title: GiANT: gene set uncertainty in enrichment analysis.
abstract: Over the past years growing knowledge about biological processes and pathways revealed complex interaction networks involving many genes. In order to understand these networks, analysis of differential expression has continuously moved from single genes towards the study of gene sets. Various approaches for the assessment of gene sets have been developed in the context of gene set analysis (GSA). These approaches are bridging the gap between raw measurements and semantically meaningful terms.We present a novel approach for assessing uncertainty in the definition of gene sets. This is an essential step when new gene sets are constructed from domain knowledge or given gene sets are suspected to be affected by uncertainty. Quantification of uncertainty is implemented in the R-package GiANT. We also included widely used GSA methods, embedded in a generic framework that can readily be extended by custom methods. The package provides an easy to use front end and allows for fast parallelization.
  
  
  
  The package GiANT is available on CRAN.
  
  
  
  hans.kestler@leibniz-fli.de or hans.kestler@uni-ulm.de.
authors.affiliation: Institute of Medical Systems Biology, Ulm University, Ulm 89069, Germany.
authors.forename: Florian
authors.initials: F
authors.lastname: Schmid
authors.affiliation: Institut für Medizinische Biometrie, Informatik und Epidemiologie, Universität Bonn, Bonn 53127, Germany.
authors.forename: Matthias
authors.initials: M
authors.lastname: Schmid
authors.affiliation: Institute of Medical Systems Biology, Ulm University, Ulm 89069, Germany.
authors.forename: Christoph
authors.initials: C
authors.lastname: Müssel
authors.affiliation: Institute of Medical Systems Biology, Ulm University, Ulm 89069, Germany.
authors.forename: J Eric
authors.initials: JE
authors.lastname: Sträng
authors.affiliation: Institute of Experimental Cancer Research.
authors.forename: Christian
authors.initials: C
authors.lastname: Buske
authors.affiliation: Department of Internal Medicine III, Ulm University, Ulm 89069, Germany and.
authors.forename: Lars
authors.initials: L
authors.lastname: Bullinger
authors.affiliation: Institute of Medical Systems Biology, Ulm University, Ulm 89069, Germany.
authors.forename: Johann M
authors.initials: JM
authors.lastname: Kraus
authors.affiliation: Institute of Medical Systems Biology, Ulm University, Ulm 89069, Germany, Leibniz Institute on Ageing - Fritz Lipmann Institute and FSU Jena, Jena 07745, Germany.
authors.forename: Hans A
authors.initials: HA
authors.lastname: Kestler
mesh_terms: D000465:Algorithms; D000818:Animals; D003198:Computer Simulation; D053263:Gene Regulatory Networks; D016161:Genes, Retinoblastoma; D006801:Humans; D051379:Mice; D009369:Neoplasms / Q000235:genetics; D012984:Software; D035501:Uncertainty