Article (Scientific journals)
Localizing potentially active post-transcriptional regulations in the Ewing's sarcoma gene regulatory network.
Baumuratova, Tatiana; Surdez, Didier; Delyon, Bernard et al.
2010In BMC Systems Biology, 4, p. 146
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Keywords :
Cell Line, Tumor; Gene Expression Profiling; Gene Regulatory Networks; Humans; Insulin-Like Growth Factor Binding Protein 3; Insulin-Like Growth Factor Binding Proteins/genetics; Insulin-Like Growth Factor I/genetics; Oncogenes/genetics; Proto-Oncogene Protein c-fli-1/genetics; Sarcoma, Ewing/genetics; Software; Transcription, Genetic
Abstract :
[en] 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.
Disciplines :
Life sciences: Multidisciplinary, general & others
Author, co-author :
Baumuratova, Tatiana ;  University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Life Science Research Unit
Surdez, Didier;  Genetics and Biology of Cancers, Institut Curie, Paris, France > Unité 830, INSERM
Delyon, Bernard;  IRMAR, Université de Rennes 1, Rennes, France > UMR 6625, CNRS
Stoll, Gautier;  Service bioinformatique, Institut Curie, Paris, France > Unité 900, INSERM ; Service bioinformatique, Mines ParisTech
Delattre, Olivier;  Genetics and Biology of Cancers, Institut Curie, Paris, France > Unité 830, INSERM
Radulescu, Ovidiu;  IRMAR, Université de Rennes 1, Rennes, France > UMR 6625, CNRS, UMR 5235, CNRS, Symbiose project team, INRIA
Siegel, Anne;  Symbiose project team, INRIA, IRISA, Université de Rennes 1, Rennes, France > UMR 6074, CNRS
Language :
English
Title :
Localizing potentially active post-transcriptional regulations in the Ewing's sarcoma gene regulatory network.
Publication date :
2010
Journal title :
BMC Systems Biology
ISSN :
1752-0509
Publisher :
BioMed Central, United Kingdom
Volume :
4
Pages :
146
Peer reviewed :
Peer Reviewed verified by ORBi
Available on ORBilu :
since 28 May 2013

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