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pathifier specifications


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
R.oo, princurve(>=2.0.4)
Maintained Yes




No version available



  • person_outline Assif Yitzhaky

pathifier citations


Pathway and clinical factor based risk model predicts the prognosis of patients with gastric cancer

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 […]


Perturbation response genes reveal signaling footprints in cancer gene expression

Nat Commun
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 […]


Network analysis of EMT and MET micro RNA regulation in breast cancer

Sci Rep
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 […]


Finding disagreement pathway signatures and constructing an ensemble model for cancer classification

Sci Rep
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 […]


A Novel Unsupervised Algorithm for Biological Process based Analysis on Cancer

Sci Rep
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 […]


Molecular Signature for Lymphatic Invasion Associated with Survival of Epithelial Ovarian Cancer

PMCID: 5912145
PMID: 28546526
DOI: 10.4143/crt.2017.104

[…] the clinical rsf model. we then combined the molecular-level signatures more appropriate for the existing model by processing a feature-selection step against the remainders., in addition, we used pathifier (, an algorithm that calculates pathway deregulation scores (pds) for each sample based on expression data []. in brief, hastie and stuetzle’s algorithm […]

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