ToppNet statistics

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Citations per year

Number of citations per year for the bioinformatics software tool ToppNet

Tool usage distribution map

This map represents all the scientific publications referring to ToppNet per scientific context
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Associated diseases

This word cloud represents ToppNet usage per disease context

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ToppNet specifications


Unique identifier OMICS_27569
Name ToppNet
Interface Web user interface
Restrictions to use None
Input data Two gene lists (training and test).
Output format HTML
Computer skills Basic
Stability Stable
Maintained Yes


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

Publication for ToppNet

ToppNet citations


Drug Repositioning for Alzheimer’s Disease Based on Systematic ‘omics’ Data Mining

PLoS One
PMCID: 5179106
PMID: 28005991
DOI: 10.1371/journal.pone.0168812
call_split See protocol

[…] drug targets derived from our ‘omics’ mining method, we used the Toppgene tool (, which ranks candidate genes based on functional similarity to the training genes, and the Toppnet tool (, which ranks candidate genes based on topological features in protein-protein interaction networks and their similarity to the training genes []. In the curre […]


Identification of novel therapeutics for complex diseases from genome wide association data

BMC Med Genomics
PMCID: 4101352
PMID: 25077696
DOI: 10.1186/1755-8794-7-S1-S8

[…] fied potential drug targets for three neurological disorders - Alzheimer's disease, Parkinson's disease and Schizophrenia. This study involved the prediction of candidate genes using the ToppGene and ToppNet prediction systems [,]. The repositioning tools could be used as an initial screening tool for potential drugs which can be used for further evaluation []. It is important to note that not all […]


Prioritizing Disease Candidate Proteins in Cardiomyopathy Specific Protein Protein Interaction Networks Based on “Guilt by Association” Analysis

PLoS One
PMCID: 3733802
PMID: 23940716
DOI: 10.1371/journal.pone.0071191

[…] lic human PPI data . DADA was built up as a suite to prioritize disease candidate genes accounting for the degree distribution of known disease and candidate genes, using a PPI network . ToppGene and ToppNet were online candidate gene prioritization tools with high reliability based on functional similarity or network analysis in PPIN . These algorithms take a set of seed proteins (genes known to […]


Biomarker Identification for Prostate Cancer and Lymph Node Metastasis from Microarray Data and Protein Interaction Network Using Gene Prioritization Method

Sci World J
PMCID: 3354662
PMID: 22654636
DOI: 10.1100/2012/842727

[…] state Cancer as the domain for the experiments, as it is explained in the Materials section previously. The method is compared to HITS with Priors, K-step Markov and PageRank with Priors all from the ToppNet suite []; other methods in the benchmark are ENDEAVOR [], CIPHER [] and plain Random Walk with Restarts [] using Pearson Correlation Coefficient for weights of the network. These methods were […]

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ToppNet 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
ToppNet 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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