TY - JOUR
T1 - Clustering biological annotations and gene expression data to identify putatively co-regulated biological processes
AU - Henegar, Corneliu
AU - Cancello, Raffaella
AU - Rome, Sophie
AU - Vidal, Hubert
AU - Clément, Karine
AU - Zucker, Jean Daniel
PY - 2006/8
Y1 - 2006/8
N2 - Motivation: 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. Availability: Supplementary information about the FunClust er tool is available on-line at http://corneliu.henegar.info/FunCluster.htm.
AB - Motivation: 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. Availability: Supplementary information about the FunClust er tool is available on-line at http://corneliu.henegar.info/FunCluster.htm.
KW - Computational biology
KW - Functional profiling of gene expression
KW - Gene expression pattern analysis
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U2 - 10.1142/S0219720006002181
DO - 10.1142/S0219720006002181
M3 - Article
C2 - 17007070
AN - SCOPUS:33750459679
VL - 4
SP - 833
EP - 852
JO - Journal of Bioinformatics and Computational Biology
JF - Journal of Bioinformatics and Computational Biology
SN - 0219-7200
IS - 4
ER -