title: Clustering biological annotations and gene expression data to identify putatively co-regulated biological processes.
abstract: BACKGROUND
  Functional profiling is a key step of microarray gene expression data analysis. Identifying co-regulated biological processes could help for better understanding of underlying biological interactions within the studied biological frame.
  
  
  RESULTS
  We present herein an original approach designed to search for putatively co-regulated biological processes sharing a significant number of co-expressed genes. An R language implementation named "FunCluster" was built and tested on two gene expression data sets. A discriminatory functional analysis of the first data set, related to experiments performed on separated adipocytes and stroma vascular fraction cells of human white adipose tissue, highlighted the prevalent role of nonadipose cells in the synthesis of inflammatory and immunity molecules in human adiposity. On the second data set, resulting from a model investigating insulin coordinated regulation of gene expression in human skeletal muscle, FunCluster analysis spotlighted novel functional classes of putatively co-regulated biological processes related to protein metabolism and the regulation of muscular contraction.
  
  
  BACKGROUND
  Supplementary information about the FunCluster tool is available on-line at http://corneliu.henegar.info/FunCluster.htm.
authors.affiliation: Inserm, U755 Nutriomique, 75004 Paris, France. corneliu@henegar.info
authors.forename: Corneliu
authors.initials: C
authors.lastname: Henegar
authors.forename: Raffaella
authors.initials: R
authors.lastname: Cancello
authors.forename: Sophie
authors.initials: S
authors.lastname: Rome
authors.forename: Hubert
authors.initials: H
authors.lastname: Vidal
authors.forename: Karine
authors.initials: K
authors.lastname: Clément
authors.forename: Jean-Daniel
authors.initials: JD
authors.lastname: Zucker
mesh_terms: D000465:Algorithms; D001695:Biology / Q000379:methods; D016000:Cluster Analysis; D003198:Computer Simulation; D015870:Gene Expression / Q000502:physiology*; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation / Q000502:physiology; D008954:Models, Biological; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010363:Pattern Recognition, Automated / Q000379:methods*; D015398:Signal Transduction / Q000502:physiology*