232
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: not found
      • Article: not found

      clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

      1 , 2 , 1 , 1
      OMICS: A Journal of Integrative Biology
      Mary Ann Liebert Inc

      Read this article at

      ScienceOpenPublisherPMC
      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Increasing quantitative data generated from transcriptomics and proteomics require integrative strategies for analysis. Here, we present an R package, clusterProfiler that automates the process of biological-term classification and the enrichment analysis of gene clusters. The analysis module and visualization module were combined into a reusable workflow. Currently, clusterProfiler supports three species, including humans, mice, and yeast. Methods provided in this package can be easily extended to other species and ontologies. The clusterProfiler package is released under Artistic-2.0 License within Bioconductor project. The source code and vignette are freely available at http://bioconductor.org/packages/release/bioc/html/clusterProfiler.html.

          Related collections

          Most cited references18

          • Record: found
          • Abstract: found
          • Article: not found

          Gene Ontology: tool for the unification of biology

          Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. 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 and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: found
            Is Open Access

            ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks

            Summary: We have developed ClueGO, an easy to use Cytoscape plug-in that strongly improves biological interpretation of large lists of genes. ClueGO integrates Gene Ontology (GO) terms as well as KEGG/BioCarta pathways and creates a functionally organized GO/pathway term network. It can analyze one or compare two lists of genes and comprehensively visualizes functionally grouped terms. A one-click update option allows ClueGO to automatically download the most recent GO/KEGG release at any time. ClueGO provides an intuitive representation of the analysis results and can be optionally used in conjunction with the GOlorize plug-in. Availability: http://www.ici.upmc.fr/cluego/cluegoDownload.shtml Contact: jerome.galon@crc.jussieu.fr Supplementary information: Supplementary data are available at Bioinformatics online.
              Bookmark
              • Record: found
              • Abstract: not found
              • Article: not found

              A direct approach to false discovery rates

                Bookmark

                Author and article information

                Journal
                OMICS: A Journal of Integrative Biology
                OMICS: A Journal of Integrative Biology
                Mary Ann Liebert Inc
                1536-2310
                1557-8100
                May 2012
                May 2012
                : 16
                : 5
                : 284-287
                Affiliations
                [1 ]Institute of Life and Health Engineering, Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Jinan University, Guangzhou, People's Republic of China.
                [2 ]Guangdong Information Center, Guangzhou, People's Republic of China.
                Article
                10.1089/omi.2011.0118
                3339379
                22455463
                b21fe860-1553-40be-a528-1bb59cec42ca
                © 2012

                http://www.liebertpub.com/nv/resources-tools/text-and-data-mining-policy/121/

                History

                Comments

                Comment on this article