Abstract
BackgroundTranscriptional regulatory network inference (TRNI) from large compendia of DNA microarrays has become a fundamental approach for discovering transcription factor (TF)-gene interactions at the genome-wide level. In correlation-based TRNI, network edges can in principle be evaluated using standard statistical tests. However, while such tests nominally assume independent microarray experiments, we expect dependency between the experiments in microarray compendia, due to both project-specific factors (e.g., microarray preparation, environmental effects) in the multi-project compendium setting and effective dependency induced by gene-gene correlations. Herein, we characterize the nature of dependency in an Escherichia coli microarray compendium and explore its consequences on the problem of determining which and how many arrays to use in correlation-based TRNI.ResultsWe present evidence of substantial effective dependency among microarrays in this compendium, and characterize that dependency with respect to experimental condition factors. We then introduce a measure neff of the effective number of experiments in a compendium, and find that corresponding to the dependency observed in this particular compendium there is a huge reduction in effective sample size i.e., neff = 14.7 versus n = 376. Furthermore, we found that the neff of select subsets of experiments actually exceeded neff of the full compendium, suggesting that the adage 'less is more' applies here. Consistent with this latter result, we observed improved performance in TRNI using subsets of the data compared to results using the full compendium. We identified experimental condition factors that trend with changes in TRNI performance and neff , including growth phase and media type. Finally, using the set of known E. coli genetic regulatory interactions from RegulonDB, we demonstrated that false discovery rates (FDR) derived from neff -adjusted p-values were well-matched to FDR based on the RegulonDB truth set.ConclusionsThese results support utilization of neff as a potent descriptor of microarray compendia. In addition, they highlight a straightforward correlation-based method for TRNI with demonstrated meaningful statistical testing for significant edges, readily applicable to compendia from any species, even when a truth set is not available. This work facilitates a more refined approach to construction and utilization of mRNA expression compendia in TRNI.
Highlights
Transcriptional regulatory network inference (TRNI) from large compendia of DNA microarrays has become a fundamental approach for discovering transcription factor (TF)-gene interactions at the genome-wide level
With the availability of genome-wide mRNA expression data from DNA microarray experiments, transcriptional regulatory network inference (TRNI) from large compendia of these microarrays has become a fundamental task in computational systems biology
We found that peff = 14.66 for this compendium, a drastic reduction compared to the number of genes p = 4298
Summary
Transcriptional regulatory network inference (TRNI) from large compendia of DNA microarrays has become a fundamental approach for discovering transcription factor (TF)-gene interactions at the genome-wide level. In correlation-based TRNI, network edges can in principle be evaluated using standard statistical tests While such tests nominally assume independent microarray experiments, we expect dependency between the experiments in microarray compendia, due to both project-specific factors (e.g., microarray preparation, environmental effects) in the multi-project compendium setting and effective dependency induced by gene-gene correlations. With the availability of genome-wide mRNA expression data from DNA microarray experiments, transcriptional regulatory network inference (TRNI) from large compendia of these microarrays has become a fundamental task in computational systems biology In this approach, transcription factor (TF)-gene interactions are predicted. While many of these approaches have relied on userdefined or truth set-based thresholds for determining the network, the correlation- and partial correlationbased methods can in principle calibrate established tests to a desired level of prediction accuracy via control of the false discovery rate (FDR) alone Such tests nominally assume independent and identically distributed (i.i.d.) microarray experiments. Such (effective) dependency invalidates the assumption of i.i.d. experiments upon which the statistical tests are based, thereby complicating the calibration of these tests
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