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Background  Large-scale accumulation of omics data poses a pressing challenge of integrative analysis of multiple data sets in bioinformatics. An open question of such integrative analysis is how to pinpoint consistent but subtle gene activity patterns across studies. Study heterogeneity needs to be addressed carefully for this goal.    Results  This paper proposes a regulation probability model-based meta-analysis,  j GRP, for identifying differentially expressed genes (DEGs). The method integrates multiple transcriptomics data sets in a gene regulatory space instead of in a gene expression space, which makes it easy to capture and manage data heterogeneity across studies from different laboratories or platforms. Specifically, we transform gene expression profiles into a united gene regulation profile across studies by mathematically defining two gene regulation events between two conditions and estimating their occurring probabilities in a sample. Finally, a novel differential expression statistic is established based on the gene regulation profiles, realizing accurate and flexible identification of DEGs in gene regulation space. We evaluated the proposed method on simulation data and real-world cancer datasets and showed the effectiveness and efficiency of  j GRP in identifying DEGs identification in the context of meta-analysis.    Conclusions  Data heterogeneity largely influences the performance of meta-analysis of DEGs identification. Existing different meta-analysis methods were revealed to exhibit very different degrees of sensitivity to study heterogeneity. The proposed method,  j GRP, can be a standalone tool due to its united framework and controllable way to deal with study heterogeneity.    Electronic supplementary material  The online version of this article (doi:10.1186/s12859-017-1794-6) contains supplementary material, which is available to authorized users.

A regulation probability model-based meta-analysis of multiple transcriptomics data sets for cancer biomarker identification