Interampatteness - A generic property of biochemical networks

• 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.

Ämnesord

NATURVETENSKAP  -- Biologi -- Biokemi och molekylärbiologi (hsv//swe)

NATURAL SCIENCES  -- Biological Sciences -- Biochemistry and Molecular Biology (hsv//eng)

TEKNIK OCH TEKNOLOGIER  -- Elektroteknik och elektronik -- Reglerteknik (hsv//swe)

ENGINEERING AND TECHNOLOGY  -- Electrical Engineering, Electronic Engineering, Information Engineering -- Control Engineering (hsv//eng)

Nyckelord

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

Biokemi

Automatic control

Reglerteknik

Publikations- och innehållstyp

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