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Protocols

GXNA specifications

Information


Unique identifier OMICS_06987
Name GXNA
Alternative name Gene eXpression Network Analysis
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data An expression and a phenotype file, an interaction graph, and an annotation file.
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
Computer skills Advanced
Stability Stable
Source code URL http://statweb.stanford.edu/~serban/gxna/src/
Maintained Yes

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Versioning


No version available

Maintainer


  • person_outline Serban Nacu

Additional information


http://statweb.stanford.edu/~serban/gxna/quickstart.html

Publication for Gene eXpression Network Analysis

GXNA citations

 (5)
call_split

On the performance of de novo pathway enrichment

2017
NPJ Syst Biol Appl
PMCID: 5445589
PMID: 28649433
DOI: 10.1038/s41540-017-0007-2
call_split See protocol

[…] ental data. (d) GiGA is another score propagation method that first computes local minima to serve as starting points for iteratively building sub-networks with n members and a maximal rank of m. (e) GXNA is a score propagation method that selects random nodes as seeds of candidate sub-networks. These are iteratively extended by adding the neighboring node with the highest score. (f) KPM is anothe […]

library_books

Differentially Expressed Transcripts and Dysregulated Signaling Pathways and Networks in African American Breast Cancer

2013
PLoS One
PMCID: 3853650
PMID: 24324792
DOI: 10.1371/journal.pone.0082460

[…] d CA BRCa patients using DESeq; secondly, pathway analysis and gene set enrichment analysis with the Pathway Interaction Database (PID) and Gene Set Enrichment Analysis (GSEA) was performed; thirdly, Gene Expression Network Analysis (GXNA) was used to identify differentially expressed subnetworks; finally, patients were stratified to study differences in stage- or subtype-specific gene expression […]

call_split

Predicting In Silico Which Mixtures of the Natural Products of Plants Might Most Effectively Kill Human Leukemia Cells?

2013
PMCID: 3569894
PMID: 23431350
DOI: 10.1155/2013/801501
call_split See protocol

[…] icted binding proteins related to cancer; Am was the number of predicted binding proteins related to AML; Ah was the number of predicted binding proteins detected as hubs in interaction networks from gene-expression network analysis; comm was the number of common target protein(s) shared by constituent drugs in combination; sp was the specificity score defined as (the number of cancer-related pred […]

library_books

PRC2/EED EZH2 Complex Is Up Regulated in Breast Cancer Lymph Node Metastasis Compared to Primary Tumor and Correlates with Tumor Proliferation In Situ

2012
PLoS One
PMCID: 3519681
PMID: 23251464
DOI: 10.1371/journal.pone.0051239

[…] To capture subtle yet biologically important changes, the Gene eXpression Network Analysis (GXNA) program was used to determine significantly changed networks/subnetworks between lymph node metastasis and primary tumor. This produced a network of thirty-one genes with a significant score of […]

library_books

Classification and biomarker identification using gene network modules and support vector machines

2009
BMC Bioinformatics
PMCID: 2774324
PMID: 19832995
DOI: 10.1186/1471-2105-10-337

[…] termined to be linked. In applying this approach one thousand genes selected by t-test from a training set are first filtered so that the only genes that map to the gene networks database remain. The Gene Expression Network Analysis Tool (GXNA, []) is applied to these genes to form n clusters of genes that are highly connected in the network. Linear SVM is used to classify the samples using these […]

Citations

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GXNA institution(s)
Department of Statistics, Stanford University, Stanford CA, USA; Stanford School of Medicine, Stanford CA, USA; Ecole Normale Superieure, Paris, France
GXNA funding source(s)
Supported in part by NSF grant DMS-0241246.

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