functional genomics tools

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Yanhui Hu, Aram Comjean, Charles Roesel, Arunachalam Vinayagam, Ian Flockhart, Jonathan Zirin, Lizabeth Perkins, Norbert Perrimon, and Stephanie E Mohr, Yanhui Hu, Verena Chung, Aram Comjean, Jonathan Rodiger, Fnu Nipun, Norbert Perrimon, and Stephanie E Mohr, Chiao-Lin Chen, Jonathan Rodiger, Verena Chung, Raghuvir Viswanatha, Stephanie E Mohr, Yanhui Hu, and Norbert Perrimon, Yanhui Hu, Richelle Sopko, Verena Chung, Marianna Foos, Romain A Studer, Sean D Landry, Daniel Liu, Leonard Rabinow, Florian Gnad, Pedro Beltrao, and Norbert Perrimon, Yanhui Hu, Arunachalam Vinayagam, Ankita Nand, Aram Comjean, Verena Chung, Tong Hao, Stephanie E Mohr, and Norbert Perrimon, Julia Wang, Rami Al-Ouran, Yanhui Hu, Seon-Young Kim, Ying-Wooi Wan, Michael F Wangler, Shinya Yamamoto, Hsiao-Tuan Chao, Aram Comjean, Stephanie E Mohr, Undiagnosed Diseases Network, Norbert Perrimon, Zhandong Liu, and Hugo J Bellen, Yanhui Hu, Aram Comjean, Stephanie E Mohr, The FlyBase Consortium, and Norbert Perrimon, Arunachalam Vinayagam, Travis E Gibson, Ho-Joon Lee, Bahar Yilmazel, Charles Roesel, Yanhui Hu, Young Kwon, Amitabh Sharma, Yang-Yu Liu, Norbert Perrimon, and Albert-László Barabási, Arunachalam Vinayagam, Meghana M Kulkarni, Richelle Sopko, Xiaoyun Sun, Yanhui Hu, Ankita Nand, Christians Villalta, Ahmadali Moghimi, Xuemei Yang, Stephanie E Mohr, Pengyu Hong, John M Asara, and Norbert Perrimon, Stephanie E Mohr, Yanhui Hu, Benjamin Ewen-Campen, Benjamin E Housden, Raghuvir Viswanatha, and Norbert Perrimon, Lizabeth A Perkins, Laura Holderbaum, Rong Tao, Yanhui Hu, Richelle Sopko, Kim McCall, Donghui Yang-Zhou, Ian Flockhart, Richard Binari, Hye-Seok Shim, Audrey Miller, Amy Housden, Marianna Foos, Sakara Randkelv, Colleen Kelley, Pema Namgyal, Christians Villalta, Lu-Ping Liu, Xia Jiang, Qiao Huan-Huan, Xia Wang, Asao Fujiyama, Atsushi Toyoda, Kathleen Ayers, Allison Blum, Benjamin Czech, Ralph Neumuller, Dong Yan, Amanda Cavallaro, Karen Hibbard, Don Hall, Lynn Cooley, Gregory J Hannon, Ruth Lehmann, Annette Parks, Stephanie E Mohr, Ryu Ueda, Shu Kondo, Jian-Quan Ni, and Norbert Perrimon, Stephanie E Mohr, Yanhui Hu, Kirstin Rudd, Michael Buckner, Quentin Gilly, Blake Foster, Katarzyna Sierzputowska, Aram Comjean, Bing Ye, and Norbert Perrimon, Yanhui Hu, Aram Comjean, Lizabeth A Perkins, Norbert Perrimon, and Stephanie E Mohr, Benjamin E Housden, Shuailiang Lin, and Norbert Perrimon, Arunachalam Vinayagam, Jonathan Zirin, Charles Roesel, Yanhui Hu, Bahar Yilmazel, Anastasia A Samsonova, Ralph A Neumüller, Stephanie E Mohr, and Norbert Perrimon, Bahar Yilmazel, Yanhui Hu, Frederic Sigoillot, Jennifer A Smith, Caroline E Shamu, Norbert Perrimon, and Stephanie E Mohr, Xingjie Ren, Jin Sun, Benjamin E Housden, Yanhui Hu, Charles Roesel, Shuailiang Lin, Lu-Ping Liu, Zhihao Yang, Decai Mao, Lingzhu Sun, Qujie Wu, Jun-Yuan Ji, Jianzhong Xi, Stephanie E Mohr, Jiang Xu, Norbert Perrimon, and Jian-Quan Ni, Yanhui Hu, Richelle Sopko, Marianna Foos, Colleen Kelley, Ian Flockhart, Noemie Ammeux, Xiaowei Wang, Lizabeth Perkins, Norbert Perrimon, and Stephanie E Mohr, Yanhui Hu, Charles Roesel, Ian Flockhart, Lizabeth Perkins, Norbert Perrimon, and Stephanie E Mohr, Arunachalam Vinayagam, Yanhui Hu, Meghana Kulkarni, Charles Roesel, Richelle Sopko, Stephanie E Mohr, and Norbert Perrimon, Ian T Flockhart, Matthew Booker, Yanhui Hu, Benjamin McElvany, Quentin Gilly, Bernard Mathey-Prevot, Norbert Perrimon, and Stephanie E Mohr, Marcelo Perez-Pepe, Victoria Slomiansky, Mariela Loschi, Luciana Luchelli, Maximiliano Neme, María Gabriela Thomas, and Graciela Lidia Boccaccio, Matthew Booker, Anastasia A Samsonova, Young Kwon, Ian Flockhart, Stephanie E Mohr, and Norbert Perrimon, Adam A Friedman, George Tucker, Rohit Singh, Dong Yan, Arunachalam Vinayagam, Yanhui Hu, Richard Binari, Pengyu Hong, Xiaoyun Sun, Maura Porto, Svetlana Pacifico, Thilakam Murali, Russell L Finley, John M Asara, Bonnie Berger, and Norbert Perrimon, Yanhui Hu, Ian Flockhart, Arunachalam Vinayagam, Clemens Bergwitz, Bonnie Berger, Norbert Perrimon, and Stephanie E Mohr, Michael Schnall-Levin, Yong Zhao, Norbert Perrimon, and Bonnie Berger, Irene M Kaplow, Rohit Singh, Adam Friedman, Chris Bakal, Norbert Perrimon, and Bonnie Berger, Dashnamoorthy Ravi, Amy M Wiles, Selvaraj Bhavani, Jianhua Ruan, Philip Leder, and Alexander JR Bishop, Amy M Wiles, Dashnamoorthy Ravi, Selvaraj Bhavani, and Alexander JR Bishop, Jun Wang, Xiaobo Zhou, Pamela L Bradley, Shih-Fu Chang, Norbert Perrimon, and Stephen TC Wong, Copyright © 2020 The President and Fellows of Harvard College, CellExpressionLevels (fly cell transcriptome data), ScreenSummary (all DRSC cell RNAi screens), Online GESS (siRNA seed sequence analysis), MitoMax fly mitochondrial proteomics data set, Pooled CRISPR fly cell screen raw data sets, Nucleolar fly cell RNAi image-based screen data set, DRSC RNA Binding RNAi library fly cell screen data set, Table of all public DRSC cell-based RNAi screen data sets at Screen Summary, FlyBi Drosophila Y2H binary interaction data DRSC/CCSB/BDGP, FlyRNAi.org—the database of the Drosophila RNAi screening center and transgenic RNAi project: 2017 update, BioLitMine: Advanced Mining of Biomedical and Biological Literature About Human Genes and Genes from Major Model Organisms, SNP-CRISPR: A Web Tool for SNP-Specific Genome Editing, https://www.flyrnai.org/tools/snp_crispr/, iProteinDB: An Integrative Database of Post-translational Modifications, https://www.flyrnai.org/tools/iproteindb/, Molecular Interaction Search Tool (MIST): an integrated resource for mining gene and protein interaction data, MARRVEL: Integration of Human and Model Organism Genetic Resources to Facilitate Functional Annotation of the Human Genome, Gene2Function: An Integrated Online Resource for Gene Function Discovery, Controllability analysis of the directed human protein interaction network identifies disease genes and drug targets, An Integrative Analysis of the InR/PI3K/Akt Network Identifies the Dynamic Response to Insulin Signaling. Here we report an effective and inexpensive method for genome DNA editing in Drosophila melanogaster whereby plasmid DNAs encoding short sgRNAs under the control of the U6b promoter are injected into transgenic flies in which Cas9 is specifically expressed in the germ line via the nanos promoter. The resource is available online for scientists to search and view, and is editable based on community input. HFGP is a large-scale project that aims to identify the consequences that genetic variation in human DNA and the complex colonization with microbial … or cellular function (e.g. Sequencing based methods such as serial analysis of gene expression (SAGE; Velculescu et al., 1995) and massively parallel signature sequencing (MPSS; Brenner et al., 2000), also utilize the fact that the more abundant mRNA species are more highly represented in a cDNA library. The samples are mixed, protease digested, and affinity purified to capture tagged peptides, which are then separated and identified by LC‐MS‐MS. However, these tools can give different results and identification of predicted orthologs is not always straightforward. Stress granules (SGs) and processing bodies (PBs) belong to a novel family of cellular structures collectively known as mRNA silencing foci that harbour repressed mRNAs and their associated proteins. The sequence of a peptide can be determined as fragmentation occurs at the peptide bonds producing fragment mass differences that match the masses of the different amino acids (in this case the Masslinks Program, Micromass UK, was used to determine the peptide sequence). 3) (Pandey & Mann, 2000; Yates, 2000). CRISPR-Cas9 is a powerful genome editing technology in which a short guide RNA (sgRNA) confers target site specificity to achieve Cas9-mediated genome editing. Experimental organismic biology is built on a foundation of reductionism, where individual research groups specialize in small, well‐defined areas of research, and where the greatest challenge is often to collect and synthesize the results of many groups into useful models of how the various parts of a cell or complex, multicellular organism interact to produce a viable organism. Although it is now easier than ever before to isolate interesting genes using forward genetics, the approach has one important intrinsic limitation: it can only be applied to genes that produce a discernable phenotype when mutated. Altogether, our results demonstrate that the scale of biologically important miRNA targeting in ORFs is extensive and that computational tools such as ours can aid in the identification of such targets. Current 2D‐PAGE protocols suffer from some problems that limit their use for proteomics: proteins with extreme pI and molecular weight, low abundance, or high hydrophobicity (especially membrane proteins) are rarely seen on 2D‐PAGE gels. Measuring the metabolome: current analytical technologies. These methods allow the simultaneous analysis of thousands, or even millions of transcripts by generating short nucleotide signature sequences. Quantitative comparisons are achieved by labelling the proteins of one sample with a light isotope version of a chemical tag and proteins of the second sample with a heavy isotope version of the same tag. By identifying and measuring many, if not all of the molecular players that participate in a given biological process, functional genomics offers the prospect of obtaining a truly holistic picture of life. based on protein domains (kinases, transcription factors, etc.) Several technologies are now in use to identify differentially expressed genes and to analyse gene expression levels on a genomic scale. Metabolic Fingerprinting in Toxicological Assessment Using FT-ICR MS. Functional Genomics For Crop Improvement. Functional genomics uses mostly multiplex techniques to measure the abundance of many or all gene products such as mRNAs or proteins within a biological sample. Following hybridization and washing of arrays, the amount of probe bound to each spot is quantified using either a high‐sensitivity PhosphorImager or fluorescence imaging equipment. CRISPR) and support of integrated, cross-species approaches to uncovering gene function using functional genomics and other approaches. To meet community needs, predefined qPCR primer pairs for mammalian genes have been designed and sequences made available, e.g., via PrimerBank. A major issue for data management at present is the need to create standard formats for different types of data so that it can be shared and compared between labs. It has captured the imagination of thousands of scientists, perhaps in part because it empowers individual groups to work on a grander scale that promises local (and possibly patentable) insights into the ‘big picture’ of biology. A recent and potentially potent addition to the reverse genetics armoury is a procedure called Targeted Induced Local Lesions IN Genomes (TILLING) (McCallum et al., 2000). Although primary metabolism involves only a few hundred metabolites, the metabolome of a higher plant may well include tens of thousands of different metabolites that differ in concentration among cell compartments, cells, tissues, and organs. However, in cotton functional genomics, a persistent challenge is the absence of genetic and molecular tools partly due to large genome size, low transformation efficiency and long growth cycle. Such a map could have more intrinsic value than the corresponding transcriptome map, which is a more remote indicator of the biochemical activity of the organism. Learn about our remote access options, Max Plank Institute of Molecular Plant Physiology, Am Mühlenberg 1, 1446 Golm, Germany. We observed down-regulation by the miRNA in five out of seven cases, indicating our approach can recover functional sites with high confidence. Interestingly, these indispensable proteins are the primary targets of disease-causing mutations, human viruses, and drugs, suggesting that altering a network's control property is critical for the transition between healthy and disease states. Ectomycorrhizal development and function – transcriptome analysis. The authors present a framework, consisting of microscopic image segmentation and analysis components, for automatic recognition of cellular phenotypes in the context of the Rho family of small GTPases. Be sure to cite our online resources if they contribute to a published study. The metabolic phenotypes of the two ecotypes were more divergent than were the phenotypes of the single‐loci mutants and their parental ecotypes. This approach has been used successfully to identify phosphorylated proteins from thylakoid membranes of Arabidopsis (Vener et al., 2001). Therefore, tubers may be less reliant on transport of amino acids from the leaves than previously thought. In this work, we adapted and refined the algorithms used for the mammalian PrimerBank to design 45,417 primer pairs for 13,860 Drosophila melanogaster genes, with three or more primer pairs per gene. Annotation of gene groups is an ongoing effort and scientific need will typically drive decisions regarding which gene lists to pursue. GLAD: an Online Database of Gene List Annotation for Drosophila. With the tool, users can either use a built-in database or provide a database of transcripts for analysis. Technologies that allow us to monitor changes in the transcriptome, proteome, and metabolome will no doubt help us to discern subtle molecular phenotypes that elude detection at the physiological or morphological levels. Finally, we used BUHO to analyze the role of candidate genes on SG formation in an RNAi-based experiment. In a retrospective analysis, the authors describe the use of validation data to evaluate each normalization method. This makes it possible to analyze RNAi data from any organism for which the user can provide transcript sequences. The Microarray Gene Expression Database (MGED) consortium (http://www.mged.org) has proposed a data format (MAML/MIAME) that is already used by some applications and is likely to find broad acceptance by public repositories and commercial software suppliers. Bioinformatics and Functional Genomics, Second Edition serves as an excellent single-source textbook for advanced undergraduate and beginning graduate-level courses in the biological sciences and computer sciences. Automatic functional annotation is an effective approach to solve this problem. Characterizing the extent and logic of signaling networks is essential to understanding specificity in such physiological and pathophysiological contexts as cell fate decisions and mechanisms of oncogenesis and resistance to chemotherapy. These screens need not be based on macroscopic phenotypes, as should become clear from the following sections. The database and website is used as a platform for community availability of protocols, tools, and other resources useful to researchers planning, conducting, analyzing or interpreting the results of Drosophila RNAi screens. Constraints on the evolution of adaptive phenotypic plasticity in plants. 77 Avenue Louis PasteurBoston, MA 02115(Map)Fax: (617) 432-7688. You can cite our latest Nucleic Acids Research Database Issue paper and/or the publication(s) corresponding to the specific online resource(s) that you used. The multiparallel approaches of functional genomics allow one to query the ‘behaviour’ of thousands of genes, proteins, and metabolites in a single, controlled experiment in a way that allows sensible connections to be made within and between the various levels of biological organization. (2001) recently identified 1484 proteins from yeast, including a fair representation of low‐abundance proteins, proteins with extremes of pI and MW, and integral membrane proteins. The Gene Ontology Consortium, Visualization of differential gene expression using a novel method of RNA fingerprinting based on AFLP: analysis of gene expression during potato tuber development, A comparison of gel‐based, nylon filter and microarray techniques to detect differential RNA expression in plants, Fast forward genetics based on virus‐induced gene silencing, On the importance of standardisation in life sciences, Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays, An Arabidopsis mutant with a reduced level of cab140 RNA is a result of cosuppression, Patterns of protein synthesis and tolerance of anoxia in root tips of maize seedlings acclimated to a low‐oxygen environment, and identification of proteins by mass spectrometry, Use of a cDNA microarray to analyse gene expression patterns in human cancer, Differential gene expression in Arabidopsis monitored using cDNA arrays, Expression profiling using cDNA microarrays, Cluster analysis and display of genome‐wide expression patterns, Large‐scale functional analysis using peptide or protein arrays, Metabolite profiling for plant functional genomics, Microarray analysis of developing Arabidopsis seeds, Hybridization fingerprinting of high‐density cDNA‐library arrays with cDNA pools derived from whole tissues, Quantitative analysis of complex protein mixtures using isotope‐coded affinity tags, A Concise Guide to cDNA Microarray Analysis, Discovery and analysis of inflammatory disease‐related genes using cDNA microarrays, A hierarchical unsupervised growing neural network for clustering gene expression patterns, Large‐Scale Expression Measurement by Hybridisation Methods: From High Density Membranes to ‘DNA Chips’, KEGG: kyoto encyclopedia of genes and genomes, DNA microarrays for studies of higher plants and other photosynthetic organisms, An oligonucleotide hybridization approach to DNA sequencing, T‐DNA as an insertional mutagen in Arabidopsis, From library screening to microarray technology: Strategies to determine gene expression profiles and to identify differentially regulated genes in plants, High‐throughput protein expression of cDNA products as a tool in functional genomics, Importance of replication in microarray gene expression studies: Statistical methods and evidence form repetitive cDNA hybridizations, Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction, Using oligonucleotide probe arrays to access genetic diversity, Expression monitoring by hybridization to high density oligonucleotide arrays, Positional cloning in Arabidopsis. Arraying on glass slides also provides reproducible results, and it allows very high densities of spotted DNA and small hybridization volumes, although the associated costs are currently prohibitive for most laboratories. FlyRNAi (http://www.flyrnai.org), the database and website of the Drosophila RNAi Screening Center (DRSC) at Harvard Medical School, serves a dual role, tracking both production of reagents for RNA interference (RNAi) screening in Drosophila cells and RNAi screen results. The resulting spot intensity is dependant on the amount of clone‐specific transcript that was present in the starting material, and is quantified to produce a raw data set (d). Faster methods for forward and reverse genetics, which link phenotypes with genes, or vice versa, are essential for functional genomics. How will a holistic picture of the interplay between biomolecules be obtained from raw profiling data? Moreover, the authors applied this approach to analyze the whole high-content fluorescence images of Drosophila cells for further HCS-based gene function analysis. These include the amount of DNA delivered to each individual spot on the array, which in turn can be affected by PCR efficiency, pin geometry, and the degree of DNA fixation to the array surface. The accumulation of biological and biomedical literature outpaces the ability of most researchers and clinicians to stay abreast of their own immediate fields, let alone a broader range of topics. Metabolic profiling is also likely to uncover novel metabolic pathways in plants, and novel locations for known pathways. This distinguishes functional, postgenomics from traditional disciplines, which study one or a few genes, proteins, etc. Reagent and Data Resources for Investigation of RNA Binding Protein Functions in Drosophila melanogaster Cultured Cells. The results are accessible through the DIOPT diseases and traits query tool (DIOPT-DIST; http://www.flyrnai.org/diopt-dist). Hence, rather than visiting multiple separate databases for variant and gene analysis, users can obtain important information by searching once through MARRVEL. If you do not receive an email within 10 minutes, your email address may not be registered, Damage initiates a pleiotropic cellular response aimed at cellular survival when appropriate. Using the protein interactome, a significant level of connectivity was observed between Drosophila MMS survival proteins, suggesting a higher order relationship. They compare multiple normalization methods, which take advantage of different features within the data, including quantile normalization, background subtraction, scaling, cellHTS2 (Boutros et al. The final and currently most widespread technology for transcriptome analysis is DNA array technology, which relies on a reverse‐Northern approach in which DNA is attached to a solid support, and then hybridized to labelled cDNA probes derived from cellular mRNA (Fig. This review describes the tools that are currently being used for functional genomics work and considers the impact that this new discipline is likely to have in the future. This has been the most common approach for plant transcriptome analysis, in part because accurate sequence data, which is not available for many plant species, is not necessarily required. Most reverse genetics experiments in higher plants have so far relied on antisense RNA suppression or cosuppression, both of which reduce the level of endogenous transcript of the target gene (van der Krol et al., 1988; Brusslan et al., 1993). It is likely that central repositories of profiling data will emerge in the near future, analogous to databases like GenBank and SwissProt, which will enable the scientific community to share and discuss experimental results in a standardized way. 2). Altogether, BioLitMine extends the value of PubMed-indexed literature and its existing expert curation by providing a robust and gene-centric approach to retrieval of relevant information. In many model organisms, including bacteria, yeast, and even some lower plants like the moss, Physcomitrella patens, it is possible to knock‐out the function of a gene by replacing it with a mutant allele using homologous recombination (Schaefer & Zryd, 1997). Screeners must decide whether to examine genes with the most robust phenotype or the full gradient of genes that cause an effect and how to identify candidate genes. BACKGROUND: High-throughput screening using RNAi is a powerful gene discovery method but is often complicated by false positive and false negative results. All these experiments were analyzed manually and by BUHO and the results differed in less than 5% of the average value. SGs and PBs are highly dynamic and they form upon stress and dissolve thus releasing the repressed mRNAs according to changes in cell physiology. Based on our own experience and user feedback, we have made several changes. Although functional genomics is also built upon reductionism, it is nonetheless transforming the way we think about and perform biological science. We find that 21% of the proteins in the PPI network are indispensable. Comparison with genomic screen data from Saccharomyces cerevisiae revealed no overlap enrichment of individual genes between the species, but a conservation of the pathways. We constructed a Drosophila melanogaster signed PPI network consisting of 6,125 signed PPIs connecting 3,352 proteins that can be used to identify positive and negative regulators of signaling pathways and protein complexes. Such technologies may even help to discriminate the roles of genes from multigene families, which will be valuable when functional redundancy shrouds their physiological roles. Sensitivity on glass slides is very high for both oligonucleotides (Wodicka et al., 1997) and DNA fragments (Ruan et al., 1998). Specifically, we have restructured the database to accommodate new types of reagents; added information about new RNAi libraries and other reagents; updated the user interface and website; and added new tools of use to the Drosophila community and others. Upon the sequencing of the human genome, some believed that the connection of all genotypes to phenotypes could not be far behind. Insulin regulates an essential conserved signaling pathway affecting growth, proliferation, and meta- bolism. Our ability to modify the Drosophila genome has recently been revolutionized by the development of the CRISPR system. This approach relies on the fact that the set of peptides produced by protease digestion of a specific protein is nearly always unique to that protein. Although the first reported use of glass slide arrays and fluorescence hybridization was in Arabidopsis (Schena et al., 1995), most early applications of this technology searched for differentially expressed genes in the mammalian and yeast fields (DeRisi et al., 1996; Schena et al., 1996; Shalon et al., 1996; Heller et al., 1997). Furthermore, analyzing copy number alterations data from 1,547 cancer patients reveals that 56 genes that are frequently amplified or deleted in nine different cancers are indispensable. However, this ‘guilt by association’ approach is likely to reach its full potential only if it is possible to integrate information from many different organizational levels, not just the molecular level. Among the 56 genes, 46 of them have not been previously associated with cancer. We demonstrate the utility of this resource for validation of RNAi reagents in vivo. a single base‐pair change) is responsible for the phenotype, and especially when the organism has a large and complex genome, as do higher plants. Libraries of T‐DNA and transposon‐tagged mutants have also been created in many different plant species, including of course Arabidopsis. The role of PP1 is conserved in mammalian cells as judged by the effect of the PP1 inhibitor salubrinal, and involves dephosphorylation of the translation factor eIF2α. CCG’s functional genomics studies use models of cancer for high-throughput drug screens, gene perturbation experiments using RNA interference and CRISPR-Cas9 technology, and many other genome-wide … Experimental in vitro data generated with many of these functional genomics tools and technologies can now be integrated with a variety of omics data (including transcriptomics, metabolomics, proteomics, … Systems Biological Approaches in Infectious Diseases. - Serving as a forum for scientific exchange and discussion in the field of functional genomics. RESULTS: We report a simple but effective tool, the Drosophila RNAi Screening Center Integrative Ortholog Prediction Tool (DIOPT; http://www.flyrnai.org/diopt), for rapid identification of orthologs. DNA arrays are then probed with labelled cDNA reverse transcribed from poly(A) + RNA or total RNA isolated from the sample of interest.

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