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Inferring the relation between transcriptional and posttranscriptional regulation from expression compendia

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Bioinformatics: from nucleotids to networks (N2N)
Abstract
Background: Publicly available expression compendia that measure both mRNAs and sRNAs provide a promising resource to simultaneously infer the transcriptional and the posttranscriptional network. To maximally exploit the information contained in such compendia, we propose an analysis flow that combines publicly available expression compendia and sequence-based predictions to infer novel sRNA-target interactions and to reconstruct the relation between the sRNA and the transcriptional network. Results: We relied on module inference to construct modules of coexpressed genes (sRNAs). TFs and sRNAs were assigned to these modules using the state-of-the-art inference techniques LeMoNe and Context Likelihood of Relatedness (CLR). Combining these expressions with sequence-based sRNA-target interactions allowed us to predict 30 novel sRNA-target interactions comprising 14 sRNAs. Our results highlight the role of the posttranscriptional network in finetuning the transcriptional regulation, e.g. by intra-operonic regulation. Conclusion: In this work we show how strategies that combine expression information with sequence-based predictions can help unveiling the intricate interaction between the transcriptional and the posttranscriptional network in prokaryotic model systems.
Keywords
IDENTIFICATION, PROTEIN, SULFUR, ACID, BACTERIA, GENETIC-REGULATION, NONCODING RNAS, MESSENGER-RNA, sRNA, Gene, Module network, Network inference, Escherichia coli, SMALL-RNA, ESCHERICHIA-COLI K-12, IBCN

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Citation

Please use this url to cite or link to this publication:

Chicago
Ishchukov, Ivan, Yan Wu, Sandra Van Puyvelde, Jos Vanderleyden, and Kathleen Marchal. 2014. “Inferring the Relation Between Transcriptional and Posttranscriptional Regulation from Expression Compendia.” Bmc Microbiology 14.
APA
Ishchukov, I., Wu, Y., Van Puyvelde, S., Vanderleyden, J., & Marchal, K. (2014). Inferring the relation between transcriptional and posttranscriptional regulation from expression compendia. BMC MICROBIOLOGY, 14.
Vancouver
1.
Ishchukov I, Wu Y, Van Puyvelde S, Vanderleyden J, Marchal K. Inferring the relation between transcriptional and posttranscriptional regulation from expression compendia. BMC MICROBIOLOGY. 2014;14.
MLA
Ishchukov, Ivan, Yan Wu, Sandra Van Puyvelde, et al. “Inferring the Relation Between Transcriptional and Posttranscriptional Regulation from Expression Compendia.” BMC MICROBIOLOGY 14 (2014): n. pag. Print.
@article{4419827,
  abstract     = {Background: Publicly available expression compendia that measure both mRNAs and sRNAs provide a promising resource to simultaneously infer the transcriptional and the posttranscriptional network. To maximally exploit the information contained in such compendia, we propose an analysis flow that combines publicly available expression compendia and sequence-based predictions to infer novel sRNA-target interactions and to reconstruct the relation between the sRNA and the transcriptional network. 
Results: We relied on module inference to construct modules of coexpressed genes (sRNAs). TFs and sRNAs were assigned to these modules using the state-of-the-art inference techniques LeMoNe and Context Likelihood of Relatedness (CLR). Combining these expressions with sequence-based sRNA-target interactions allowed us to predict 30 novel sRNA-target interactions comprising 14 sRNAs. Our results highlight the role of the posttranscriptional network in finetuning the transcriptional regulation, e.g. by intra-operonic regulation. 
Conclusion: In this work we show how strategies that combine expression information with sequence-based predictions can help unveiling the intricate interaction between the transcriptional and the posttranscriptional network in prokaryotic model systems.},
  articleno    = {14},
  author       = {Ishchukov, Ivan and Wu, Yan and Van Puyvelde, Sandra and Vanderleyden, Jos and Marchal, Kathleen},
  issn         = {1471-2180},
  journal      = {BMC MICROBIOLOGY},
  keyword      = {IDENTIFICATION,PROTEIN,SULFUR,ACID,BACTERIA,GENETIC-REGULATION,NONCODING RNAS,MESSENGER-RNA,sRNA,Gene,Module network,Network inference,Escherichia coli,SMALL-RNA,ESCHERICHIA-COLI K-12,IBCN},
  language     = {eng},
  pages        = {14},
  title        = {Inferring the relation between transcriptional and posttranscriptional regulation from expression compendia},
  url          = {http://dx.doi.org/10.1186/1471-2180-14-14},
  volume       = {14},
  year         = {2014},
}

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