ToppCluster protocols

ToppCluster specifications

Information


Unique identifier OMICS_02225
Name ToppCluster
Interface Web user interface
Restrictions to use None
Input data Some separate lists of genes which can be successively added and named, or a two-column list with genes in the first column and the name of the gene list in the second column.
Output data A result matrix that has columns that relate to each input gene list, and rows that represent the overrepresented features of any of the gene lists.
Output format TSV,CSV,HTML,PDF
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Maintainer


  • person_outline Bruce Aronow <>

Additional information


https://toppcluster.cchmc.org/help/

Publication for ToppCluster

ToppCluster IN pipelines

 (5)
2017
PMCID: 5319840
PMID: 28219480
DOI: 10.7554/eLife.22914.039

[…] samples. we generated a list of differentially regulated genes by comparing cd34-high samples to cd34-negative samples, with a fold change cutoff of 2.0 (n = 896 entities). entities were exported to toppcluster in order to identify enrichment in previously published microarray datasets (coexpression ontologies). a network consisting of genes and associated studies was generated […]

2017
PMCID: 5319840
PMID: 28219480
DOI: 10.7554/eLife.22914.039

[…] to toppcluster in order to identify enrichment in previously published microarray datasets (coexpression ontologies). a network consisting of genes and associated studies was generated through toppcluster and cytoscape., chromatin immunoprecipitation was performed as previously described (mccauley et al., 2014). briefly, nih3t3 cells were seeded in 10 cm plates at 80% confluence […]

2017
PMCID: 5575162
PMID: 28852045
DOI: 10.1038/s41598-017-10127-1

[…] obtain functional pathways and go term. relevant go terms for those gene set were analyzed by using funrich software (http://www.funrich.org)19. enriched pathways and drugs were identified by using toppcluster (https://toppcluster.cchmc.org/)20. the functional annotations for the go term level were mainly focused on biological process in this study. hypergeometric test and multiple-testing […]

2017
PMCID: 5575162
PMID: 28852045
DOI: 10.1038/s41598-017-10127-1

[…] and go term. relevant go terms for those gene set were analyzed by using funrich software (http://www.funrich.org)19. enriched pathways and drugs were identified by using toppcluster (https://toppcluster.cchmc.org/)20. the functional annotations for the go term level were mainly focused on biological process in this study. hypergeometric test and multiple-testing corrections (bonferroni) […]

2015
PMCID: 4460046
PMID: 26053627
DOI: 10.1371/journal.pone.0129023

[…] (http://eqtl.uchicago.edu/cgi-bin/gbrowse/eqtl/) and extracted genes associated with selected variants in ceu populations. next, a multigene feature based enrichment analysis was performed using toppcluster (http://toppcluster.cchmc.org/) [46], which uses all the available resources related to the given genes. statistically significant enrichment (false discovery rate; fdr correction […]

ToppCluster institution(s)
Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA; Department of Biomedical Engineering, University of Cincinnati, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
ToppCluster funding source(s)
Supported by National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Diseases (NIH/NIDDK) 1U01 DK70219 (Murine Atlas of a Genitourinary Development Molecular Anatomy Project); PHS Grant P30 DK078392 (Cincinnati Digestive Health Center); U54 RR025216 (CTSA: Cincinnati Center for Clinical and Translational Sciences); and U01DE020049 NIDCR (FACEBASE Consortium).

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