• Brief summaries describing the function of each gene's product are of great value to the research community, especially when interpreting genome-wide studies that reveal changes to hundreds of genes. (stanford.edu)
  • 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)
  • Two such genes in Drosophila encode the enzymes dopa decarboxylase (Ddc) and tyrosine hydroxylase (ple) . (sdbonline.org)
  • Gene coexpression analysis refers to the en masse discovery of coexpressed genes from a large variety of transcriptomic experiments. (mdpi.com)
  • We determined and documented embryonic expression patterns for 6,003 (44%) of the 13,659 protein-coding genes identified in the Drosophila melanogaster genome with over 70,000 images and controlled vocabulary annotations. (biomedcentral.com)
  • This file reports nomenclature and functional data (GO annotations, EC annotations, gene group membership) for ''D. melanogaster'' genes encoding enzymes, as defined by membership of the ENZYMES (FBgg0001715) gene group. (flybase.org)
  • Complete sequences of the rRNA genes of Drosophila melanogaster. (research.com)
  • Evolution of genes and genomes on the Drosophila phylogeny. (kb.se)
  • Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. (kb.se)
  • In Drosophila , the BX-C cluster contains the three most posterior Hox genes, where their collinear activation incorporates progressive replacement of histone modifications, reorganization of 3D chromatin architecture and sequential activation of boundary elements and cis -regulatory regions. (biorxiv.org)
  • In D. melanogaster , the eight Hox genes are organized in two separate clusters on chromosome 3R: the Antennapedia cluster (ANT-C) and the Bithorax cluster (BX-C). The 350 kb BX-C contains the Ubx, abd-A and Abd-B genes, which specify the identity of the more posterior embryonic parasegments 5 to 14 (PS5 to PS14). (biorxiv.org)
  • Therefore, robustness of genome annotation depends on accurate identification of orthologs. (biomedcentral.com)
  • the Genomes FTP repository , containing genome and genome annotation data files (including FASTA, GFF and GTF files) for D. melanogaster and other Drosophila species, organized by genome/FlyBase release number. (flybase.org)
  • In particular, we gained significant insight into DNA sequences that do not encode proteins, which we knew very little about before," said Ewan Birney, Ph.D., head of genome annotation at the European Molecular Biology Laboratory's European Bioinformatics Institute (EBI) in Hinxton, England, who led ENCODE's massive data integration and analysis effort. (nih.gov)
  • Data were compared with equivalent data for two long germ-band holometabolan species Drosophila melanogaster and Drosophila virilis , and the short germ-band holometabolan species Tribolium castaneum . (biomedcentral.com)
  • Short germ-band development is typical of basal insects such as locusts and cockroaches, whereas more derived species such as those of the genus Drosophila predominantly undergo long germ-band development [ 2 ]. (biomedcentral.com)
  • miRNA commonalities between B. germanica and T. castaneum , as opposed to those of the two Drosophila species studied, were assumed to be associated with the germ-band type, whereas those of T. castaneum and the Drosophila species, as opposed to B. germanica , were assumed to be associated with the mode of metamorphosis followed. (biomedcentral.com)
  • This track shows the multiple alignments of 26 Drosophila species and measurements of evolutionary conservation using two methods ( phastCons and phyloP ) from the PHAST package . (wustl.edu)
  • 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)
  • 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)
  • 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)
  • Drosophila has been extensively studied in the fields of genetics and developmental biology. (elifesciences.org)
  • These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. (kb.se)
  • PMID:14996496, table 1 provides links to papers that describe subcellular location of many pro- and anti-apoptotic proteins. (geneontology.org)
  • BCL2 proteins are described as 'crucial regulators of apoptosis' (PMID:15868100)and the intrinsic apoptosis pathway is initiated by the release of mitochondrial cytochrome c into the cytoplasm, which results in the activation of caspases (15102863) - help in generating a defintion for intrinsic apoptosis? (geneontology.org)
  • We describe a computational methodology allowing to systematically and quantitatively characterize a Boolean mathematical model of a biological network in terms of genetic interactions between all loss of function and gain of function mutations with respect to all model phenotypes or outputs. (researchgate.net)
  • To identify novel regulators of JNK-dependent cell death, this study performed a dominant-modifier screen in Drosophila and found that the Toll pathway participates in JNK-mediated cell death. (sdbonline.org)
  • the process that governs the early embryonic patterning of the Drosophila body plan is now the best understood example of a complex cascade of transcriptional regulation during development [ 14 , 15 ]. (biomedcentral.com)
  • We produced a map of the Drosophila melanogaster regulatory genome on the basis of more than 300 chromatin immunoprecipitation data sets for eight chromatin features, five histone deacetylases and thirty-eight site-specific transcription factors at different stages of development. (duke.edu)
  • 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)
  • 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)
  • We describe emerging approaches for representing and visualizing systems data and for achieving semantic zooming, or changes in information density concordant with scale. (nature.com)
  • The incumbent in this position plays a critical role in data annotation and curation for the Gene Ontology (GO) and Protein Ontology (PRO) programs at The Jackson Laboratory in Bar Harbor Maine, through diverse activities to gather, analyze, evaluate and integrate information and analysis results using biomedical ontologies. (bytesizebio.net)
  • In this post, I'll describe how I updated IGB to the latest sorghum genome assembly using data from Phytozome and a few easy-to-use command line tools. (lorainelab.org)
  • HTML file to describe "Gclust Server" data. (biosciencedbc.jp)
  • In this study, model simulations based on fluid mechanics are described to derive the loads on the objects caused by currents and waves and combined with knowledge of the known burial condition of the objects. (bvsalud.org)
  • Using Google searches, I found a page describing the new assembly and associated gene annotations. (lorainelab.org)
  • Leonardo da Vinci's embryological drawings of the fetus in the womb and his accompanying observational annotations are found in the third volume of his private notebooks. (asu.edu)
  • Figure 5: Using a metagraph to integrate two annotation methods. (nature.com)
  • This study aims to understand the function and mechanism of Drosophila Glycine N-acyltransferase (GLYAT) in cell invasion. (sdbonline.org)
  • This study describes 8 image rendering techniques that are essential for the identification and visualization of postmortem findings in stranded cetaceans, which will help clinicians, veterinarians and stranding response personnel worldwide to fully utilize the radiological modality. (jove.com)
  • The levels of catalase (CAT) and glutathione (GSH) were measured in PC12 cells and Drosophila brain tissue. (sdbonline.org)
  • GSOs also mitigated the deleterious effects of GLU on the mitochondrial membrane potential and Cyt C release, thus alleviating mitochondrial dysfunction, and increased GSH levels and CAT activity in both cells and Drosophila brain tissue. (sdbonline.org)
  • Comment Open annotations (there are currently 0 annotations on this page). (elifesciences.org)
  • The genome assembly is called "version 2.0" and the annotations are called "version 2.1. (lorainelab.org)
  • This new item refers to the genome annotations, not the genome assembly, but probably the two were released about the same time, so I decided to use this. (lorainelab.org)
  • Here we describe results from the modENCODE cis-regulatory annotation project. (duke.edu)
  • We reported the identification of a new family of DNA-binding proteinsfrom our characterization of the dead ringer (dri) gene of Drosophilamelanogaster. (embl.de)
  • Here, we have developed DIAMonDS ( Drosophila Individual Activity Monitoring and Detection System) comprising time-lapse imaging by a charge-coupled device (CCD) flatbed scanner and Sapphire, a novel algorithm and web application. (elifesciences.org)
  • Since the physical position of inparalogs corresponding to recent speciations is not likely to have changed since the duplication, we also use our predictions to estimate the types of duplications that have occurred in some vertebrates and drosophila. (biomedcentral.com)
  • He observed and diagramed the previously undemonstrated position of the fetus in the womb with detailed accompanying annotations of his observations. (asu.edu)