NetGestalt protocols

View NetGestalt computational protocol

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NetGestalt specifications

Information


Unique identifier OMICS_08041
Name NetGestalt
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Bing Zhang <>

Publications for NetGestalt

NetGestalt in pipeline

2014
PMCID: 3945913
PMID: 24429493
DOI: 10.1074/mcp.M113.032953

[…] sensitivity to electrophile exposure, we used the kruskal-wallis test implemented in r (). to visualize the network impact of protein alkylation by ahne and aone in both cell types, we used the netgestalt tool ()., cell pellets were resuspended in m-per® mammalian protein extraction reagent (thermo scientific, rockford, il) and sonicated (10 pulses at 20% duty cycle). lysates were cleared […]


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NetGestalt in publications

 (9)
PMCID: 4838525
PMID: 27103885
DOI: 10.5808/GI.2016.14.1.2

[…] applied for integration of proteomic data with other types of global data, they have been used mainly for integration of disparate genomic and transcriptomic data. recently, shi et al. [] developed netgestalt that can be used for integration of multi-dimensional global datasets including proteomic data. for example, using neggestalt, zhu et al. [] identified kras and akap12 subnetworks […]

PMCID: 4856749
PMID: 27211549
DOI: 10.1016/j.ebiom.2016.02.028

[…] from t-47d, we identified the target coding genes and generated the correlation plot showing both fold changes of lncrnas and target coding genes., for protein–protein interaction, we utilized the netgestalt previously described (). we selected the iref database as a network view and uploaded differentially expressed genes of rna-seq outcomes with fold changes (log2 scale) in a single binary […]

PMCID: 4705461
PMID: 26742467
DOI: 10.1038/srep18764

[…] knowledge from databases and literature. the integrated methods have an advantage over traditional, single-analysis microarray approaches and other enrichment-analysis methods, such as david and netgestalt and ensure the reliability and accuracy of the results. key candidates were also validated in chinese patients, indicating the generalization of molecular mechanisms among different ethnic […]

PMCID: 4779376
PMID: 26653538
DOI: 10.1021/acs.jproteome.5b00859

[…] p values below 0.05 to be significant., we also interpreted the genes expressed significantly highly in whim2 or in whim16 against the context of a global protein–protein interaction network using netgestalt. the network used in this article was downloaded from iref. we first identified the hierarchical modules from the iref network based on the netsam algorithm. then, based on fisher’s exact […]

PMCID: 4642299
PMID: 26559152
DOI: 10.1038/srep16473

[…] were used to fish out remaining variants located in genes linking up with recurrent genes and genes previously implicated hscr candidate genes; these were done by kggseq, dapple, genemania and netgestalt. joint effects for the genes from the same pathway/network were examined by tracing their combined cosegregation in those families not explainable by recurrent genes., finally, we checked […]


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NetGestalt institution(s)
Department of Biomedical Informatics, Advanced Computing Center for Research and Education, Department of Electrical Engineering and Computer Science and Department of Cancer Biology, Vanderbilt University, Nashville, TN, USA

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