ArticleBMC genomics2014
Categorizer: a tool to categorize genes into user-defined biological groups based on semantic similarity.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
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- GCN2 is required to maintain core body temperature in mice during acute cold.American journal of physiology. Endocrinology and metabolism · 2023Article
- Regulated IRE1α-dependent decay (RIDD)-mediated reprograming of lipid metabolism in cancer.Nature communications · 2022Article
- Whether Gametophytes are Reduced or Unreduced in Angiosperms Might Be Determined Metabolically.Genes · 2020Article
- Graph-based exploitation of gene ontology using GOxploreR for scrutinizing biological significance.Scientific reports · 2020Article
- Epigenomic and Transcriptomic Changes During Human RPE EMT in a Stem Cell Model of Epiretinal Membrane Pathogenesis and Prevention by Nicotinamide.Stem cell reports · 2020Article
- GOcats: A tool for categorizing Gene Ontology into subgraphs of user-defined concepts.PloS one · 2020Article
- Indoxyl Sulfate Induces Apoptosis Through Oxidative Stress and Mitogen-Activated Protein Kinase Signaling Pathway Inhibition in Human Astrocytes.Journal of clinical medicine · 2019Article
- Advances in gene ontology utilization improve statistical power of annotation enrichment.PloS one · 2019Article
- A new method for evaluating the impacts of semantic similarity measures on the annotation of gene sets.PloS one · 2018Article
- Article
- In-Cardiome: integrated knowledgebase for coronary artery disease enabling translational research.Database : the journal of biological databases and curation · 2017Article
- Quantitative Identification of Compound-Dependent On-Modules and Differential Allosteric Modules From Homologous Ischemic Networks.CPT: pharmacometrics & systems pharmacology · 2016Article
- Role of plant MicroRNA in cross-species regulatory networks of humans.BMC systems biology · 2016Article
- Total Lipopolysaccharide from the Human Gut Microbiome Silences Toll-Like Receptor Signaling.mSystemsArticle
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3 authors.
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Abstract
backgroundCommunalities between large sets of genes obtained from high-throughput experiments are often identified by searching for enrichments of genes with the same Gene Ontology (GO) annotations. The GO analysis tools used for these enrichment analyses assume that GO terms are independent and the semantic distances between all parent-child terms are identical, which is not true in a biological sense. In addition these tools output lists of often redundant or too specific GO terms, which are difficult to interpret in the context of the biological question investigated by the user. Therefore, there is a demand for a robust and reliable method for gene categorization and enrichment analysis.
resultsWe have developed Categorizer, a tool that classifies genes into user-defined groups (categories) and calculates p-values for the enrichment of the categories. Categorizer identifies the biologically best-fit category for each gene by taking advantage of a specialized semantic similarity measure for GO terms. We demonstrate that Categorizer provides improved categorization and enrichment results of genetic modifiers of Huntington's disease compared to a classical GO Slim-based approach or categorizations using other semantic similarity measures.
conclusionCategorizer enables more accurate categorizations of genes than currently available methods. This new tool will help experimental and computational biologists analyzing genomic and proteomic data according to their specific needs in a more reliable manner.
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