Clustering biological annotations and gene expression data to identify putatively co-regulated biological processes.
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.
Henegar
Corneliu
C
Inserm, U755 Nutriomique, 75004 Paris, France. corneliu@henegar.info
Cancello
Raffaella
R
Rome
Sophie
S
Vidal
Hubert
H
Clément
Karine
K
Zucker
Jean-Daniel
JD
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*