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sigPathway specifications

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Unique identifier OMICS_19177
Name sigPathway
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.48.0
Stability Stable
Requirements
R(>=2.10), hgu133a.db(>=1.10.0), XML(>=1.6-3), AnnotationDbi(>=1.3.12)
Maintained Yes

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  • person_outline Peter J. Park <>

Publication for sigPathway

sigPathway in publications

 (17)
PMCID: 5378997
PMID: 28345670
DOI: 10.1038/ncomms14892

[…] the 6 h mock treated cells. statistical significance of probe sets was assessed with empirical bayesian linear modelling using the limma package, and significance of gene sets was assessed with the sigpathway package. heatmaps were created with the gplots package, and volcano plots and scatterplots were created with the ggplot2 package., overall, 1 μg of rna was reverse transcribed using a high […]

PMCID: 4744442
PMID: 26852017
DOI: 10.1186/s12859-016-0928-6

[…] proposed methods are denoted by sdr t and sdr v, corresponding to t in () and v in (), respectively. the competing methods in the assessment include: (1) gsea by subramanian et al. [] with r package sigpathway; (2) global test (gt) by goeman et al. with r package globaltest; (3) mvat by tsai and chen []; (4) pca-based test (pcot) by kong et al. [] with r package pcot2; (5) gsnca by rahmatallah […]

PMCID: 3829842
PMID: 24260172
DOI: 10.1371/journal.pone.0079217

[…] derive a score from all genes that belong to a given gene set regardless of whether or not they are differentially expressed. such methods include gene set enrichment analysis (gsea) , globaltest , sigpathway with two alternative null hypotheses (q1 and q2), gene set analysis (gsa) , generally applicable gene set enrichment (gage) , significance analysis of functional categories in gene […]

PMCID: 3757743
PMID: 24052943
DOI: 10.1016/j.stemcr.2013.03.004

[…] and rma normalized. to construct the heatmap, the normalized values of stat3 target gene expression were log2 transformed and centered around the median. pathway analysis was performed using the sigpathway package (http://bioconductor.org/packages/release/bioc/html/sigpathway.html). to create a customized gene set object, the g file specific for the human microarray used in this study, […]

PMCID: 3359832
PMID: 22666299
DOI: 10.1155/2012/986427

[…] 564 gene expression profiles, representing 453 individual instances at http://www.broad.mit.edu/cmap/., gene sets were needed to sort out genes according to meaningful signal pathways. a set called sigpathway [] was used in our method. these gene sets are an integration of different pathway databases, including biocarta, kegg, biocyc, pathway-specific microarray annotations, and >5,000 gene […]

sigPathway institution(s)
Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Department of Neurology, Brigham and Women’s Hospital, Boston, MA, USA; Children’s Hospital Informatics Program, Boston, MA, USA; Bauer Center for Genomics Research, Harvard University, Cambridge, MA, USA; Molecular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA; Harvard-Partners Center for Genetics and Genomics, Boston, MA, USA
sigPathway funding source(s)
Supported by grants from the National Institute of General Medical Sciences; the Muscular Dystrophy Association and the National Institute of Neurological Disorders and Stroke; and Specialized Centers of Clinically Oriented Research in Pediatric Heart Development and Disease.

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