ToppNet statistics

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Citations per year

Number of citations per year for the bioinformatics software tool ToppNet
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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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Popular tool citations

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Protocols

ToppNet specifications

Information


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

Maintainers


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

Publication for ToppNet

ToppNet citations

 (4)
call_split

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

2016
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 (https://toppgene.cchmc.org), which ranks candidate genes based on functional similarity to the training genes, and the Toppnet tool (https://toppgene.cchmc.org), which ranks candidate genes based on topological features in protein-protein interaction networks and their similarity to the training genes []. In the curre […]

library_books

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

2014
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 […]

library_books

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

2013
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 […]

library_books

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

2012
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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