A Statistical Method to Incorporate Biological Knowledge for Generating Testable Novel Gene Regulatory Interactions from Microarray Experiments

Overview

Journal BMC Bioinformatics

Publisher Biomed Central

Specialty Biology

Date 2007 Aug 31

PMID 17727721

Citations 7

Authors

Peter Larsen

Eyad Almasri

Guanrao Chen

Yang Dai

Affiliations

Soon will be listed here.

Abstract

Background: The incorporation of prior biological knowledge in the analysis of microarray data has become important in the reconstruction of transcription regulatory networks in a cell. Most of the current research has been focused on the integration of multiple sets of microarray data as well as curated databases for a genome scale reconstruction. However, individual researchers are more interested in the extraction of most useful information from the data of their hypothesis-driven microarray experiments. How to compile the prior biological knowledge from literature to facilitate new hypothesis generation from a microarray experiment is the focus of this work. We propose a novel method based on the statistical analysis of reported gene interactions in PubMed literature.

Results: Using Gene Ontology (GO) Molecular Function annotation for reported gene regulatory interactions in PubMed literature, a statistical analysis method was proposed for the derivation of a likelihood of interaction (LOI) score for a pair of genes. The LOI-score and the Pearson correlation coefficient of gene profiles were utilized to check if a pair of query genes would be in the above specified interaction. The method was validated in the analysis of two gene sets formed from the yeast Saccharomyces cerevisiae cell cycle microarray data. It was found that high percentage of identified interactions shares GO Biological Process annotations (39.5% for a 102 interaction enriched gene set and 23.0% for a larger 999 cyclically expressed gene set).

Conclusion: This method can uncover novel biologically relevant gene interactions. With stringent confidence levels, small interaction networks can be identified for further establishment of a hypothesis testable by biological experiment. This procedure is computationally inexpensive and can be used as a preprocessing procedure for screening potential biologically relevant gene pairs subject to the analysis with sophisticated statistical methods.

Citing Articles

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Larsen P, Sreedasyam A, Trivedi G, Desai S, Dai Y, Cseke L Front Plant Sci. 2016; 6:1061.

PMID: 26834754 PMC: 4717292. DOI: 10.3389/fpls.2015.01061.

Dynamic Bayesian Network Modeling of the Interplay between EGFR and Hedgehog Signaling.

Frohlich H, Bahamondez G, Gotschel F, Korf U PLoS One. 2015; 10(11):e0142646.

PMID: 26571415 PMC: 4646463. DOI: 10.1371/journal.pone.0142646.

Boosting probabilistic graphical model inference by incorporating prior knowledge from multiple sources.

Praveen P, Frohlich H PLoS One. 2013; 8(6):e67410.

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Quantitative utilization of prior biological knowledge in the Bayesian network modeling of gene expression data.

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