pathifier protocols

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pathifier specifications

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Unique identifier OMICS_16077
Name pathifier
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 1.20.0
Stability Stable
Requirements
R.oo, princurve(>=2.0.4)
Maintained Yes

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  • person_outline Assif Yitzhaky <>

pathifier in pipelines

 (4)
2018
PMCID: 5750219
PMID: 29295995
DOI: 10.1038/s41467-017-02391-6

[…] for a braf inhibitor, we show additional stratification on top of braf mutations, and for nutlin-3a on top of tp53 mutations., starting from the pathway scores derived with go/reactome gsea, spia, pathifier, paradigm, and our method on the tcga data as described above, we used cox proportional hazard model (r package survival) to calculate survival associations for pan-cancer […]

2018
PMCID: 5928624
PMID: 29532879
DOI: 10.3892/mmr.2018.8722

[…] expression matrix of the prognosis-associated genes was converted into a pathway deregulation score (pds) matrix of the relevant pathways using the principal components analysis algorithm in the r pathifier package (bioconductor.org/packages/pathifier) (). the optimal prognosis-associated pathways were screened subsequent to importing the pds matrix using the cox proportional hazards (cox-ph) […]

2017
PMCID: 5374559
PMID: 28361683
DOI: 10.1186/s12859-017-1462-x

[…] t-test and genes associated with the studied disease taken from genecard []. meanwhile, the biomarkers identified by frsvm and stsvm are general gene sets rather than functional gene groups by gsva, pathifier and aep; that’s why we first functionally label them with the top enriched terms by g:profiler []., the enrichment ratio boxplots are shown in fig. . it seems cns has the best performance […]

2016
PMCID: 5342415
PMID: 27409342
DOI: 10.18632/oncotarget.10509

[…] for gsea pre-ranked test at the pathway level result., for pathway-level analysis on the paired tcga rna-seq data, we first applied deseq2 [] to normalize the expression among samples. we then used pathifier [] algorithm to transform gene-level expression information into pathway-level information, represented by pathway deregulation score (pds) per patient. personalized pds is derived […]


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pathifier in publications

 (18)
PMCID: 5928624
PMID: 29532879
DOI: 10.3892/mmr.2018.8722

[…] and clinical factors may improve prognostic accuracy in gc., huang et al () developed a novel computational model for breast cancer prognosis by combining the pathway deregulation score (pds)-based pathifier algorithm, cox proportional hazards regression and the l1-lasso penalization method to select promising targets for therapeutic intervention. huang et al () developed a novel computational […]

PMCID: 5750219
PMID: 29295995
DOI: 10.1038/s41467-017-02391-6

[…] normals available, in order to make full use of the pathway methods that require them. we calculated pathway scores for those using progeny, reactome and gene ontology enrichment, spia, pathifier, paradigm, a modified version of speed, and the gatza et al. signatures (supplementary table ). we used an anova to calculate significant associations between the presence and absence […]

PMCID: 5648819
PMID: 29051564
DOI: 10.1038/s41598-017-13903-1

[…] wikipathways, and kegg pathways which contained at least one gene that corresponds to mrna nodes in the mir-200 and dlk1-dio3 first neighbour networks inferred from tumour data (see methods). using pathifier, we estimated the pathway deregulation score (pds) of each sample and for the selected pathways. we used pathifier as it allows to integrate the mrna expression and pathway information […]

PMCID: 5577098
PMID: 28855608
DOI: 10.1038/s41598-017-10258-5

[…] on biological functions for disease diagnosis. this method is a typical representative of pathway-based method for disease diagnosis. it converts omics-level data to pathway-level data by the pathifier algorithm, . a pathway dysregulation score matrix in which each score measures the deregulation of a specific pathway for a specific sample is obtained. then, correlation feature selection […]

PMCID: 5498659
PMID: 28680165
DOI: 10.1038/s41598-017-04961-6

[…] method). to validate the effectiveness and robustness of our bps matrix, we compared our bps matrix with pam50 gene expression matrix and pathway-based deregulation score (pds) matrix yielded by pathifier respectively. here, pam50 is a gene set designed for subtyping breast cancer, and also has satisfactory performance in breast cancer prognosis, and pathifier is derived […]


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