ToppFun protocols

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ToppFun specifications

Information


Unique identifier OMICS_27567
Name ToppFun
Interface Web user interface
Restrictions to use None
Input data A single gene list.
Output format HTML+TSV
Computer skills Basic
Stability Stable
Maintained Yes

Maintainers


  • person_outline Bruce Aronow <>
  • person_outline Anil Jegga <>
  • person_outline Eric Bardes <>

Publication for ToppFun

ToppFun in pipelines

 (7)
2018
PMCID: 5858605
PMID: 29593587
DOI: 10.3389/fpsyt.2018.00081

[…] the experiments using the sva package in bioconductor (). mirnas with a p-value <0.05 were considered to be significantly different between two groups., for gene set enrichment analysis, we used toppfun in toppgene suite () to infer significantly enriched gene ontology (go) () terms, pathway, and disease terms. as the input for this approach, we used 1,230 predicted target genes […]

2017
PMCID: 5329963
PMID: 28241754
DOI: 10.1186/s12881-017-0370-2

[…] reported, which is more conservative relative to the generally suggested threshold enrichment score of > 1.3 []. genes from the human genome were used as background. in the toppgene suite, the toppfun module was used to analyze functional enrichment in biological processes of differentially methylated genes. enrichment for genes from input ≥ 3 and fdr ≤ 0.05 after benjamini-hochberg […]

2016
PMCID: 5073979
PMID: 27766949
DOI: 10.1186/s12859-016-1226-z

[…] tprs versus threshold values were then compared graphically for both fdr and t-statistic calculated p-values., lists of cell type-specific differentially expressed gene names were analyzed using toppfun module of the toppgene suite [] using default settings., rstudio [] v.0.99.491. r packages: geoquery [] v.2.36.0, proc [] v.1.8, cellmix [] 1.6.2. cssam [] version 1.2.4, computer […]

2016
PMCID: 5133834
PMID: 27827897
DOI: 10.3390/ijms17111833

[…] performed using the benjamini and hochberg method. to analyze lists of significantly deregulated genes after dep extract treatments (cut-off p-value < 0.05, fold change > 1.5, or < 0.6), a toppfun tool was used []. functional analysis identified numerous over-represented terms in several categories; pathways as a functional category were considered for the analysis., the detection […]

2014
PMCID: 4274761
PMID: 25538794
DOI: 10.1186/s13073-014-0111-5

[…] they had the expressed variant or not. subjects without adequate sequencing coverage across the variant were excluded from the analysis. pathway gene list enrichment analysis was performed using the toppfun algorithm of the toppgene suite []., vcf files for sepsis survivors and non-survivors were analyzed using the snp and variation suite v8.1.4 (goldenhelix). to assess the association […]


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ToppFun in publications

 (69)
PMCID: 5928158
PMID: 29740474
DOI: 10.3389/fgene.2018.00125

[…] expressed in ds samples; (2) expression ratios ≥1.30 and (3) expression ratios ≤0.76., a functional enrichment analysis of over-expressed genes in the “total transcriptome map” was performed using ‘toppfun’ from the ‘toppgene suite’ gene ontology tool (). we submitted a list of human genes with expression ratio ≥1.30 and a list of genes of all the chromosomes with expression ratio ≤0.76, […]

PMCID: 5915558
PMID: 29691416
DOI: 10.1038/s41598-018-23916-z

[…] species, mir-1-3p, mir-1-5p, and mir-t3-3p. as human mirna-mrna interactions are currently better annotated through experimental validation, we used the human target gene predictions as input into toppfun to explore possible effects on biological function through enrichment analyses. the top three viral mirnas appear to regulate divergent biological processes (table ). genes targeted […]

PMCID: 5858605
PMID: 29593587
DOI: 10.3389/fpsyt.2018.00081

[…] the experiments using the sva package in bioconductor (). mirnas with a p-value <0.05 were considered to be significantly different between two groups., for gene set enrichment analysis, we used toppfun in toppgene suite () to infer significantly enriched gene ontology (go) () terms, pathway, and disease terms. as the input for this approach, we used 1,230 predicted target genes […]

PMCID: 5818516
PMID: 29459674
DOI: 10.1038/s41598-018-21691-5

[…] atcl6a (7), bcl6 (6), senp5 (5) and kras (3). these 28 genes have been implicated in several biological and cellular processes including cell-cell junction and cell-cell junction assembly. using toppfun, the functional enrichment results show that these 20 genes are enriched with regulation of translation and cell aging. translational regulation has been shown to play an important role […]

PMCID: 5794889
PMID: 29391432
DOI: 10.1038/s41598-018-20266-8

[…] the assigned human orthologs, we performed enrichment analysis with the ‘transcriptome, ontology, phenotype, proteome, and pharmacome annotations’ based gene list functional enrichment analysis (toppfun) tool and observed that exposure to dehp and ee2 both had a significant impact on metabolism (table , supplementary tables –), including the organonitrogen compound biosynthetic process (dehp […]


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ToppFun institution(s)
Department of Environmental Health, University of Cincinnati, Cincinnati, OH, USA; Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
ToppFun funding source(s)
Supported by the State of Ohio Computational Medicine Center (ODD TECH 04-042); National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Diseases (NIH/NIDDK) 1U01 DK70219 (Murine Atlas of a Genitourinary Smooth Muscle Development); PHS Grant P30 DK078392 (Cincinnati Digestive Health Center).

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