PathScore specifications

Information


Unique identifier OMICS_12538
Name PathScore
Interface Web user interface
Restrictions to use None
Programming languages Python
Database management system MySQL
License GNU General Public License version 3.0
Computer skills Basic
Stability Stable
Source code URL https://codeload.github.com/sggaffney/pathscore/zip/master
Maintained Yes

Maintainer


  • person_outline Stephen G. Gaffney <>

Publication for PathScore

PathScore in publications

 (4)
PMCID: 5549357
PMID: 28789679
DOI: 10.1186/s12920-017-0286-x

[…] \left\langle {consenscore}_i^m\right\rangle $$\end{document}consenscoreim is the average of the consenscore i of all genes presents in the pathway “m”.the final score associated with the pathway “m” (pathscore m)is calculated as the geometrical mean between pathgenescore m and the normalized pathrankscore m. , each community “k” was weighted as: \documentclass[12pt]{minimal} \usepackage{amsmat […]

PMCID: 5547992
PMID: 28713927
DOI: 10.3892/mmr.2017.7003

[…] each enriched pathway in each sample were determined by the expression value of degs involved in the enriched pathway. the score of indicated pathway was determined by the following formula:, where pathscore of indicated the score of pathway p; m indicated the number of upregulated degs in the enriched pathway of p; n indicated the number of downregulated degs in the enriched pathway of p; di […]

PMCID: 5562048
PMID: 28586067
DOI: 10.3892/mmr.2017.6699

[…] the fisher hypergeometric distribution test () was applied, p<0.05 was the threshold. the significant pathways were then performed hierarchical clustering analysis, the changes of pathways (the pathscore) in every sample was presented by gene expression in the pathways. the pathscore was computed using the following formula., m represents the upregulated genes and n represents […]

PMCID: 5360351
PMID: 28204826
DOI: 10.3892/ijmm.2017.2878

[…] the degs. subsequently, the important genes were uploaded to david for pathway enrichment analysis. pathway correlation analysis was carried out using spearman's rank correlation coefficient of the pathscore. in total, 1,333 degs, 391 upregulated and 942 downregulated, were obtained between the arlc-sccs and narlc-sccs. a total of 524 important genes for arlc-scc were significantly enriched […]


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PathScore institution(s)
Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT, USA; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
PathScore funding source(s)
This work was supported by Gilead Sciences, Inc.

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