ArticleBMC bioinformatics2011
Consistent Differential Expression Pattern (CDEP) on microarray to identify genes related to metastatic behavior.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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6 citing papers in PubMed.
- Mechanical Strain Induces Transcriptomic Reprogramming of Saphenous Vein Progenitors.Frontiers in cardiovascular medicine · 2022Article
- Reporters to mark and eliminate basal or luminal epithelial cells in culture and in vivo.PLoS biology · 2018Article
- A fast algorithm for determining bounds and accurate approximate p-values of the rank product statistic for replicate experiments.BMC bioinformatics · 2014Article
- Knowledge-based compact disease models identify new molecular players contributing to early-stage Alzheimer's disease.BMC systems biology · 2013Article
- Reuse of public genome-wide gene expression data.Nature reviews. Genetics · 2013Review
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4 authors.
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Abstract
backgroundTo utilize the large volume of gene expression information generated from different microarray experiments, several meta-analysis techniques have been developed. Despite these efforts, there remain significant challenges to effectively increasing the statistical power and decreasing the Type I error rate while pooling the heterogeneous datasets from public resources. The objective of this study is to develop a novel meta-analysis approach, Consistent Differential Expression Pattern (CDEP), to identify genes with common differential expression patterns across different datasets.
resultsWe combined False Discovery Rate (FDR) estimation and the non-parametric RankProd approach to estimate the Type I error rate in each microarray dataset of the meta-analysis. These Type I error rates from all datasets were then used to identify genes with common differential expression patterns. Our simulation study showed that CDEP achieved higher statistical power and maintained low Type I error rate when compared with two recently proposed meta-analysis approaches. We applied CDEP to analyze microarray data from different laboratories that compared transcription profiles between metastatic and primary cancer of different types. Many genes identified as differentially expressed consistently across different cancer types are in pathways related to metastatic behavior, such as ECM-receptor interaction, focal adhesion, and blood vessel development. We also identified novel genes such as AMIGO2, Gem, and CXCL11 that have not been shown to associate with, but may play roles in, metastasis.
conclusionsCDEP is a flexible approach that borrows information from each dataset in a meta-analysis in order to identify genes being differentially expressed consistently. We have shown that CDEP can gain higher statistical power than other existing approaches under a variety of settings considered in the simulation study, suggesting its robustness and insensitivity to data variation commonly associated with microarray experiments. AVAILABILITY: CDEP is implemented in R and freely available at: http://genomebioinfo.musc.edu/CDEP/. CONTACT: zhengw@musc.edu.
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