sigPathway statistics

info info

Citations per year

Number of citations per year for the bioinformatics software tool sigPathway
info

Tool usage distribution map

This map represents all the scientific publications referring to sigPathway per scientific context
info info

Associated diseases

This word cloud represents sigPathway usage per disease context
info

Popular tool citations

chevron_left Gene set enrichment analysis chevron_right
Want to access the full stats & trends on this tool?

Protocols

sigPathway specifications

Information


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

Download


download.png

Versioning


No version available

Documentation


Maintainer


  • person_outline Peter J. Park

Publication for sigPathway

sigPathway citations

 (10)
call_split

Domain dependent effects of insulin and IGF 1 receptors on signalling and gene expression

2017
Nat Commun
PMCID: 5378997
PMID: 28345670
DOI: 10.1038/ncomms14892
call_split See protocol

[…] h 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. […]

library_books

A Comparison of Gene Set Analysis Methods in Terms of Sensitivity, Prioritization and Specificity

2013
PLoS One
PMCID: 3829842
PMID: 24260172
DOI: 10.1371/journal.pone.0079217

[…] s 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 Express […]

library_books

Rebuilding Pluripotency from Primordial Germ Cells

2013
Stem Cell Reports
PMCID: 3757743
PMID: 24052943
DOI: 10.1016/j.stemcr.2013.03.004

[…] kage 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, hgu133 […]

library_books

Statistical Test of Expression Pattern (STEPath): a new strategy to integrate gene expression data with genomic information in individual and meta analysis studies

2011
BMC Bioinformatics
PMCID: 3094239
PMID: 21481242
DOI: 10.1186/1471-2105-12-92

[…] see Additional file ).We compared STEPath meta-analysis results with a meta-analysis approach based on different GSA scores. Similarly for STEPath, we built a MGS matrix using scores derived by both sigPathway and GSEA (as implemented in limma). Clustering results of the MGS matrix from both sigPathway and GSEA failed to co-segregate the two LGMD2A datasets and the entire group of LGMDs (Figure […]

library_books

Distinct Early Molecular Responses to Mutations Causing vLINCL and JNCL Presage ATP Synthase Subunit C Accumulation in Cerebellar Cells

2011
PLoS One
PMCID: 3040763
PMID: 21359198
DOI: 10.1371/journal.pone.0017118

[…] onds, and 72°C for 10 seconds.The DAVID Bioinformatics Resource 6.7 , was used for further gene ontology analysis of significant probes.For identification of significantly enriched pathways, we used sigPathway (1.6.0) (http://bioconductor.org/packages/release/bioc/html/sigPathway.html) . Following analysis using sigPathway software, ‘NEk statistics’ and ‘NTk statistics’ were output as measures of […]

library_books

Meta analysis of glioblastoma multiforme versus anaplastic astrocytoma identifies robust gene markers

2009
Mol Cancer
PMCID: 2743637
PMID: 19732454
DOI: 10.1186/1476-4598-8-71

[…] 0 and 500 genes. This gave 178 Biocarta pathways. Gene set elements were converted from gene symbols to U133A probe sets using GSEA's chip2chip tool [,]. Analysis of gene sets was performed using our SigPathway Bioconductor package [], which compares each gene set to a column and row permutation null distribution separately, giving two normalized enrichment scores per gene set. These enrichment sc […]


Want to access the full list of citations?
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.

sigPathway reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review sigPathway