  • This annotation can be used together with Gene Set Enrichment Analysis (GSEA) approach to determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes). (rug.nl)
  • WEGO (Web Gene Ontology Annotation Plot) is a simple but useful tool for visualizing, comparing and plotting GO (Gene Ontology) annotation results. (genomics.cn)
  • Gene coexpression analysis refers to the en masse discovery of coexpressed genes from a large variety of transcriptomic experiments. (mdpi.com)
  • Title: A genetic screen for maternal-effect suppressors of decapentaplegic identifies the eukaryotic translation initiation factor 4A in Drosophila. (genscript.com)
  • We applied RNAi in Drosophila to 260 unknown genes that are conserved between flies and humans. (biorxiv.org)
  • Our work demonstrates the importance of poorly understood genes, provides a resource for future research acceleration, and highlights a need for our awareness of ignorance to be protected from erosion by automated database annotation. (biorxiv.org)
  • This package is for the visualization of multi-omics data that can be integrated into any analysis pipeline in R. trackViewer can be used not only to visualize coverage and annotation tracks, but also to generate lollipop and dandelion plots that depict sparse and dense methylation/mutation/variant data to facilitate an integrative analysis of diverse datasets. (umassmed.edu)
  • This study aims to understand the function and mechanism of Drosophila Glycine N-acyltransferase (GLYAT) in cell invasion. (sdbonline.org)
  • It provides unique identifiers, names and synonyms, list of complex members with their unique identifiers (UniProt, ChEBI, RNAcentral), function, binding and stoichiometry annotations, descriptions of their topology, assembly structure, ligands and associated diseases as well as cross-references to the same complex in other databases (e.g. (stanford.edu)
  • The annotation data is stored in an SQLite database, while the structure information is stored in Structure Definition Files (SDF). (bioconductor.org)
  • The hub is a repository of annotation data parsed from original file format to R objects for convient computing. (bioconductor.org)
  • NADfinder is the first software designed specifically for the bioinformatic analysis of the NAD-seq data, including baseline correction, smoothing, normalization, peak calling, and annotation. (umassmed.edu)
  • The intracellular domains of Ten-a, Ten-m/Odz and C. elegans Ten-1 are significantly different, both in size and structure, from the comparable domains of vertebrate teneurins, but the extracellular domains of all of these proteins are remarkably similar. (embl.de)
  • The climbing index in GSO-treated Drosophila was significantly higher than that in the tert-butyl-hydroperoxide-treated flies. (sdbonline.org)
  • The compound annotation tables are stored in an SQLite database. (bioconductor.org)
  • Database represents the result of the manual annotation work aimed at making the DNAtraffic database much more useful for a wide range of systems biology applications. (vifabio.de)
  • Accurate annotation has traditionally been maintained manually with the experience of individual experts and the experimental characterisation of sequences. (biomedcentral.com)
  • eIF4A controls germline stem cell self-renewal by directly inhibiting BAM function in the Drosophila ovary. (genscript.com)
  • Title: A novel function of Drosophila eIF4A as a negative regulator of Dpp/BMP signalling that mediates SMAD degradation. (genscript.com)
  • This circuit was obtained with great effort using manually cut sections and purely manual annotation on photographic film. (wikipedia.org)
  • Figure 5: Using a metagraph to integrate two annotation methods. (nature.com)
  • The connectome of C. elegans was the seminal work in this field. (wikipedia.org)
  • The levels of catalase (CAT) and glutathione (GSH) were measured in PC12 cells and Drosophila brain tissue. (sdbonline.org)