ToppGene Suite statistics

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Citations per year

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Popular tool citations

chevron_left Functional annotation Gene prioritization Gene set enrichment analysis Phenotype enrichment analysis chevron_right
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Associated diseases

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ToppGene Suite specifications

Information


Unique identifier OMICS_06533
Name ToppGene Suite
Alternative name ToppGene
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input data Two gene lists (training and test).
Output data HTML
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Documentation


Maintainers


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

Publications for ToppGene Suite

ToppGene Suite in pipelines

 (11)
2018
PMCID: 5775307
PMID: 29352121
DOI: 10.1038/s41598-017-19114-y

[…] escs) were derived from previous data. fpkm value 0 was set to 0.1, to be able to avoid erratic deviations in fold-change values. the functional annotation of the genes was performed using toppgene suite., c2c12 myoblast cells expressing h2b-mcherry were differentiated in a differentiation medium consisting dmem-f12 (gibco) supplemented with 2% horse serum with igf for 5 days […]

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

[…] 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 of the candidate […]

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

[…] and p < 0.05 were 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 […]

2017
PMCID: 5498581
PMID: 28680106
DOI: 10.1038/s41467-017-00050-4

[…] relative to the normal na12878 samples were identified using both our pipeline and the tuxedo approach. for the top 10 overexpressed genes, functional enrichment analysis was conducted using the toppgene suite (supplementary table  and supplementary data –). on mcf7-100 and mcf7-300 samples, cufflinks-tophat prediction sets were not enriched in any mcf7 or breast cancer-related gene […]

2017
PMCID: 5596511
PMID: 28604704
DOI: 10.1038/nm.4346

[…] employed, which amasses ontological data from over 30 individual repositories., we performed candidate gene prioritization on differentially regaled genes between tn and ts animals on hfd. using the toppgene suite candidate prioritization tool, we ranked genes based on their functional similarity to nash-related genes (extracted from the nash-profiler; healthy obese v nash at fdr-p-value<0.05 […]


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ToppGene Suite in publications

 (108)
PMCID: 5958137
PMID: 29773794
DOI: 10.1038/s41467-018-04420-4

[…] by er-464195-01 (fig.  and supplementary data )., to explore whether 894 genes were involved in the inflammatory response of ibd, we then conducted gene ontology (go) enrichment analysis using the toppgene suite. as shown in fig. , for these genes the molecular function terms revealed the activity of cytokines and chemokines, their receptor binding, the structural constituent of muscle […]

PMCID: 5923024
PMID: 29703138
DOI: 10.1186/s12864-018-4679-9

[…] with the likelihood ratio tests of the glmlrt function in edger package and considered significant if the p-value was ≤0.05 and the absolute fold change (fc) ≥1.2. degs were annotated with the toppgene suite (https://toppgene.cchmc.org/) [] and prioritized by literature mining using pubmatrix []., enrichment analysis was performed using the pre-ranked tool of gene set enrichment analysis […]

PMCID: 5928158
PMID: 29740474
DOI: 10.3389/fgene.2018.00125

[…] (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, excluding est clusters. […]

PMCID: 5929452
PMID: 29732009
DOI: 10.18632/oncotarget.24893

[…] genes within a particular imaging group with already existing functional gene pathway annotations; the cancer gene pathways in the kyoto encyclopaedia of genes and genomes (kegg) database [, ]. the toppgene suite software (division of biomedical informatics, cincinnati children's hospital medical center, cincinatti, oh; https://toppgene.cchmc.org/)) was used for gene pathway analysis based […]

PMCID: 5897339
PMID: 29651138
DOI: 10.1038/s41467-018-03811-x

[…] gene coexpression network analysis to cluster genes with similar profiles of expression across all of the cell types (supplementary fig. ). all enrichment analyses were conducted using the online toppgene suite., as gene co-expression is associated with structural connectivity,, we examine whether the 505 limbic network-associated genes were particularly expressed in deeper cortical layers […]


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ToppGene Suite 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
ToppGene Suite 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).

ToppGene Suite review

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Anonymous user #1216

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Web
Best part is the ease of use. Powerful and quite up-to-date annotations in the back end database.