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ToppCluster: a multiple gene list feature analyzer for comparative enrichment clustering and network-based dissection of biological systems.

Nucleic acids research | Jul 25, 2010

ToppCluster is a web server application that leverages a powerful enrichment analysis and underlying data environment for comparative analyses of multiple gene lists. It generates heatmaps or connectivity networks that reveal functional features shared or specific to multiple gene lists. ToppCluster uses hypergeometric tests to obtain list-specific feature enrichment P-values for currently 17 categories of annotations of human-ortholog genes, and provides user-selectable cutoffs and multiple testing correction methods to control false discovery. Each nameable gene list represents a column input to a resulting matrix whose rows are overrepresented features, and individual cells per-list P-values and corresponding genes per feature. ToppCluster provides users with choices of tabular outputs, hierarchical clustering and heatmap generation, or the ability to interactively select features from the functional enrichment matrix to be transformed into XGMML or GEXF network format documents for use in Cytoscape or Gephi applications, respectively. Here, as example, we demonstrate the ability of ToppCluster to enable identification of list-specific phenotypic and regulatory element features (both cis-elements and 3'UTR microRNA binding sites) among tissue-specific gene lists. ToppCluster's functionalities enable the identification of specialized biological functions and regulatory networks and systems biology-based dissection of biological states. ToppCluster can be accessed freely at http://toppcluster.cchmc.org.

Pubmed ID: 20484371 RIS Download

Mesh terms: Animals | Cluster Analysis | Gene Expression Profiling | Gene Regulatory Networks | Genes | Humans | Internet | Kidney | Liver | Mice | MicroRNAs | Phenotype | Software | Transcription Factors

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GenitoUrinary Development Molecular Anatomy Project

International consortium providing a molecular atlas of gene expression for the developing organs of the GenitoUrinary (GU) tract; a high resolution molecular anatomy highlighting development of the GU system; mouse strains to facilitate developmental and functional studies within the GU system; experimental protocols and standard specifications; tutorials describing GU organogenesis and primary data via the database. The data are from large-scale in situ hybridization screens (wholemount and section) and microarray gene expression data of microdissected, laser-captured and FACS-sorted components of the developing mouse genitourinary (GU) system. These expression data are annotated using a high-resolution anatomy ontology specific to the developing murine GU system.

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A bibliographic database that provides access to over 22 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites. PubMed citations and abstracts include the fields of biomedicine and health, covering portions of the life sciences, behavioral sciences, chemical sciences, and bioengineering. PubMed also provides access to additional relevant web sites and links to the other NCBI molecular biology resources. Publishers of journals can submit their citations to NCBI and then provide access to the full-text of articles at journal web sites using LinkOut.

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