Prediction of a gene regulatory network linked to prostate cancer from gene expression, microRNA and clinical data.
BACKGROUND
Cancer is a complex disease, triggered by mutations in multiple genes and pathways. There is a growing interest in the application of systems biology approaches to analyze various types of cancer-related data to understand the overwhelming complexity of changes induced by the disease.


RESULTS
We reconstructed a regulatory module network using gene expression, microRNA expression and a clinical parameter, all measured in lymphoblastoid cell lines derived from patients having aggressive or non-aggressive forms of prostate cancer. Our analysis identified several modules enriched in cell cycle-related genes as well as novel functional categories that might be linked to prostate cancer. Almost one-third of the regulators predicted to control the expression levels of the modules are microRNAs. Several of them have already been characterized as causal in various diseases, including cancer. We also predicted novel microRNAs that have never been associated to this type of tumor. Furthermore, the condition-dependent expression of several modules could be linked to the value of a clinical parameter characterizing the aggressiveness of the prostate cancer. Taken together, our results help to shed light on the consequences of aggressive and non-aggressive forms of prostate cancer.


BACKGROUND
The complete regulatory network is available as an interactive supplementary web site at the following URL: http://bioinformatics.psb.ugent.be/webtools/pronet/.
Bonnet
Eric
E
Department of Plant Systems Biology, VIB, Ghent University, Gent, Belgium.
Michoel
Tom
T
Van de Peer
Yves
Y
D000368:Aged; D000465:Algorithms; D045744:Cell Line, Tumor; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D006801:Humans; D008297:Male; D035683:MicroRNAs / Q000096:biosynthesis; D011471:Prostatic Neoplasms / Q000235:genetics* / Q000378:metabolism / Q000503:physiopathology; D049490:Systems Biology
D035683:MicroRNAs
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