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Open Access Open Badges Methodology article

A bag-of-words approach for Drosophila gene expression pattern annotation

Shuiwang Ji12, Ying-Xin Li3, Zhi-Hua Zhou3, Sudhir Kumar14 and Jieping Ye12*

Author Affiliations

1 Center for Evolutionary Functional Genomics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA

2 Department of Computer Science and Engineering, Arizona State University, Tempe, AZ 85287, USA

3 National Key Laboratory for Novel Software Technology, Nanjing University, Nanjing 210093, PR China

4 School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA

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BMC Bioinformatics 2009, 10:119  doi:10.1186/1471-2105-10-119

Published: 21 April 2009



Drosophila gene expression pattern images document the spatiotemporal dynamics of gene expression during embryogenesis. A comparative analysis of these images could provide a fundamentally important way for studying the regulatory networks governing development. To facilitate pattern comparison and searching, groups of images in the Berkeley Drosophila Genome Project (BDGP) high-throughput study were annotated with a variable number of anatomical terms manually using a controlled vocabulary. Considering that the number of available images is rapidly increasing, it is imperative to design computational methods to automate this task.


We present a computational method to annotate gene expression pattern images automatically. The proposed method uses the bag-of-words scheme to utilize the existing information on pattern annotation and annotates images using a model that exploits correlations among terms. The proposed method can annotate images individually or in groups (e.g., according to the developmental stage). In addition, the proposed method can integrate information from different two-dimensional views of embryos. Results on embryonic patterns from BDGP data demonstrate that our method significantly outperforms other methods.


The proposed bag-of-words scheme is effective in representing a set of annotations assigned to a group of images, and the model employed to annotate images successfully captures the correlations among different controlled vocabulary terms. The integration of existing annotation information from multiple embryonic views improves annotation performance.