Gene Ontology

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Gene Ontology (GO) ist eine internationale Bioinformatik-Initiative zur Vereinheitlichung eines Teils des Vokabulars der Biowissenschaften. Resultat ist die gleichnamige Ontologie - Datenbank , die inzwischen weltweit von vielen biologischen Datenbanken verwendet und ständig weiterentwickelt wird The Gene Ontology (GO) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species. More specifically, the project aims to: 1) maintain and develop its controlled vocabulary of gene and gene product attributes; 2) annotate genes and gene products, and assimilate and disseminate annotation data; and 3) provide tools for easy access to. Gene Ontology (GO) describes gene products with three independent categories: biological process, cellular component, and molecular function (Ashburner et al., 2000), which may produce multiple GO terms assigned to one query sequence. From: Methods in Enzymology, 2016. Download as PDF

In general, an ontology such as the gene ontology consists of a number of explicitly defined terms that are names for biological objects or events. These terms are depicted as nodes (also called vertices) in a graph that describe the relationships between the nodes. For instance, The Gene Ontology (GO) project provides a set of hierarchical controlled vocabulary split into 3 categories: Biological process; Molecular function; Cellular component; UniProtKB lists selected terms derived from the GO project. The GO terms derived from the 'Biological process' and Molecular function' categories are listed in the 'Function' section; the GO terms derived from the 'Cellular component' category are listed in the 'Subcellular location' section Interactively searchthe Gene Ontology data for annotations, gene products, and terms using a powerful search syntax and filters. Search. Annotations. Ontology. Genes and gene products. Browse the Ontology. Use the drill-down browserto view the ontology structure with annotation counts. Go »

Gene Ontology - Wikipedi

The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating. This book provides a practical and self-contained overview of the Gene Ontology (GO), the leading project to organize biological knowledge on genes and their products across genomic resources. Written for biologists and bioinformaticians, it covers the state-of-the-art of how GO annotations are made, how they are evaluated, and what sort of analyses can and cannot be done with the GO. In the spirit of th Parent. No parent directory Directories. annotations; bin; lib; metadata; ontology; products; release_stats; reports; Files. summary.tx Gene Ontology annotations report connections between gene products and the biological types that are represented in the GO using GO evidence codes. The evidence codes record the process by which these connections are established and reflect either the experimental analysis of actual instances of gene products or inferential reasoning from such analysis. We believe that an understanding of the role of instances in the spatiotemporal reality upon which experiments are performed can.

The Gene Ontology Consortium (GOC) provides the most comprehensive resource currently available for computable knowledge regarding the functions of genes and gene products. Here, we report the advances of the consortium over the past two years. The new GO-CAM annotation framework was notably improved, and we formalized the model with a computational schema to check and validate the rapidly increasing repository of 2838 GO-CAMs. In addition, we describe the impacts of several collaborations. Gene Ontology. Gene Ontology (GO) describes gene products with three independent categories: biological process, cellular component, and molecular function (Ashburner et al., 2000), which may produce multiple GO terms assigned to one query sequence. From: Methods in Enzymology, 2016. Download as PDF Any process that activates or increases the frequency, rate or extent of metanephric mesenchymal cell migration. Any process that stops, prevents or reduces the frequency, rate or extent of metanephric mesenchymal cell migration. Any process that modulates the frequency, rate or extent of optic nerve formation

vocabularies - gene ontology (GO) - to describe key domains of molecular biology, gene - To apply GO terms in the annotation of genes in biological databases - To provide a centralized public resource allowing universal access to the GO, annotation data sets and software tools developed for use with GO data . GO Data Descriptive Vocabularies. GO Vocabularies (Terms) • Define all gene.

Skip to local navigation; Skip to EBI global navigation menu; Skip to expanded EBI global navigation menu (includes all sub-sections Overview. The gene association files ingested from GO Consortium members are shown in the table below. Files are in the GO annotation file format and are compressed using the UNIX gzip utility. Please see the upstream resource information for further details on the annotation set. Any errors or omissions in annotations should be reported. Code for converting between BioPAX pathways and Gene Ontology Causal Activity Models (GO-CAM) Java 0 1 26 0 Updated May 4, 2021. neo noctua entity ontology Perl 2 1 22 (3 issues need help) 2 Updated Apr 29, 2021. obographs Basic and Advanced OBO Graphs: specification and reference implementation json graphs owl gene-ontology ontologies obofoundry ontology-standards Java 9 36 42 6 Updated Apr. The Gene Ontology archive provides GO data - ontology, annotations, and associated files - starting from March 2004. The archive was built from the legacy GO CVS, SVN and archive products to reconstruct GO releases on a monthly basis, similar to our current release cycle

Download Gene Ontology for free. The home of the Gene Ontology project on SourceForge, including ontology requests, software downloads, bug trackers, and much, much more Welcome to the Gene Ontology Tools developed within the Bioinformatics Group at the Lewis-Sigler Institute. The GO Help Page at SGD gives the following description of the Gene Ontology: The Gene Ontology (GO) project was established to provide a common language to describe aspects of a gene product's biology. The use of a consistent vocabulary allows genes from different species to be.

Gene ontology - Wikipedi

  1. 遺伝子オントロジー. 遺伝子オントロジー (いでんしオントロジー、 英: gene ontology 、 GO )とは、 生物学 的概念を記述するための、共通の語彙を策定しようとするプロジェクトである。. 1990年代後半から、生物学における実験手法の革新( DNAシーケンサー や DNAマイクロアレイ など)や、 バイオインフォマティクス 的手法の発達により、様々な 種 の遺伝子.
  2. The Gene Ontology Consortium is supported by NIH/NHGRI grant HG02273, and by grants from the European Union RTD Programme 'Quality of Life and Management of Living Resources' (QLRI‐CT‐2001‐00981 and QLRI‐CT‐2001‐00015). Open in new tab Download slide. Figure 1. Application of a GO slim set in genome annotation. The number of gene products annotated to each term in each of four.
  3. It initiated the Gene Ontology Annotation (GOA) project ( 6, 7) to provide assignments of GO terms to all well characterized proteins and in particular to that of the human proteome. The initial aims and objectives of the GOA project have already been achieved. GOA has organized, shared and integrated protein knowledge using the GO structured vocabulary. This was facilitated with the help of.
  4. Gene Ontology: tool for the unification of biology. Nature Genetics, 2000, 25: 25-29. Acknowledgements. Plant Ontology has been developed and contributed by the Plant Ontology Consortium. Gramene is collaborating with The.
  5. Gene Ontology is a term that comprises three broad biological aspects- cellular component, molecular functions, and biological processes. There are many gene ontology tools available that help in identifying the GO terms associated with a gene or protein. Some of the best gene ontology tools are free to use as public web- browsers. Some are.

Gene Ontology - an overview ScienceDirect Topic

dict.cc | Übersetzungen für 'Gene Ontology' im Englisch-Deutsch-Wörterbuch, mit echten Sprachaufnahmen, Illustrationen, Beugungsformen,. The Gene Ontology (GO) provides core biological knowledge representation for modern biologists, whether computationally or experimentally based. GO resources include biomedical ontologies that cover molecular domains of all life forms as well as extensive compilations of gene product annotations to these ontologies that provide largely species-neutral, comprehensive statements about what gene. Gene Ontology的结构是一个有向无环图,有点类似于分类树,不同点在于Gene Ontology 的结构中一 个 term可以有不止一个parent. image **GO term关系 ** GO的本体被构造为有向无环图,其中术语作为图中的节点,并且术语之间的关系作为边缘。 正如每个术 语被定义一样,因此GO术语之间的关系也被分类和定义.

Understanding Gene Ontology Analysis - Advaita Bioinformatic

Data available from TAIR includes the complete genome sequence along with gene structure, gene product information, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community. Gene product function data is updated every week from the latest published research literature and community data submissions. Schematischer Aufbau eines eukaryotischen Gens. Vor der Transkriptionseinheit oder auch innerhalb der Exons (hellblau und dunkelblau) und Introns(rosa und rot) liegen regulatorische Elemente, wie zum Beispiel Enhancer oder Promotor.An diese binden, abhängig von der Sequenz, verschiedene Proteine, wie beispielsweise die Transkriptionsfaktoren und die RNA-Polymerase © STRING Consortium 2020. SIB - Swiss Institute of Bioinformatics; CPR - Novo Nordisk Foundation Center Protein Research; EMBL - European Molecular Biology Laborator Gene Ontology Ribbon Sandbox. The GO Ribbon provides a visual summary of gene functions and a quick way to browse the GO annotations for a gene or gene set. To further investigate the GO annotations grouped under a high level term, click on the colored cells for your gene of interest..

Provides structured controlled vocabularies for the annotation of gene products with respect to their molecular function, cellular component, and biological role. The Gene Ontology consists of three Vocabularies. Cancer Biomedical Informatics Grid, Clinical and Translational Science Awards, OBO Foundry, Unified Medical Language System Lentiviral gene ontology (LeGO) vectors equipped with novel drug-selectable fluorescent proteins: new building blocks for cell marking and multi-gene analysis. Kristoffer Weber, Ulrike Mock, Bettina Petrowitz, Udo Bartsch & Boris Fehse. Gene Therapy (2010), 17 (4): 511-520 The Gene Ontology archive provides GO data - ontology, annotations, and associated files - starting from March 2004. The archive was built from the legacy GO CVS, SVN and archive products to reconstruct GO releases on a monthly basis, similar to our current release cycle. The file structure and file format were made consistent with the current GO monthly releases produced since 2018. File. Gene Ontology. An ontology for describing the function of genes and gene products. The goal of the GeneOntology (GO) project is to provide a uniformway to describe the functions of gene products from organisms across all kingdoms of life and thereby enable analysis of genomic data

Gene Ontology (GO) term enrichment is a technique for interpreting sets of genes making use of the Gene Ontology system of classification, in which genes are assigned to a set of predefined bins depending on their functional characteristics. For example, the gene FasR is categorized as being a receptor, involved in apoptosis and located on the plasma membrane Gene Ontology (GO) ist eine internationale Bioinformatik-Initiative zur Vereinheitlichung eines Teils des Vokabulars der Biowissenschaften.Resultat ist die gleichnamige Ontologie-Datenbank, die inzwischen weltweit von vielen biologischen Datenbanken verwendet und ständig weiterentwickelt wird.Weitere Bemühungen sind die Zuordnung von GO-Termini (Annotation) zu einzelnen Genen und ihren. A set of annotation maps describing the entire Gene Ontology. Bioconductor version: Release (3.13) A set of annotation maps describing the entire Gene Ontology assembled using data from GO. Author: Marc Carlson . Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org> Citation (from within R, enter citation(GO.db)): Installation. To install this package, start R (version. SourceForge Gene Ontology main page: the main Gene Ontology project page at SourceForge Downloads: all the GO-related files hosted on the SourceForge site GO mailing lists on SourceForge: subscription information and archives for the automated e-mail notification system that operates with SourceForge trackers Back to to Term/Gene Co-Occurrence Probability: Ranking functional categories based on co-occurrence with sets of genes in a gene list can rapidly aid in unraveling new biological processes associated with cellular functions and pathways. DAVID 6.8 allows investigators to sort gene categories from dozens of annotation systems. Sorting can be based either the number of genes within each category or by the.

ontologyOperations on Ontology Terms and Subsets. GET /ontology/ribbon/. Fetch the summary of annotations for a given gene or set of genes. GET /ontology/shared/ {subject}/ {object} Returns the ancestor ontology terms shared by two ontology terms. GET /ontology/subset/ {id The Gene Ontology (GO) considers three distinct aspects of how gene functions can be described: molecular function, cellular component, and biological process (note that throughout this chapter, bold text will denote specific concepts, or classes, from the Gene Ontology). In order to understand what these aspects mean and how they relate to each other, it may be helpful to consider the. De Gene Ontology of GO is een belangrijke ontologie binnen de bio-informatica.Het doel ervan is om de weergave van de eigenschappen van genen en de genproducten te standaardiseren, onafhankelijk van de soort waaruit ze komen.. Het doel van het GO-project bestaat uit drie delen: onderhouden en ontwikkelen van een vocabularium voor eigenschappen van genen en hun producten

Gene Ontology (GO) - UniPro

Video: Gene ontology - AmiGO 2: Welcom

Gene Ontology: tool for the unification of biology

  1. Gene ontology (GO) is a bioinformatic concept that was originally proposed to unify the representation of genes and gene products of many species [15, 16]. The ontology covers three main domains, namely, (I) cellular component, (II) molecular function, and (III) biological process, which can easily cluster all genes and gene products with a directed acyclic graph (DAG) [ 16 ]
  2. The Gene Ontology (GO) Project. We are part of the Gene Ontology Consortium which seeks to provide controlled vocabularies for the description of the molecular function, biological process, and cellular component of gene products. These terms are to be used as attributes of gene products by collaborating databases, facilitating uniform queries.
  3. Gene Ontology (GO)简介 . Gene Ontology(GO)包含了基因参与的生物过程,所处的细胞位置,发挥的分子功能三方面功能信息,并将概念粗细不同的功能概念组织成DAG(有向无环图)的结构。Gene Ontology是一个使用有控制的词汇表和严格定义的概念关系,以有向无环图的形式统一表示各物种的基因功能分类.
  4. The Gene Ontology is a hierarchical controlled-vocabulary system deployed to derive functional insights from gene lists. From my understanding, protein motifs are the gold standard for GO.
  5. Gene Ontology. The Gene Ontology (GO) provides a framework and set of concepts for describing the functions of gene products from all organisms. Ontology Homepage
  6. The Gene Ontology Analysis Viewer allows direct browsing of the Gene Ontology, and also the visualization of GO Term analysis results. The viewer presents the GO both in tabular form (Table tab) as well as in a tree form (Tree tab). In addition, three windows provide additional details: A list below the selection windows shows all genes annotated with a selected term. The Single Term View.
  7. Welcome to the Gene Ontology Helpdesk.. Do you have general questions about GO? Check our Frequently Asked Questions, as your query may have already been answered.. Do you have a specific question about the GO, its data, usage, software, or services

The Gene Ontology Handbook SpringerLin

  1. Gene Ontology & Pathway Analysis are done to understand more about a group of genes and there combined effect. After a gene expression study, the significant genes that came up in the study are used for these analyses. Here we are using ShinyGO app for doing this analysis. Tutorial Difficulty : Eas
  2. Gene Ontology (GO) Frequently used. apoptotic process; binding; kinase activity; transporter activity; ALL: biological_process: cellular_component: molecular_function: associated chemicals · associated genes · associated diseases · associated exposure references associated phenotypes is a · negatively regulates · part of · positively regulates · regulates. Home | Site Map | FAQ.
  3. Gene ontology characterizes the relationship between genes by specifically annotating and categorizing a gene product's molecular function (function of the gene product) and associated.
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The Gene Ontology Annotation (GOA) project provides high-quality functional annotations to gene products, such as proteins, protein complexes and non-coding. This group's purpose is to ensure that the Gene Ontology represents biology in a way that is useful for gene product annotation of reference genomes and other MODs using the GO for annotation. The group serves as the link between biological knowledge that is gained from wet-bench scientists and the representation of that knowledge in the GO Gene Ontology website (www.geneontology.org) or from the NCBI. Additionally, the bioconductor AnnotationDbi library has recently added a function makeOrgPackageFromNCBI, which can be used to create an organism package from within R, using the NCBI data. Once created, this package can then be used to obtain the mapping between genes and gene ontology. 4. 6 Case study: Prostate cancer data 6.1. The Gene Ontology and the Meaning of Biological Function Paul D. Thomas 3. Primer on the Gene Ontology Pascale Gaudet, Nives Skunca, James C. Hu, and Christophe Dessimoz Part II: Making Gene Ontology Annotations 4. Best Practices in Manual Annotation with the Gene Ontology Sylvain Poux and Pascale Gaudet 5 FlyBase uses Gene Ontology (GO) controlled vocabulary (CV) terms for cellular component, biological process and molecular function to describe properties of gene products. Although GO terms are intended to describe the properties of gene products, FlyBase currently assigns GO terms to genes rather than protein or RNA. FlyBase is one of the founding members of the Gene Ontology (GO) Consortium.

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Gene ontology (GO) enrichment analysis was performed using GOrilla [21]. Each list from the limma analysis was ranked from smallest to largest p-value and analyzed for enriched biological process ontology terms found near the top of the list. Functional classification summary for the nhr-49 mutant were presented as a scatter plot using the GO visualization tool REViGO [51]. Eden E, Navon R. MATA1 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 literature, as well as computational, or predicted. Gene Ontology term obtained by mapping which can directly be associated with one or more BLAST hits. (GO-Accession, maximum hit e-value assigned, max. hit similarity assigned, number of hits belonging to this) Non-annotated GO term node (GO term name, mean e-value of all hits contributing to this node, max. e-value, max. Similarity, number of Hits contributing to this node, Annotation. The Gene Ontology database is dated Saturday, May 01, 2021. The UniProt-to-GO mapping database from the EBI GOA project (goa_uniprot_gcrp.gaf.gz) is dated Friday, April 09, 2021. If you found REVIGO useful in your work, please cite the following reference:. All genes/features with GO annotations in the database, 2. All annotations in the database (manually curated, high-throughput, and computational), and 3. All hits with p-value < 0.01 will be displayed on results page.. Step 1. Query Set (Your Input) Step 2. Choose Ontology. Step 3. (Optional) Specify your background set of genes

High-throughput network maps are used to automatically (or semi-automatically) reconstruct an ontology that recapitulates much of the Gene Ontology and finds additional terms and relations Gene Ontology (Daily build accessed on 01/14/2019.) Pathway; KEGG (Release 88.2, 11/01/2018), WikiPathways (Release 02/10/2020), Reactome (Version 66, September 2018), PANTHER (v3.6.1, 01/22/2018) Network; Hierarchical mRNA co-expression modules: The modules are computationally derived from the RNA-Seq data sets across 33 TCGA (The Cancer Genome Atlas, Release 01/28/2016) and 6 CPTAC (Clinical. ToppFun: Transcriptome, ontology, phenotype, proteome, and pharmacome annotations based gene list functional enrichment analysis Detect functional enrichment of your gene list based on Transcriptome, Proteome, Regulome (TFBS and miRNA), Ontologies (GO, Pathway), Phenotype (human disease and mouse phenotype), Pharmacome (Drug-Gene associations), literature co-citation, and other features

The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information Gene Ontology (GO) è un progetto bioinformatico atto a unificare la descrizione delle caratteristiche dei prodotti dei geni in tutte le specie. In particolare, il progetto si propone di: Mantenere e sviluppare un vocabolario controllato atto a descrivere i geni e i prodotti genici per ogni organismo vivente; Annotare i geni e i prodotti genici, e diffondere tali dati; Fornire strumenti per un.

Gene Ontology annotations: what they mean and where they

If Gene Ontology is chosen, your genes are grouped by functional categories defined by high-level GO terms. The characteristics of your genes are compared with the rest in the genome. Chi-squared and Student's t-tests are run to see if your genes have special characteristics when compared with all the other genes or, if uploaded a customized background. Your genes are marked in each of the. Gene Ontology Consortium. We are leaders in the application of ontologies to aid communication between biologists and bioinformatic resources. The Cherry lab was a founding member of GO in 1998 in collaboration with FlyBase and MGI. The GO Consortium created a standard language to describe protein and RNA function Gene Ontology annotations report connections between gene products and the biological types that are represented in the GO using GO evidence codes. The evidence codes record the process by which these connections are established and reflect either the experimental analysis of actual instances of gene products or inferential reasoning from such analysis. We believe that an understanding of the. MG1655 Gene-Ontology-Terms How to Navigate: A class hierarchy (ontology) allows you to retrieve information according to categories of interest. In the class hierarchy that follows, each line names a single class of biological objects. The levels of indentation indicate a subclass relationship to the class above. The numbers in parentheses indicate the number of instances of that class. Gene Ontology est un projet bio-informatique destiné à structurer la description des gènes et des produits géniques dans le cadre d'une ontologie commune à toutes les espèces [1].Ce projet, qui s'inscrit dans la démarche plus large d'Open Biomedical Ontologies (OBO) regroupant d'autres projets bio-informatiques dans le domaine biomédical, poursuit trois objectifs

The Gene Ontology resource: enriching a GOld min

Gene ontology and KEGG enrichment analyses of known AMD-related genes were performed, and a classification system was established. In detail, each gene was encoded into a vector by extracting enrichment scores of the gene set, including it and its direct neighbors in STRING, and gene ontology terms or KEGG pathways. Then certain feature. La Gene Ontology ( GO) est une initiative bioinformatique majeure visant à unifier la représentation des attributs des gènes et des produits génétiques dans toutes les espèces.Plus précisément, le projet vise à: 1) maintenir et développer son vocabulaire contrôlé des attributs des gènes et des produits géniques; 2) annoter les gènes et les produits géniques, assimiler et. The GOA database: Gene Ontology annotation updates for 2015. Huntley RP, Sawford T, Mutowo-Muellenet P, Shypitsyna A, Bonilla C, Martin MJ, O'Donovan C. Nucleic Acids Research 2014 43:D1057-D1063. QuickGO: a web-based tool for Gene Ontology searching. Binns D, Dimmer E, Huntley R, Barrell D, O'Donovan C, Apweiler R. Bioinformatics 2009 25. Gene Ontology, abreviada como GO (Ontoloxía Xénica), é unha importante iniciativa bioinformática para unificar a representación dos atributos dos xenes e produtos xénicos de todas as especies de seres vivos. [1] O proxecto ten os seguintes obxectivos concretos: 1) Manter e desenvolver o seu vocabulario controlado de atributos de xenes e produtos xénicos; 2) anotar xenes e produtos. dict.cc | Übersetzungen für 'Gene Ontology' im Latein-Deutsch-Wörterbuch, mit echten Sprachaufnahmen, Illustrationen, Beugungsformen,.

The Gene Ontology Term Analysis component will automatically make use of Affymetrix 3' Expression microarray annotation data if it was loaded along with the microarray dataset. Although the Affymetrix Human Gene 1.0 ST and Human Exon 1.0 ST annotation files can be used by geWorkbench, they cannot currently be used by the ontology analysis code. For any other microarray platform type except the. Gene Ontology enrichment analysis. The Gene Ontology Enrichment Analysis is a popular type of analysis that is carried out after a differential gene expression analysis has been carried out. There are many tools available for performing a gene ontology enrichment analysis. Online tools include DAVID, PANTHER and GOrilla Gene Ontology Tools • The Gene Ontology Consortium itself has created tools to help create, search, and analyze its data and also supports 3rd party applications on their website • The GOC created AmiGO and OBO-edit to read and edit the database data respectfully • 3rd party developers have created GO browsers, annotators, and data analyzers, among other tools 36. AmiGO • Browser and. dict.cc | Übersetzungen für 'Gene Ontology' im Ungarisch-Deutsch-Wörterbuch, mit echten Sprachaufnahmen, Illustrationen, Beugungsformen,.

Using the Gene Ontology data objects Daniel Greene 2021-02-10. ontologySimliarity comes with data objects encapsulating the GO (Gene Ontology) annotation of genes [1]:. gene_GO_terms, a list of character vectors of term IDs of GO terms annotating each gene, named by gene,; GO_IC, a numeric vector containing the information content of Gene Ontology terms based on frequencies of annotation in. Gene Ontologyの意味や使い方 *** シソーラス 共起表現 Scholar, Entrez, Google, WikiPedia (遺伝子の機能定義と分類体系)ジーンオントロジー関連語GO同義語(異表記)Gene Ontology... - 約1174万語ある英和辞典・和英辞典。発音・イディオムも分かる英語辞書 Among existing ontologies, Gene Ontology (GO) is one of the earliest and most frequently used vocabularies, which focuses on describing biological process (BP), molecular function (MF), and cell component (CC) of genes. Since appearing in 2000, a large number of databases recording the functions of genes were annotated to the GO. The functional annotation of human protein-coding genes was.

AmiGO 2: Search - Gene ontolog

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