• proteins
  • The moss is also a promising model for green biotechnology [ 5 - 9 ], which allows the production of safe recombinant proteins with eukaryotic post-translational modifications in competitive quantities. (biomedcentral.com)
  • When human proteins are mapped to yeast, we find a strong positive correlation (r = 0.50, P = 3.9 × 10 -4 ) between evolutionary conservation and the number of interacting proteins, which is also found when mapped to other model organisms. (biomedcentral.com)
  • The preferential conservation of proteins with higher degree leads to enrichment in protein complexes when interactions are transferred between organisms using interologs. (biomedcentral.com)
  • of California) Pfam Protein families database of alignments and HMMs (Sanger Institute) PRINTS a compendium of protein fingerprints from (Manchester University) SUPERFAMILY Library of HMMs representing superfamilies and database of (superfamily and family) annotations for all completely sequenced organisms neXtProt - a human protein centric knowledge resource InterPro Classifies proteins into families and predicts the presence of domains and sites. (wikipedia.org)
  • The entity markup pipeline results in links from over nine classes of objects including genes, proteins, alleles, phenotypes and anatomical terms. (biomedcentral.com)
  • whereas understanding the science in a research paper often requires a reader to understand more about the research system in which these genes and proteins are assayed and concluded to work. (biomedcentral.com)
  • The cytosolic arrestin proteins mediate desensitization of activated G protein-coupled receptors (GPCRs) via competition with G proteins for the active phosphorylated receptors. (beds.ac.uk)
  • Many of these proteins are similar to characterized proteins from other organisms, but much of this information is missing from annotation databases and is hidden in the scientific literature. (asm.org)
  • Given a protein of interest, PaperBLAST quickly finds similar proteins that are discussed in the literature and presents snippets of text from relevant articles or from the curators. (asm.org)
  • To help find articles about similar proteins, PaperBLAST searches the full text of scientific articles for protein identifiers or gene identifiers, and it links these articles to protein sequences. (asm.org)
  • Then, given a protein of interest, it can quickly find similar proteins in its database by using standard software (BLAST), and it can show snippets of text from relevant papers. (asm.org)
  • Specifically, we are not aware of any text-mining tools that, given a protein of interest, search for information about similar proteins. (asm.org)
  • Given a protein identifier or a protein sequence, PaperBLAST rapidly finds similar proteins that are discussed in the literature and provides links to those proteins and to articles about them. (asm.org)
  • In general, each mRNA molecule goes on to make a specific protein (or set of proteins). (wikipedia.org)
  • Some proteins though serve only to activate other genes, and these are the transcription factors that are the main players in regulatory networks or cascades. (wikipedia.org)
  • In parallel with this process of building structure, the gene cascade turns on genes that make structural proteins that give each cell the physical properties it needs. (wikipedia.org)
  • A typical gene regulatory network looks something like this: The nodes of this network can represent genes, proteins, mRNAs, protein/protein complexes or cellular processes. (wikipedia.org)
  • Information of microbial genes stored in MicrobesOnline includes sequences (genes, transcripts and proteins), genomic loci, gene annotations and some statistics of sequences. (wikipedia.org)
  • Gene
  • Examining overlapping PPI networks, Gene Ontology (GO) terms, and gene expression data, we are able to demonstrate that protein complexes are conserved preferentially, compared to transient interactions in the network. (biomedcentral.com)
  • Bioinformatic Harvester Gene Disease Database SNPedia Ensembl provides automatic annotation databases for human, mouse, other vertebrate and eukaryote genomes. (wikipedia.org)
  • Reflect identifies and highlights gene names, protein names and small molecules. (biomedcentral.com)
  • A gene that is turned on in one cell may make a product that leaves the cell and diffuses through adjacent cells, entering them and turning on genes only when it is present above a certain threshold level. (wikipedia.org)
  • Saccharomyces cerevisiae is a commonly used model organism for understanding eukaryotic gene function. (springer.com)
  • In this study, we examined the interplay between genes encoding components of the PAF1 complex and VPS36 , the gene located next to CDC73 on chromosome XII. (springer.com)
  • 2016 ). Such a high density of genes in yeast often leads to adjacent gene effects where deletion of one gene affects the function of the adjacent gene, for example by interfering with 5′ UTR (untranslated regions) or 3′ UTRs sequences (Ben-Shitrit et al. (springer.com)
  • In yeast, CDC73 , encoding a component of the PAF1 complex, is adjacent to VPS36 , encoding a component of the ESCRT machinery and the two genes have been suggested to show an adjacent gene effect (Ben-Shitrit et al. (springer.com)
  • artificial intelligence, drug combination, combination therapy, machine learning, genomic profile Introduction It is becoming increasingly clear that targeted combination therapy is the treatment of choice in many complex human diseases, particularly those resulting from biological dysfunction driven by alterations/mutations in several genes or/and gene networks as is usually the case in cancer . (deepdyve.com)
  • It also provides tools to search or browse the database with genes, species, sequences, orthologous groups, gene ontology (GO) terms or pathway keywords, etc. (wikipedia.org)
  • Another one of its main features is the Gene Cart, which allows users to keep a record of their genes of interest. (wikipedia.org)
  • Gene expression data is available for 113 species, and fitness data is available for 4 organisms. (wikipedia.org)
  • We performed a chromosome 10-specific association study with 1,412 gene-based single-nucleotide polymorphisms (SNPs), to identify susceptibility genes for developing LOAD. (genes2cognition.org)
  • These results indicate that variants in the RPS3A homologue are associated with LOAD and implicate this gene, adjacent genes, or other functional variants (e.g., noncoding RNAs) in the pathogenesis of this disorder. (genes2cognition.org)
  • interactions
  • Despite the preferential conservation of complexes, and the fact that the human interactome comprises an abundance of transient interactions, we demonstrate how transferring human PPIs to yeast augments this well-studied protein interaction network, using the coatomer complex and replisome as examples. (biomedcentral.com)
  • The signaling outcome is believed to be a result of structural and sequence-dependent interactions of arrestins with GPCRs and other protein partners. (beds.ac.uk)
  • Together, our results outline complex interactions, in cis and in trans , between genes encoding PAF1 and ESCRT-II complex components that affect telomere function and cell viability in yeast. (springer.com)
  • Repository
  • A survey of microarray databases reveals that most of the repository contents and data models are heterogeneous (i.e., data obtained from different chip manufacturers), and that the repositories provide only basic biological keywords linking to PubMed. (biomedcentral.com)
  • Combining information from all organisms in one central repository makes it possible to integrate knowledge from different databases, to infer the functionality of newly discovered genes, and to gain insight into the conservation and divergence of biological subsystems. (springer.com)
  • species
  • and whereas this information, such as species specific anatomy and phenotypes are available in databases, access to the relevant pages in the database may not be inherently obvious to the non-initiated database user. (biomedcentral.com)
  • Comparisons of PK data across species is a potential problem drug researchers need to deal with, as model organism studies are the primary source of such data. (blogspot.com)
  • kinase
  • Despite the progress made during the past few decades, our knowledge about regulation of protein function by phosphorylation and the basis of kinase specificity remains incomplete, mainly because of lack of data. (biomedcentral.com)
  • In addition to protein kinase cascades, the targets of reversible phosphorylation include ubiquitin ligases, guanine nucleotide exchange factors, and at least 46 different transcriptional regulators. (genes2cognition.org)
  • sequence
  • Entrez (National Center for Biotechnology Information) Primary Databases International Nucleotide Sequence Database (INSD) consists of the following databases. (wikipedia.org)
  • All three databases accept nucleotide sequence submissions, and then exchange new and updated data on a daily basis to achieve optimal synchronisation between them. (wikipedia.org)
  • These three databases are primary databases, as they house original sequence data. (wikipedia.org)
  • Often a protein whose sequence is similar, and which is likely to have a similar function, has been studied already, but this information is not available in any database. (asm.org)
  • For the sequence search tool, MicrobesOnline integrates BLAT, FastHMM and FastBLAST to search protein sequences, and uses MEGABLAST to search nucleotide sequences. (wikipedia.org)
  • repositories
  • ArrayWiki improves on existing microarray repositories by providing an open interface for community curation (either through human or automated means), variance heatmaps and quality scores for every imported chip data file, and a convenient and compact data transport format that allows for storing data at a higher detail level and also provides visual assurance that the provided data is complete and is not corrupt. (biomedcentral.com)
  • Plant
  • Given its phylogenetic key position as an early diverging land plant that bridges the gap of about one billion years between the unicellular green algae and flowering plants, the moss Physcomitrella patens (Physcomitrella) unites most of the attributes desirable for a model organism, including a short generation time, small stature, comparatively low morphological complexity, a haplo-dominant life cycle, traceable cell lineage, high growth rate and simplicity of genetic transformation. (biomedcentral.com)
  • Eliminating the need to go through the difficult process of shifting data from various databases from different platforms provides a strong incentive to create better, more integrated and easily accessible integrated plant portals. (biomedcentral.com)
  • cellular processes
  • The current challenge is to place this information within the dynamic context of the cell in order to elucidate how individual molecules interact to achieve the complex behavior of cellular processes, which translates into the ability of living organisms to adapt and thrive in a myriad of environments and conditions. (biomedcentral.com)
  • molecular
  • For the drugs, hundreds of 2D and 3D molecular descriptors for medicines are now available, while for patients, large data sets related to genetic/proteomic and metabolomics profiles of the patients are now available, as well as the more traditional data relating to the histology, history of treatments, pretreatment state of the organism, etc. (deepdyve.com)
  • data
  • Meta databases are databases of databases that collect data about data to generate new data. (wikipedia.org)
  • For example, in an animal model study, which may be carried out on a compound as it passes through the drug development pipeline, is it meaningful to compare clearance or bioavailability data from a mouse or rat to human? (blogspot.com)
  • The new system is called ADME SARfari and it aims to centralise all ADME data currently stored in ChEMBL and other related databases, as well as providing new tools to help interrogate the data. (blogspot.com)
  • The Human Protein Atlas - Protein expression data for human ADME Targets. (blogspot.com)
  • The genotyping data of diploid organisms obtained by current laboratory techniques provides unordered allele pairs for each marker. (eccb06.org)
  • Large and growing public databases of transcriptome sequencing data (RNA-seq) derived from tumors and normal tissues hold the potential of yielding tumor-specific molecules, but because the data are new they have not been fully explored for this purpose. (pnas.org)
  • human
  • PharmaADME - An online resource providing a list ADME related human genes. (blogspot.com)
  • The first column of the table corresponds to the human ADME targets and additional columns correspond to targets found in model organisms. (blogspot.com)
  • describe
  • There has been a tendency to enrich annotation records of many of the existing expert-curated databases with previously missing but biologically relevant aspects by incorporating new fields or extending the inventory of terms used to describe these aspects. (biomedcentral.com)
  • database
  • Projects focused on bridging the gap between journals and databases have been on the rise over the last five years and have resulted in the development of automated tools that can recognize entities within a document and link those entities to a relevant database. (biomedcentral.com)
  • Automated tools have become excellent at identifying entities that exist in a database, but are necessarily limited in accuracy to those entities that are unique i.e., they are not ambiguous within or across databases. (biomedcentral.com)
  • MetNetDB is the underlying database and draws the majority of its information from external databases (Table 1 - also available on our website). (biomedcentral.com)
  • A relational database with advanced query interfaces (Open Source). (biosupplynet.com)
  • networks
  • In single-celled organisms, regulatory networks respond to the external environment, optimising the cell at a given time for survival in this environment. (wikipedia.org)
  • results
  • ADME studies are focused on understanding the disposition of a compound within an organism and the results of such studies play a critical role in the drug development process. (blogspot.com)
  • different
  • They are capable of merging information from different sources and making it available in a new and more convenient form, or with an emphasis on a particular disease or organism. (wikipedia.org)
  • Reference
  • As an alternative to expert curation, text-mining tools can find scientific articles that discuss a protein of interest (see, i.e., reference 6 ). (asm.org)
  • tools
  • With these tools, biologists can quickly find articles about a protein of interest and determine its function by reading the articles themselves, instead of relying on curators to do this for them. (asm.org)
  • However, most of these text-mining tools have focused on model organisms and are not suitable for annotation by homology. (asm.org)
  • family
  • Beyond their "arresting"-function that gave the protein family its name, diverse other biological functions of arrestins have been described in the last two decades. (beds.ac.uk)
  • Text
  • To make this information accessible, PaperBLAST uses EuropePMC to search the full text of scientific articles for references to genes. (asm.org)