Essential gene database

DEG: a database of essential gene

Essential genes are genes that are indispensable to support cellular life. These genes constitute a minimal gene set required for a living cell. We have constructed a Database of Essential Genes (DEG), which contains all the essential genes that are currently available. The functions encoded by esse If a predicted essential gene codes for an enzyme, the database provides the EC number and the KEGG linkage describing the metabolic pathway in which the enzyme is involved. Users can search a predicted essential gene by their functions and names. Users can also browse and extract all the records in pDEG We would like to show you a description here but the site won't allow us Essential genes are genes that are indispensable to support cellular life. These genes constitute a minimal gene set required for a living cell. We have constructed a Database of Essential Genes (DEG), which contains all the essential genes that are currently available

CEG (Cluster of Essential Genes) is a database containing clusters of orthologous essential genes developed by CEFG Group in UESTC. Original data for generating CEG are derived from the database DEG, which has been published in NAR in 2004 and 2009 In the most recent release, the number of prokaryotic essential genes in DEG has increased about 10-fold, mainly owing to genome-wide gene essentiality screens performed in a wide range of bacteria. The number of eukaryotic essential genes has increased more than 5-fold, because DEG 1.0 only had yeast ones, but DEG 5.0 also has those in humans. The DEG [ 12, 13] is the first database of essential genes, and only collects genes determined by genome-wide experiments. Since its publication, the DEG database has been widely used in areas such as antibacterial drug target discovery and synthetic biology OGEE is an Online GEne Essentiality database. Gene essentiality is not a static and binary property, rather a context-dependent and evolvable property in all forms of life. In OGEE we collect not only experimentally tested essential and non-essential genes, but also associated gene properties that contributes to gene essentiality

On the basis of genome-wide experimental studies and systems biology analysis, an essential gene database has been developed by Kong et al. (2019) for predicting > 4000 bacterial species DESCRIPTION: Here we describe the Cluster of Essential Genes (CEG) database, which contains clusters of orthologous essential genes. Based on the size of a cluster, users can easily decide whether an essential gene is conserved in multiple bacterial species or is species-specific

Database of Predicted Essential Gene

  1. excellent source is the PEC(Profiling of Escherichia coli chromosome) database, which is lists essential genes identified from literature searches. It may also contain some experimental data, but this is not totally clear
  2. OGE
  3. OGEE is an Online GEne Essentiality database. To enhance our understanding of the essentiality of genes, in OGEE we collected experimentally tested essential and non-essential genes, as well as associated gene properties known to contribute to gene essentiality. We focus on large-scale experiments, OGEE is an Online GEne Essentiality database

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DEG: a database of essential genes Nucleic Acids

Database Of Essential Genes - Biostar:

DEG -- A Database of Essential Genes HSL

  1. The non-homologous protein sequences were further analyzed by DEG (Database of Essential genes) server [9] with expected value of < 0.0001 and bit score ≥ 100 [10] for predicting essential genes.
  2. In 2013, the first database to store prokaryotic essential genes in clusters, CEG (Clusters of Essential Genes), was constructed. Afterward, the amount of available data for essential genes.
  3. CEG (Cluster of Essential Genes) is a database containing clusters of orthologous essential genes developed by CEFG Group in UESTC. Original data for generating CEG are derived from the database DEG, which has been published in NAR in 2004 and 2009
  4. CEG (Cluster of Essential Genes) is a database containing clusters of orthologous essential genes developed by CEFG Group in UESTC. If you have any suggestion, please contact us by sending an e-mail to liushuo20022020@gmail.com
  5. Essential genes contain fewer insertions in the inactivating orientation. Sample data for two neighboring genes— RPL14, encoding an essential ribosomal protein, and ZNF619, encoding a dispensable..
  6. gene: Information on experimentally tested essential and non-essential genes: G-MtfPathways: 22,552: gene: Network motifs of genes: G-SynMiner: 35,654: gene: Gene synopses: Se-DoDecagon: 562: side-effect: Mapping of side effects to side-effect categorie

Home Categories Regulon list Essential Genes NetVis Random gene Citation Log in. Go Search. Subti-Apps. Pathways. Expression. Interactions. Regulations. Genome. Quick links. Labs. Plasmids. Methods. Citation. Zhu B, Stülke J SubtiWiki in 2018: from genes and proteins to functional network annotation of the model organism Bacillus subtilis. Gene database 'essential' to fight diseases Lack of awareness identified as the other main hurdle in preventing serious health disorders Published: March 15, 2010 00:00 By Mahmood Saberi, Senior. The analysis of each sequencing run is performed by the EMBL-EBI's Gene Expression Team using the iRAP pipeline (see above). Expression Atlas R Package on Bioconductor Search and download pre-packaged data from Expression Atlas inside an R session. Raw counts are provided for RNA-seq datasets and normalized intensities are available for.

Experiments with Drosophila for Biology Courses. Experiments with Drosophila for Biology Courses, a fully open access e-book, edited by two experienced fly researchers and with contributions by many fly researchers in India, meets the need for development of new methods and paradigms for laboratory experiments at under- and post-graduate levels so that the young students and future academics. Essential thrombocythemia may be caused by a person acquiring (not inheriting) a somatic mutation in any of several genes, such as the JAK2 gene (most frequently), CALR gene, and rarely, the MPL, THPO, or TET2 gene. The reason why some people acquire mutations that cause the disease is unknown MGI Workshops. If you would like to host an MGI workshop at your institution, contact User Support to discuss the details. A typical MGI workshop includes a brief presentation and a hands-on, interactive tutorial ().If you would like to schedule a remote interactive session to learn to use MGI, contact User Support to discuss the details CiteSeerX - Document Details (Isaac Councill, Lee Giles, Pradeep Teregowda): Essential genes are genes that are indispensable to support cellular life. These genes constitute a minimal gene set required for a living cell. We have constructed a Database of Essential Genes (DEG), which contains all the essential genes that are currently available

Infection, Immunity Immunophenotyping. The Infection and Immunity Immunophenotyping (3i) consortium conducts a high-throughput immunological phenotyping of approximately 550 knockout mouse lines generated by the Wellcome Trust Sanger Institute (WTSI).The project is entirely open access and all data is made available online via this website and the website of the International Mouse Phenotyping. GeneNet -- A database on structure and functional organization of gene networks Search for information on gene networks, such as metabolic pathways and signal transduction pathways. GenePath -- from mutations to genetic networks and back Analyze mutant-based experiments and synthesize genetic networks

Essential Genes in E

ePath (e ssential genes in Path way) database provides information for essential gene prediction in bacteria The database contains > 4000 strains of prokaryotic genomes (as of 10/09/2017). The database is currently designed for genes with KEGG Ortholog numbers (KO#) only The results of the CRISPR-Cas9 and gene trapping approaches agree very closely, confirming the robustness of the data. Interestingly, RNAi-based screens for essential genes correlated less well with either approach and appeared specifically poor at detecting essential genes that have low expression Essential genes are defined as required for the survival of an organism or a cell. They are of particular interests, not only for their essential biological functions, but also in practical applications, such as identifying effective drug targets to pathogenic bacteria and fungi The comparative genomics aim of this effort is to characterize the gene pool of horizontally transferred elements and virulence determinants known as the pathosphere. The ASAP database, developed in collaboration with Nicole Perna, is a platform for community sharing of annotation information and data which is made available for downloading by.

CEG: a database of essential gene clusters BMC Genomics

The use of metabolic networks to study all essential genes as a whole indicates that essential genes are related to the biological functions of genetic information processing, cell envelope and energy production. An essential genes database (ePath) for >4000 bacterial species is developed based on this finding In the statistics below, fitness genes are counted as non-essential genes. In sum, our database contains 167 799 genes tested for essentiality from 48 species, increased significantly from the 91 436 genes and 24 species respectively from the last version (22). In total 43 961 genes are covered by multiple data sets (in each species the text. Gene Ontology GO Annotations consist of four mandatory components: a gene product, a term from one of the three Gene Ontology (GO) controlled vocabularies (Molecular Function, Biological Process, and Cellular Component), a reference, and an evidence code. SGD has manually curated and high-throughput GO Annotations, both derived from the.

OGEE v3: Online GEne Essentiality database with increased

determining essential genes in a wide range of organisms. This paper represents an update, DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes. SUMMARY OF DATABASE UPDATES In parallel to the rapid progress of the essential-gene field, DEG 5.0 has significant advances over DEG 1.0 by the following changes Gene essentiality is condition dependent. For example, while the referred DEG database lists 1617 E. coli MG1655 genes as essential, other experimentally more rigorous studies list only around 300 essential genes Gene name: collagen type I alpha 1 chain: Gene symbol: COL1A1: Chromosome Location: 17q21.33: Database location: Dalgleish Laboratory, Department of Genetics, University of Leicester, UK: Curator: Raymond Dalgleish, Ivana Osredek and Wei Kheng Teh: PubMed references: View all (unique) PubMed references in the COL1A1 database: Date of creation. Our results show that 18.2% of the genes are essential for growth on rich gluose media and approximately 15% of the homozygous diploid disruptions cause slow growth in this type of media. When the Yeast Knock-out (YKO) deletion collection was released in 2000, the deletion strains were based on the annotation of the available yeast genome sequence

Candida auris Data in CGD; We are pleased to announce the addition of Candida auris B8441 information into CGD.C. auris B8441 was sequenced by the Centers for Disease Control and Prevention (Lockhart et al. 2017).Sequence and annotation were obtained by CGD from GenBank. C. auris is the fifth Candida species for which manually curated data are available in our database, joining C. albicans, C. Chan JD, Zhang D, Liu X, Zarowiecki MZ, Berriman M, Marchant JS. Data Brief 2016 Dec;9:1044-1047. PMID: 27909700 Abstract. This data article provides a transcriptomic resource for the free living planarian flatworm Dugesia japonica related to the research article entitled 'Utilizing the planarian voltage-gated ion channel transcriptome to resolve a role for a Ca(2+) channel in neuromuscular. To estimate the minimal gene set required to sustain bacterial life in nutritious conditions, we carried out a systematic inactivation of Bacillus subtilis genes. Among ≈4,100 genes of the organism, only 192 were shown to be indispensable by this or previous work. Another 79 genes were predicted to be essential. The vast majority of essential genes were categorized in relatively few domains. The 3-letter gene symbol should stand for a description of a phenotype, gene product, or gene function. In addition, it is strongly preferable that a given gene symbol have only one associated description (i.e., all genes which use a given 3-letter symbol should have a related phenotype, gene product, or gene function, and that 3-letter symbols.

KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies Search gene using symbol or synonym, chromosome location, keywords (a protein function for example) or a variety of external database accessions. Evolution More than being a simple autophagy repository, HADb will provide different tools for analysis, search and visualization to facilitate explorations, predictions and studies OGEEis an Online GEne Essentiality database. To enhance our understanding of the essentiality of genes, in OGEEwe collected experimentally tested essential and non-essential genes, as well as as-sociated gene properties known to contribute to gene essentiality. We focus on large-scale experi-ments, and complement our data with text-mining results

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1. Methods Mol Biol. 2015;1279:219-33. doi: 10.1007/978-1-4939-2398-4_14. Gene essentiality analysis based on DEG 10, an updated database of essential genes Essential tremor (ET) is a progressive, neurological disease characterized by tremor, most often of the hands or arms. Dominant genetic disorders occur when only a single copy of an abnormal gene is necessary for the appearance of the disease. The abnormal gene can be inherited from either parent, or can be the result of a new mutation.

We used operon database (DOOR) to assess the essential gene modules. These essential genes were fallen in 307, 326, 297, 310 and 316 operons in H37Rv, H37Ra, CDC1511, F11 and KZN1435, respectively (Table 1). Statistical analysis showed that there is no relationship between the size of the operon and the number of essential genes identified HumanCyc: Encyclopedia of Human Genes and Metabolism . HumanCyc provides an encyclopedic reference on human metabolic pathways. It provides a zoomable human metabolic map diagram, and it has been used to generate a steady-state quantitative model of human metabolism. HumanCyc is part of the larger BioCyc collection of thousands of Pathway/Genome Databases for sequenced genomes Yamamoto et al. (2002) screened the ALAP gene (ERAP1; 606832) gene for mutations in 488 unrelated Japanese individuals and identified one polymorphism, lys528 to arg (K528R), that showed an association with essential hypertension. The estimated odds ratio for essential hypertension was 2.3 for presence of the arg allele at codon 528, in.

The resources on this site should not be used as a substitute for professional medical care or advice. Users with questions about a personal health condition should consult with a qualified healthcare professional Interestingly, a Gene Ontology (GO) analysis and a pathway analysis from the Reactome database revealed cell-cycle genes to be significantly enriched among the top depleted sgRNAs in our screen (Additional file 4a-d). Additionally, a transcription factor enrichment analysis revealed that MYC is an upstream transcription factor for the genes identified in the negative-selection screen. The Universal Protein Resource (UniProt) provides the scientific community with a single, centralized, authoritative resource for protein sequences and functional information

Database analysis revealed close orthologs of Meig1 protein in human, rat, frog, fish, and cow. Mapping Hartz (2011) mapped the MEIG1 gene to chromosome 10p13 based on an alignment of the sequence (GenBank AA971146) with the genomic sequence (GRCh37) A curated database of genes associated with dietary restriction in model organisms either from genetic manipulation experiments or gene expression profiling. Search gene manipulations. When deemed to contain essential information for DrugAge (e.g. a large scale assay), certain papers were included without analysing the statistical.

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A PCR-generated (Baudin 1993; Wach 1994) deletion strategy was used to systematically replace each yeast open reading frame from its start- to stop- codon with a KanMX module and two unique 20mer molecular bar codes. The presence of the tags can be detected via hybridization to a high-density oligonucleotide array, enabling growth phenotypes of individual strains to be analyzed in parallel Transcription factors (TFs) are essential for the regulation of gene expression and are found in all living organisms. P2TF is an integrated and comprehensive database of TF proteins, which contains a compilation of the TF genes within completely sequenced genomes and metagenomes Because these genes play an integral role in normal blood pressure control, researchers suspect that variations in them might impair blood pressure control and contribute to hypertension. Other genes associated with essential hypertension are important for the normal function of the lining of blood vessels (the vascular endothelium). Changes in.

T1 - Conditional gene deletion with DiCre demonstrates an essential role for CRK3 in Leishmania mexicana cell cycle regulation. AU - Duncan, Samuel M. AU - Myburgh, Elmarie. AU - Philipon, Cintia. AU - Brown, Elaine. AU - Meissner, Markus. AU - Brewer, James. AU - Mottram, Jeremy Charles. PY - 2016/3/16. Y1 - 2016/3/1 A multicenter study of NS5b hepatitis C virus (HCV) genotype determination involving 12 laboratories demonstrates that any laboratory with expertise in sequencing techniques would be able to provide a reliable HCV genotype for clinical and epidemiological purposes as long as they are provided a consensus reference sequence database GeneCards is a searchable, integrative database that provides comprehensive, user-friendly information on all annotated and predicted human genes. The knowledgebase automatically integrates gene-centric data from ~150 web sources, including genomic, transcriptomic, proteomic, genetic, clinical and functional information Essential reading for making sense of this web site. It will be constantly updated. Gene expression database Search the entire data set for the expression profiles of your favourite genes or search for specific expression profiles. Also download the entire data for importing into your spreadsheet or database

Essential gene - Wikipedi

Item Type: Article: Title: OGEE v2: an update of the online gene essentiality database with special focus on differentially essential genes in human cancer cell lines: Creators N CEG: a database of essential gene clusters . By Yuan-Nong Ye, Zhi-Gang Hua, Jian Huang, Nini Rao and Feng-Biao Guo. Cite . BibTex; Full citation; Publisher: Springer Nature. Year: 2013. DOI identifier: 10.1186/1471-2164-14-769. OAI identifier: Provided by: MUCC. UW E. coli Genome Project Overview We sequenced the E. coli K-12 genome, and continue to maintain and update its annotation. We created knockouts of many genes, archive clones of many ORFs, and an extensive gene expression data set under a variety of physiological conditions The synthetic organism, Syn 3, has a minimal genome of 473 essential genes and quasi-essential genes (necessary for fast growth), although 149 have unknown function. [105] Essential genes include housekeeping genes (critical for basic cell functions) [112] as well as genes that are expressed at different times in the organisms development or. Heterozygous gene deletion mutants for essential genes. The data sheets here are the results created by reanalyzing the images in Ohnuki and Ohya (under review). Cell images of the mutants are available at here. 1112 heterzygous gene deletion mutants for essential genes; Average data (9,425 KB) Number of cells for ratio parameter (200 KB

CEG: a database of essential gene clusters

The theoretical foundation of CEG_match is as follows: If a gene with unknown essentiality happens to be essential in multiple species, the possibility of being essential gene increases. Such possibility increases with the matching species' number. The information of matching species is important for prediction NORD, a 501(c)(3) organization, is the leading patient advocacy organization dedicated to improving the lives of individuals and families living with rare diseases Gene Effect: Outcome from DEMETER2 or CERES. A lower score means that a gene is more likely to be dependent in a given cell line. A score of 0 is equivalent to a gene that is not essential whereas a score of -1 corresponds to the median of all common essential genes Regulatory subunit of the IKK core complex which phosphorylates inhibitors of NF-kappa-B thus leading to the dissociation of the inhibitor/NF-kappa-B complex and ultimately the degradation of the inhibitor. Its binding to scaffolding polyubiquitin seems to play a role in IKK activation by multiple signaling receptor pathways. However, the specific type of polyubiquitin recognized upon cell.

Essential Genes in E

BIOINFORMATICS INSTITUTE OF INDIA GenBank GenBank® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences DDBJ DDBJ (DNA Data Bank of Japan) began DNA data bank activities in earnest in 1986 at the National Institute of Genetics (NIG) with the endorsement of the Ministry of Education, Science, Sport and Culture This subsection of the Names and taxonomy section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'. 1. Name. The recommended name is used to officially represent a gene

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Env genes are found in LTR retrotransposon types Ty1-copia (Pseudoviridae), Ty3-gypsy (Metaviridae) and BEL/Pao. They encode glycoproteins on the retrovirus envelope needed for entry into the host cell. Retroviruses can move between cells whereas LTR retrotransposons can only move themselves into the genome of the same cell. Many vertebrate. Ribosomal ribonucleic acid (rRNA) is a type of non-coding RNA which is the primary component of ribosomes, essential to all cells. rRNA is a ribozyme which carries out protein synthesis in ribosomes. Ribosomal RNA is transcribed from ribosomal DNA (rDNA) and then bound to ribosomal proteins to form small and large ribosome subunits. rRNA is the physical and mechanical factor of the ribosome.

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OGEE v2: an update of the online gene essentiality

Related Publications: Human DNA Repair Genes. Wood RD, Mitchell M, Sgouros JG, Lindahl T, Science 291, 1284 (2001) Abstract Human DNA Repair Genes, 2005 Wood RD, Mitchell M, Lindahl T, Mutation Res. 577, 275 (2005) Abstract DNA Repair and Mutagenesis, 2nd edition (ASM Press, Washington, DC Role of duplicate genes in genetic robustness against null mutations. Nature, 42, 63-66. (2003) abstract Steinmetz, L., et al. Systematic screen for human disease genes in yeast. Nature Genetics. 31, 400-404. (2002) abstract Fraser, H. B., et al. Evoluationary Rate in the Protein Interaction Network

Non-essential gene in S288C and W303, essential gene in Sigma1278b; null mutant is auxotrophic for methionine, displays abnormal vacuolar morphology, reduced competitive fitness, and decreased resistance to both pH and oxidative stresses; null displays increased resistance to DNA-damaging agents and antivirals; heterozygous null is. The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families Essential thrombocythemia (ET) is a chronic myeloproliferative neoplasm (MPN) that primarily involves the megakaryocytic lineage. It is characterized by sustained thrombocytosis in the peripheral blood and increased numbers of large, mature megakaryocytes in the bone marrow and clinically by the occurrence of thrombocytosis and/or hemorrhage. Because there is no known genetic or biological. The EGFR gene provides instructions for making a receptor protein called the epidermal growth factor receptor, which spans the cell membrane so that one end of the protein remains inside the cell and the other end projects from the outer surface of the cell National Institute of Allergy and Infectious Disease: The Database for Annotation, Visualization and Integrated Discover

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