title: Improved detection of overrepresentation of Gene-Ontology annotations with parent child analysis.
abstract: BACKGROUND
  High-throughput experiments such as microarray hybridizations often yield long lists of genes found to share a certain characteristic such as differential expression. Exploring Gene Ontology (GO) annotations for such lists of genes has become a widespread practice to get first insights into the potential biological meaning of the experiment. The standard statistical approach to measuring overrepresentation of GO terms cannot cope with the dependencies resulting from the structure of GO because they analyze each term in isolation. Especially the fact that annotations are inherited from more specific descendant terms can result in certain types of false-positive results with potentially misleading biological interpretation, a phenomenon which we term the inheritance problem.
  
  
  RESULTS
  We present here a novel approach to analysis of GO term overrepresentation that determines overrepresentation of terms in the context of annotations to the term's parents. This approach reduces the dependencies between the individual term's measurements, and thereby avoids producing false-positive results owing to the inheritance problem. ROC analysis using study sets with overrepresented GO terms showed a clear advantage for our approach over the standard algorithm with respect to the inheritance problem. Although there can be no gold standard for exploratory methods such as analysis of GO term overrepresentation, analysis of biological datasets suggests that our algorithm tends to identify the core GO terms that are most characteristic of the dataset being analyzed.
authors.affiliation: Max-Planck-Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany.
authors.forename: Steffen
authors.initials: S
authors.lastname: Grossmann
authors.forename: Sebastian
authors.initials: S
authors.lastname: Bauer
authors.forename: Peter N
authors.initials: PN
authors.lastname: Robinson
authors.forename: Martin
authors.initials: M
authors.lastname: Vingron
mesh_terms: D000465:Algorithms; D020869:Gene Expression Profiling / Q000379:methods*; D005796:Genes / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010802:Phylogeny; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity