Localizing potentially active post-transcriptional regulations in the Ewing's sarcoma gene regulatory network.
BACKGROUND
A wide range of techniques is now available for analyzing regulatory networks. Nonetheless, most of these techniques fail to interpret large-scale transcriptional data at the post-translational level.


RESULTS
We address the question of using large-scale transcriptomic observation of a system perturbation to analyze a regulatory network which contained several types of interactions - transcriptional and post-translational. Our method consisted of post-processing the outputs of an open-source tool named BioQuali - an automatic constraint-based analysis mimicking biologist's local reasoning on a large scale. The post-processing relied on differences in the behavior of the transcriptional and post-translational levels in the network. As a case study, we analyzed a network representation of the genes and proteins controlled by an oncogene in the context of Ewing's sarcoma. The analysis allowed us to pinpoint active interactions specific to this cancer. We also identified the parts of the network which were incomplete and should be submitted for further investigation.


CONCLUSIONS
The proposed approach is effective for the qualitative analysis of cancer networks. It allows the integrative use of experimental data of various types in order to identify the specific information that should be considered a priority in the initial - and possibly very large - experimental dataset. Iteratively, new dataset can be introduced into the analysis to improve the network representation and make it more specific.
Systems Biology Group, Life Science Research Unit, University of Luxembourg,162A Avenue de la Faiencerie, Luxembourg, L-1511, Luxembourg. tatiana.baumuratova@uni.lu
Tatiana
T
Baumuratova
Didier
D
Surdez
Bernard
B
Delyon
Gautier
G
Stoll
Olivier
O
Delattre
Ovidiu
O
Radulescu
Anne
A
Siegel
D045744:Cell Line, Tumor; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D006801:Humans; D018972:Insulin-Like Growth Factor Binding Protein 3; D018969:Insulin-Like Growth Factor Binding Proteins / Q000235:genetics; D007334:Insulin-Like Growth Factor I / Q000235:genetics; D009857:Oncogenes / Q000235:genetics; D051789:Proto-Oncogene Protein c-fli-1 / Q000235:genetics; D012512:Sarcoma, Ewing / Q000235:genetics*; D012984:Software; D014158:Transcription, Genetic
C078433:FLI1 protein, human; C515497:IGFBP3 protein, human; D018972:Insulin-Like Growth Factor Binding Protein 3; D018969:Insulin-Like Growth Factor Binding Proteins; D051789:Proto-Oncogene Protein c-fli-1; D007334:Insulin-Like Growth Factor I