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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 | 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

Research resources used in this publication

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Associated grants

  • Agency: NIDDK NIH HHS, United States
    Id: 1U01 DK70219
  • Agency: NCATS NIH HHS, United States
    Id: UL1 TR000077
  • Agency: NCRR NIH HHS, United States
    Id: U54 RR025216
  • Agency: NIDCR NIH HHS, United States
    Id: U01DE020049
  • Agency: NIDDK NIH HHS, United States
    Id: P30 DK078392

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This is a list of tools and resources that we have found mentioned in this publication.


GenitoUrinary Development Molecular Anatomy Project (tool)

RRID:SCR_001554

Project aggregates and provides experimental gene expression data from genito-urinary system. International consortium providing molecular atlas of gene expression for developing organs of GenitoUrinary (GU) tract. Mouse strains to facilitate developmental and functional studies within GU system. Experimental protocols and standard specifications. Tutorials describing GU organogenesis and primary data via database. 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 developing mouse genitourinary (GU) system.

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TreeView (tool)

RRID:SCR_013503

Software to graphically browse results of clustering and other analyses from Cluster.

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