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Popular tool citations

chevron_left Gene prioritization Gene set enrichment analysis chevron_right
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Associated diseases

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Lynx specifications

Information


Unique identifier OMICS_04645
Name Lynx
Interface Web user interface, Application programming interface
Restrictions to use None
Computer skills Basic
Version 2.5
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Maintainer


  • person_outline Lynx <>

Publications for Lynx

Lynx in pipeline

2014
PMCID: 4266634
PMID: 25506935
DOI: 10.1371/journal.pone.0114903

[…] here however is different from these resources. it is based on seamless integration of data and services across multiple independently developed analytical systems and databases, namely the lynx and the vista systems, the developmental brain disorders database (dbdb) , and the raptorx server , . this environment, depicted in , allows end users to easily direct and analyze their data […]


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Lynx in publications

 (5)
PMCID: 5849294
PMID: 29534074
DOI: 10.1371/journal.pone.0193334

[…] of go categories, diseases, phenotypes, pathways, and other features over-represented in the sets of differentially expressed genes, was performed using online analytical tools available in the lynx integrated system []. statistical significance was estimated using bayes factor and p-value calculated for each category under consideration. bonferroni correction was applied to the results […]

PMCID: 5717815
PMID: 29208006
DOI: 10.1186/s13046-017-0651-9

[…] analysed, while specificity was defined as the ratio (1 - false positive)/(total tested - total positive)., enrichment analysis of gene ontology and molecular pathways was performed using the lynx systems biology tool []. all significance tests were two-sided, and a false discovery rate less than 0.05 was considered significant. biological network analysis was performed […]

PMCID: 5516010
PMID: 28720766
DOI: 10.1038/s41598-017-05878-w

[…] multiqc, samtools, and bioawk (https://github.com/lh3/bioawk). we used r for all statistics and data visualization. we obtained gene annotation information from the ensembl and lynx databases. the computational resources were provided by the university of chicago research computing center. all code is available for viewing and reuse […]

PMCID: 4423863
PMID: 25950834
DOI: 10.1371/journal.pgen.1005216

[…] with donor. eqtl data were downloaded from the pritchard group eqtl browser: http://eqtl.uchicago.edu. functional group enrichment was assessed using the web-based gene annotation database lynx: http://lynx.ci.uchicago.edu using all expressed genes subjected to our filtering criteria as background., gene expression data are available at the geo database, accession #gse64263., we thank […]

PMCID: 4266634
PMID: 25506935
DOI: 10.1371/journal.pone.0114903

[…] developed by multiple groups becomes inevitable. here we present a case study of a use of the distributed analytical environment integrating four complementary specialized resources, namely the lynx platform, vista rviewer, the developmental brain disorders database (dbdb), and the raptorx server, for the identification of high-confidence candidate genes contributing to pathogenesis […]


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Lynx institution(s)
Department of Human Genetics, University of Chicago, Chicago, IL, USA; Computation Institute, University of Chicago, Chicago, IL, USA; Department of Computer Science, Illinois Institute of Technology, Chicago, IL, USA; Toyota Technological Institute at Chicago, Chicago, IL, USA; Department of Medicine, University of Chicago, Chicago, IL, USA
Lynx funding source(s)
Mr and Mrs Lawrence Hilibrand, the Boler Family Foundation and National Institutes of Health/National Institute of Neurological Disorders and Stroke grant [NS050375, in part]; The Genetic Basis of Mid-Hindbrain Malformations; National Institute of Mental Health [1U24MH081810, in part]

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