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Joint analysis of transcriptional and post- transcriptional brain tumor data: searching for emergent properties of cellular systems

Raffaele Fronza12, Michele Tramonti13, William R Atchley4 and Christine Nardini1*

Author Affiliations

1 Key Laboratory of Computational Biology, MPG-CAS PICB, Shanghai, PR China

2 Biocomputing Unit, University of Bologna, Bologna, Italy

3 DEIS, University of Bologna, Bologna, Italy

4 Department of Genetics, North Carolina State University, Raleigh, NC, USA

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BMC Bioinformatics 2011, 12:86  doi:10.1186/1471-2105-12-86

Published: 30 March 2011



Advances in biotechnology offer a fast growing variety of high-throughput data for screening molecular activities of genomic, transcriptional, post-transcriptional and translational observations. However, to date, most computational and algorithmic efforts have been directed at mining data from each of these molecular levels (genomic, transcriptional, etc.) separately. In view of the rapid advances in technology (new generation sequencing, high-throughput proteomics) it is important to address the problem of analyzing these data as a whole, i.e. preserving the emergent properties that appear in the cellular system when all molecular levels are interacting. We analyzed one of the (currently) few datasets that provide both transcriptional and post-transcriptional data of the same samples to investigate the possibility to extract more information, using a joint analysis approach.


We use Factor Analysis coupled with pre-established knowledge as a theoretical base to achieve this goal. Our intention is to identify structures that contain information from both mRNAs and miRNAs, and that can explain the complexity of the data. Despite the small sample available, we can show that this approach permits identification of meaningful structures, in particular two polycistronic miRNA genes related to transcriptional activity and likely to be relevant in the discrimination between gliosarcomas and other brain tumors.


This suggests the need to develop methodologies to simultaneously mine information from different levels of biological organization, rather than linking separate analyses performed in parallel.