A knowledge-based clustering algorithm driven by Gene Ontology.
We have developed an algorithm for inferring the degree of similarity between genes by using the graph-based structure of Gene Ontology (GO). We applied this knowledge-based similarity metric to a clique-finding algorithm for detecting sets of related genes with biological classifications. We also combined it with an expression-based distance metric to produce a co-cluster analysis, which accentuates genes with both similar expression profiles and similar biological characteristics and identifies gene clusters that are more stable and biologically meaningful. These algorithms are demonstrated in the analysis of MPRO cell differentiation time series experiments.
Affymetrix, Inc, Santa Clara, CA 95051, USA. jill_cheng@affymetrix.com
Jill
J
Cheng
Melissa
M
Cline
John
J
Martin
David
D
Finkelstein
Tarif
T
Awad
David
D
Kulp
Michael A
MA
Siani-Rose
D000465:Algorithms; D001185:Artificial Intelligence; D002454:Cell Differentiation / Q000187:drug effects / Q000502:physiology; D016000:Cluster Analysis; D006801:Humans; D009504:Neutrophils / Q000187:drug effects; D020411:Oligonucleotide Array Sequence Analysis / Q000706:statistics & numerical data*; D014212:Tretinoin / Q000494:pharmacology
D014212:Tretinoin