SAFE statistics

info info

Citations per year

Number of citations per year for the bioinformatics software tool SAFE

Tool usage distribution map

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

Associated diseases


Popular tool citations

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

SAFE specifications


Unique identifier OMICS_19179
Alternative name Significance Analysis of Function and Expression
Software type Framework/Library, Package/Module
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 3.20.0
Stability Stable
AnnotationDbi, methods, Biobase, survival, foreach, GO.db, SparseM, GOstats, reactome.db, Rgraphviz, hgu133a.db, R(>=2.4.0), breastCancerUPP, PFAM.db, doRNG
Maintained Yes




No version available



  • person_outline Andrew Nobel
  • person_outline Fred Wright
  • person_outline William Barry

Publication for Significance Analysis of Function and Expression

SAFE citations


Pathway Based Genomics Prediction using Generalized Elastic Net

PLoS Comput Biol
PMCID: 4784899
PMID: 26960204
DOI: 10.1371/journal.pcbi.1004790

[…] ctors to obtain a set of discriminative scores—one for each feature / gene—and then using gene sets to elucidate pathways saturated with highly discriminative scores. Gene Set Enrichment Analysis [], Significance Analysis of Function and Expression [], and a method by Lee, et al. [] do exactly this to arrive at a single differential score for each gene set of interest. Rather than using curated se […]


Investigating the concordance of Gene Ontology terms reveals the intra and inter platform reproducibility of enrichment analysis

BMC Bioinformatics
PMCID: 3644270
PMID: 23627640
DOI: 10.1186/1471-2105-14-143

[…] improve the sensitivity and selectivity of GSEA []. Kim et al. used z-statistics and permutation test to identify significantly enriched gene sets []. In addition, other statistical methods including significance analysis of function and expression (SAFE) [], BayGO [], ProbCD [], EasyGO [], ProfCom [], GlobalANCOVA [], GOEAST [] and LRpath [] were also developed for enrichment analysis.Based on th […]


Chapter 8: Biological Knowledge Assembly and Interpretation

PLoS Comput Biol
PMCID: 3531281
PMID: 23300429
DOI: 10.1371/journal.pcbi.1002858

[…] level applications. For example, researchers developed genomic signatures to identify the activation status of oncogenic pathways and predict the sensitivity to individual chemotherapeutic drugs , . Significance Analysis of Function and Expression (SAFE) extends GSEA to cover multiclass, continuous and survival phenotypes. It also provides more options for the test statistic, including Wilcoxon […]


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

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

[…] Kyoto Encyclopedia of Genes and Genomes; GEO: Gene Expression Omnibus; RMA: Robust Multiarray Averaging; PAM: Predicted Analysis of Microarray; PCOT2: Principal Coordinates and Hotelling's T2; SAFE: Significance Analysis of Function and Expression, LGMDs: Limb Girdle Muscular Dystrophies; CTRL: Control; MAPE, Meta-Analysis of Pathway Enrichment; MGS: Main Gene set Signature; ATP: Adenosine tripho […]


Pathway analysis reveals functional convergence of gene expression profiles in breast cancer

BMC Med Genomics
PMCID: 2447843
PMID: 18588682
DOI: 10.1186/1755-8794-1-28

[…] proaches have emerged in recent years to identify sets of biologically related genes that are deregulated as a group. Examples of gene-set analysis include the Gene Set Enrichment Analysis (GSEA) [], Significance Analysis of Function and Expression (SAFE) [], and the globaltest package [] These methods focus on groups of genes that share common biological functions such as cell cycle regulation; m […]


A Low Dose of Dietary Resveratrol Partially Mimics Caloric Restriction and Retards Aging Parameters in Mice

PLoS One
PMCID: 2386967
PMID: 18523577
DOI: 10.1371/journal.pone.0002264

[…] are postulated to impact aging (IGF-1, insulin, Sirt1, oxidative stress), we analyzed the gene expression data for functional categories that may be affected with age, CR or resveratrol. We used the significance analysis of function and expression (SAFE), a two-stage, permutation-based method that can be applied to various experimental designs, accounts for the unknown correlation among genes and […]

Want to access the full list of citations?
SAFE institution(s)
Department of Cardiology, Children’s Hospital Boston, Boston, MA, USA; Informatics Program, Children’s Hospital Boston, Boston, MA, USA; Harvard-Partners Center for Genetics and Genomics, Boston, MA, USA
SAFE funding source(s)
Supported in part by NIH grants P30 HD003110, T32 ES07018 and P30 ES10126.

SAFE reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review SAFE