Elucidation of gene interaction networks through time-lagged correlation analysis of transcriptional data

The photosynthetic cyanobacterium Synechocystis sp. strain PCC 6803 uses a complex genetic program to control its physiological response to alternating light conditions. To study this regulatory program time-series experiments were conducted by exposing Synechocystis sp. to serial perturbations in l...

Full description

Saved in:
Bibliographic Details
Published in:Genome research 2004-08, Vol.14 (8), p.1654-1663
Main Authors: Schmitt, Jr, William A, Raab, R Michael, Stephanopoulos, Gregory
Format: Article
Language:English
Subjects:
Cyanobacteria - genetics
Gene Expression Profiling
Gene Expression Regulation, Bacterial
Genes, Bacterial
Genome, Bacterial
Light
Methods
Models, Biological
Oligonucleotide Array Sequence Analysis - methods
Time Factors
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:The photosynthetic cyanobacterium Synechocystis sp. strain PCC 6803 uses a complex genetic program to control its physiological response to alternating light conditions. To study this regulatory program time-series experiments were conducted by exposing Synechocystis sp. to serial perturbations in light intensity. In each experiment whole-genome DNA microarrays were used to monitor gene transcription in 20-min intervals over 8- and 16-h periods. The data was analyzed using time-lagged correlation analysis, which identifies genetic interaction networks by constructing correlations between time-shifted transcription profiles with different levels of statistical confidence. These networks allow inference of putative cause-effect relationships among the organism's genes. Using light intensity as our initial input signal, we identified six groups of genes whose time-lagged profiles possessed significant correlation, or anti-correlation, with the light intensity. We expanded this network by using the average profile from each group of genes as a seed, and searching for other genes whose time-lagged profiles possessed significant correlation, or anti-correlation, with the group's average profile. The final network comprised 50 different groups containing 259 genes. Several of these gene groups possess known light-stimulated gene clusters, such as Synechocystis sp. photosystems I and II and carbon dioxide fixation pathways, while others represent novel findings in this work.
ISSN:1088-9051
DOI:10.1101/gr.2439804