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Protocols

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 citations

 (8)
library_books

MyGeneFriends: A Social Network Linking Genes, Genetic Diseases, and Researchers

2017
J Med Internet Res
PMCID: 5493784
PMID: 28623182
DOI: 10.2196/jmir.6676

[…] example, the ExAC browser [] provides clear visualization of variations in a gene, the Semantic Body Browser [] shows gene expression in a human and a mouse with a heat map on a schematized body, and NetGestalt [] introduces 1-dimensional visualization of network modules to facilitate network comparisons.Conversely, other tools aim to extract relationships between entities. For example, Chilibot [ […]

library_books

Network Based Protein Biomarker Discovery Platforms

2016
PMCID: 4838525
PMID: 27103885
DOI: 10.5808/GI.2016.14.1.2

[…] e 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 that can […]

library_books

The Nuclear Receptor, RORγ, Regulates Pathways Necessary for Breast Cancer Metastasis

2016
PMCID: 4856749
PMID: 27211549
DOI: 10.1016/j.ebiom.2016.02.028

[…] 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 tr […]

library_books

Reproducibility of Differential Proteomic Technologies in CPTAC Fractionated Xenografts

2015
J Proteome Res
PMCID: 4779376
PMID: 26653538
DOI: 10.1021/acs.jproteome.5b00859

[…] h significant hits occurring in an additional 10 pathways appearing in by SPC analysis. The permutation analysis also found 5 additional pathways to be significant in by XIC analysis. At this time, NetGestalt has not yet gained the ability to perform permutation-based FDR correction. […]

call_split

Exome sequencing reveals a high genetic heterogeneity on familial Hirschsprung disease

2015
Sci Rep
PMCID: 4642299
PMID: 26559152
DOI: 10.1038/srep16473
call_split See protocol

[…] tions) 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 the […]

library_books

Proteomic analysis of colon and rectal carcinoma using standard and customized databases

2015
Sci Data
PMCID: 4477697
PMID: 26110064
DOI: 10.1038/sdata.2015.22

[…] oteomic analysis tools such as the Trans Proteomic Pipeline (TPP), or commercial packages such as Scaffold.To facilitate access to the TCGA colorectal dataset we created a Colorectal Cancer Portal in NetGestalt that encompasses data from all analyses types performed on this set of clinical specimens (http://www.netgestalt.org), including genomic, epigenomic, transcriptomic, proteomic, and clinical […]

Citations

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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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