Reporting FDR analogous confidence intervals for the log fold change of differentially expressed genes

BMC Bioinformatics

Research Article

Klaus Jung¹  Tim Beißbarth¹  Tim Friede¹ 

[1] Department of Medical Statistics, University Medical Center Göttingen, D-37099, Göttingen, Germany;

关键词: Gene Ontology;    Fold Change;    False Discovery Rate;    Relevance Category;    Volcano Plot;   

DOI  :  10.1186/1471-2105-12-288

 received in 2011-02-24, accepted in 2011-07-15,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundGene expression experiments are common in molecular biology, for example in order to identify genes which play a certain role in a specified biological framework. For that purpose expression levels of several thousand genes are measured simultaneously using DNA microarrays. Comparing two distinct groups of tissue samples to detect those genes which are differentially expressed one statistical test per gene is performed, and resulting p-values are adjusted to control the false discovery rate. In addition, the expression change of each gene is quantified by some effect measure, typically the log fold change. In certain cases, however, a gene with a significant p-value can have a rather small fold change while in other cases a non-significant gene can have a rather large fold change. The biological relevance of the change of gene expression can be more intuitively judged by a fold change then merely by a p-value. Therefore, confidence intervals for the log fold change which accompany the adjusted p-values are desirable.ResultsIn a new approach, we employ an existing algorithm for adjusting confidence intervals in the case of high-dimensional data and apply it to a widely used linear model for microarray data. Furthermore, we adopt a concept of different relevance categories for effects in clinical trials to assess biological relevance of genes in microarray experiments. In a brief simulation study the properties of the adjusting algorithm are maintained when being combined with the linear model for microarray data. In two cancer data sets the adjusted confidence intervals can indicate significance of large fold changes and distinguish them from other large but non-significant fold changes. Adjusting of confidence intervals also corrects the assessment of biological relevance.ConclusionsOur new combination approach and the categorization of fold changes facilitates the selection of genes in microarray experiments and helps to interpret their biological relevance.

【 授权许可】

CC BY   
© Jung et al; licensee BioMed Central Ltd. 2011