Identification of self-consistent modulons from bacterial microarray expression data with the help of structured regulon gene sets
AuthorsPermina, Elizaveta A.
Baeck, Pia M.
Hegde, Shubhada R.
Mande, Shekhar C.
Makeev, Vsevolod J.
KAUST DepartmentComputational Bioscience Research Center (CBRC)
MetadataShow full item record
AbstractIdentification of bacterial modulons from series of gene expression measurements on microarrays is a principal problem, especially relevant for inadequately studied but practically important species. Usage of a priori information on regulatory interactions helps to evaluate parameters for regulatory subnetwork inference. We suggest a procedure for modulon construction where a seed regulon is iteratively updated with genes having expression patterns similar to those for regulon member genes. A set of genes essential for a regulon is used to control modulon updating. Essential genes for a regulon were selected as a subset of regulon genes highly related by different measures to each other. Using Escherichia coli as a model, we studied how modulon identification depends on the data, including the microarray experiments set, the adopted relevance measure and the regulon itself. We have found that results of modulon identification are highly dependent on all parameters studied and thus the resulting modulon varies substantially depending on the identification procedure. Yet, modulons that were identified correctly displayed higher stability during iterations, which allows developing a procedure for reliable modulon identification in the case of less studied species where the known regulatory interactions are sparse. Copyright © 2013 Taylor & Francis.
SponsorsWe are grateful to Dmitri Ravcheev for the fruitful consultation and for information provided about PurR regulon and Alexander Favorov for kindly providing a module for calculation of exact Fisher test. This study was partially supported with Russian Fund of Basic Research grant 10-04-92,663-IND-a and Department of Science and Technology, India grant INT/RFBR/P-31.
PublisherInforma UK Limited
- [Regulation of respiration in enterobacteria: comparison of microarray and comparative genomic data].
- Authors: Tsyganova MO, Gel'fand MS, Ravcheev DA
- Issue date: 2007 May-Jun
- Reconstruction of Escherichia coli transcriptional regulatory networks via regulon-based associations.
- Authors: Zare H, Sangurdekar D, Srivastava P, Kaveh M, Khodursky A
- Issue date: 2009 Apr 14
- Identification of regulatory network topological units coordinating the genome-wide transcriptional response to glucose in Escherichia coli.
- Authors: Gutierrez-Ríos RM, Freyre-Gonzalez JA, Resendis O, Collado-Vides J, Saier M, Gosset G
- Issue date: 2007 Jun 8
- The NsrR regulon of Escherichia coli K-12 includes genes encoding the hybrid cluster protein and the periplasmic, respiratory nitrite reductase.
- Authors: Filenko N, Spiro S, Browning DF, Squire D, Overton TW, Cole J, Constantinidou C
- Issue date: 2007 Jun
- Genomics of the marA/soxS/rob regulon of Escherichia coli: identification of directly activated promoters by application of molecular genetics and informatics to microarray data.
- Authors: Martin RG, Rosner JL
- Issue date: 2002 Jun