ToppGene Suite statistics

Tool stats & trends

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Protocols

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 citations

 (143)
library_books

Calreticulin and integrin alpha dissociation induces anti inflammatory programming in animal models of inflammatory bowel disease

2018
Nat Commun
PMCID: 5958137
PMID: 29773794
DOI: 10.1038/s41467-018-04420-4

[…] 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 and grow […]

library_books

Transcriptional profiling of human bronchial epithelial cell BEAS 2B exposed to diesel and biomass ultrafine particles

2018
BMC Genomics
PMCID: 5923024
PMID: 29703138
DOI: 10.1186/s12864-018-4679-9

[…] design 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 [] ( […]

library_books

Integrated Quantitative Transcriptome Maps of Human Trisomy 21 Tissues and Cells

2018
Front Genet
PMCID: 5928158
PMID: 29740474
DOI: 10.3389/fgene.2018.00125

[…] The results of functional enrichment analysis, performed by ‘ToppFun’ from the ‘ToppGene Suite’ Gene Ontology tool, of over- and under-expressed genes (with expression ratios ≥1.30 and ≤0.76, respectively) in the “Total transcriptome map” (comparing all DS samples for any tissue […]

library_books

Altered function and maturation of primary cortical neurons from a 22q11.2 deletion mouse model of schizophrenia

2018
PMCID: 5904157
PMID: 29666363
DOI: 10.1038/s41398-018-0132-8

[…] ribed previously in vivo, suggesting that cultured neurons recapitulate key transcriptional changes occurring in vivo (Fig. ).Fig. 5To determine key functional effects, we conducted GO analysis using Toppgene. This analysis revealed that upregulated genes in mutant neurons were enriched in GO terms related to “transmembrane transporter activity (GO:0022857)”, “trans-synaptic signaling (GO:0099537) […]

call_split

Transcriptome Analysis of Orbital Adipose Tissue in Active Thyroid Eye Disease Using Next Generation RNA Sequencing Technology

2018
PMCID: 5906971
PMID: 29760827
DOI: 10.2174/1874364101812010041
call_split See protocol

[…] To detect molecular functions, biological processes, and pathways associated with the differential expression signature, Gene Ontology (GO, http://www.geneontology.org) analysis was performed using ToppGene (https://toppgene.cchmc.org/enrichment.jsp). Additional databases utilized included: Kyoto Encyclopedia of Genes and Genomes (http://www.genome.jp/kegg/pathway.html), WikiPathways (www.wikipa […]

library_books

Gene expression links functional networks across cortex and striatum

2018
Nat Commun
PMCID: 5897339
PMID: 29651138
DOI: 10.1038/s41467-018-03811-x

[…] ted 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. […]

Citations

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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.