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GLay specifications


Unique identifier OMICS_18236
Name GLay
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C++, Java
Computer skills Medium
Stability Stable
Maintained No


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Publication for GLay

GLay citations


Co expression network analysis and cis regulatory element enrichment determine putative functions and regulatory mechanisms of grapevine ATL E3 ubiquitin ligases

Sci Rep
PMCID: 5816651
PMID: 29453355
DOI: 10.1038/s41598-018-21377-y

[…] individual atl-centered co-expression clusters were also merged, and nodes with < 2 connecting edges were discarded, before partitioning into communities of densely connected nodes using glay, prior to visualization in cytoscape v3.0., enrichment p-values, based on a fdr-adjusted hypergeometric distribution of mapman bin categories was determined using 29,424 genes with annotated bin […]


Gastric cancer biomarkers; A systems biology approach

PMCID: 5857180
PMID: 29556568
DOI: 10.1016/j.bbrep.2018.01.001

[…] in order to identify topologically highly dense areas in the network, clusters were determined using cytoscape plugins including allegromcode and clustermaker which is based on community clustering (glay) and markov clustering (mcl) algorithms. the clustering algorithm of allegromcode plugin is molecular complex detection (mcode), based on node weighting according to the local neighborhood […]


A gene network regulated by FGF signalling during ear development

Sci Rep
PMCID: 5522468
PMID: 28733657
DOI: 10.1038/s41598-017-05472-0

[…] to perform hierarchical clustering (using euclidean distance) and to generate heatmaps using the r package gplots. to identify modules in the network, community clustering was performed using the glay plugin in cytoscape. the advantage of girvan and newman’s clustering algorithm is that it does not require the number of clusters to be fixed as in other clustering techniques such as k-means. […]


Gene network analysis identifies rumen epithelial cell proliferation, differentiation and metabolic pathways perturbed by diet and correlated with methane production

Sci Rep
PMCID: 5155297
PMID: 27966600
DOI: 10.1038/srep39022

[…] including the genes clustered in the ‘muscle’ and ‘type i interferon’ related sub-networks. a lower correlation coefficient threshold (>+0.75) was used to build the epithelium network and the glay community clustering plugin in cytoscape was used to subdivide the network into clusters (). sets of genes were mapped to the networks using standard procedures in cytoscape., we performed […]


An Integrative Analysis of Preeclampsia Based on the Construction of an Extended Composite Network Featuring Protein Protein Physical Interactions and Transcriptional Relationships

PLoS One
PMCID: 5089765
PMID: 27802351
DOI: 10.1371/journal.pone.0165849

[…] 50 hub genes including zbtb16, cask, fos, bhlhe40, tgfb1 and nos3., the ppi network was further subdivided into connectivity modules using the fast-greedy he (g) algorithm of the community clusters glay []. this resulted in the identification of nine connectivity modules closely connected. the modules were analyzed for functionality enrichment using the gene ontology (go) database ()., thus, […]


A Network Biology Approach Identifies Molecular Cross Talk between Normal Prostate Epithelial and Prostate Carcinoma Cells

PLoS Comput Biol
PMCID: 4849722
PMID: 27124473
DOI: 10.1371/journal.pcbi.1004884

[…] (nt network)., the nt network, representing statistically significant correlations between genes expressed in normal and tumour tissues, was modularized using the community finding algorithm glay [], as implemented in the network analysis tool cytoscape []., the algorithm begins by setting each node into a separate community and progressively merges those with the maximum increase […]

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GLay institution(s)
Bioinformatics Program, University of Michigan, Ann Arbor, MI, USA; Agilent Technologies, Santa Clara, CA, USA; Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA; School of Health Information Sciences, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, TX, USA; Psychiatry Department and Molecular Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA; National Center for Integrative Biomedical Informatics, University of Michigan, Ann Arbor, MI, USA
GLay funding source(s)
Supported by National Center for Integrated Biomedical Informatics through National Institutes of Health (grant 1U54DA021519-01A1 to the University of Michigan), also partly supported by a NIH NCRR grant P41-RR01081 to the University of California, San Francisco.

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