Interampatteness - A generic property of biochemical networks
2009 (English)In: IET Systems Biology, ISSN 1751-8849, Vol. 3, no 5, 388-403 p.Article in journal (Refereed) Published
Analysis of gene expression data sets reveals that the variation in expression is concentrated to significantly fewer 'characteristic modes' or 'eigengenes' than the number of both recorded assays and measured genes. Previous works have stressed the importance of these characteristic modes, but neglected the equally important weak modes. Herein a generic system property - interampatteness - is defined that explains the previous feature, and assigns equal weight to the characteristic and weak modes. An interampatte network is characterised by strong INTERactions enabling simultaneous AMPlification and ATTEnuation of different signals. It is postulated that biochemical networks are interampatte, based on published experimental data and theoretical considerations. Existence of multiple time-scales and feedback loops is shown to increase the degree of interampatteness. Interampatteness has strong implications for the dynamics and reverse engineering of the network. One consequence is highly correlated changes in gene expression in response to external perturbations, even in the absence of common transcription factors, implying that interampatte gene regulatory networks erroneously may be assumed to have co-expressed/ co-regulated genes. Data compression or reduction of the system dimensionality using clustering, singular value decomposition, principal component analysis or some other data mining technique results in a loss of information that will obstruct reconstruction of the underlying network.
Place, publisher, year, edition, pages
2009. Vol. 3, no 5, 388-403 p.
Biochemical network, Characteristic modes, Co-regulated genes, Data mining techniques, Experimental data, External perturbations, Feed-back loop, Gene Expression Data, Gene regulatory networks, Generic properties, Generic system, Highly-correlated, Multiple timescales, Strong interaction, Underlying networks, Amplification, Bioactivity, Data mining, Genes, Principal component analysis, Reengineering, Reverse engineering, Singular value decomposition, Transcription, Transcription factors, Data compression, biochemistry, conference paper, feedback system, gene expression, genetic regulation, information processing, signal processing, statistical analysis
Biochemistry and Molecular Biology Control Engineering
IdentifiersURN: urn:nbn:se:kth:diva-28512DOI: 10.1049/iet-syb.2009.0008ISI: 000270483700010ScopusID: 2-s2.0-70349548793OAI: oai:DiVA.org:kth-28512DiVA: diva2:390141
2nd q-bio Conference on Cellular Information Processing St John Coll, Santa Fe, NM, AUG 06-09, 2008
QC 201101212011-01-212011-01-142016-05-18Bibliographically approved