Joint Stage Recognition and Anatomical Annotation of Drosophila Gene Expression Patterns

Xiao Cai, Hua Wang, Heng Huang, Chris Ding.

Bioinformatics - 2012

Motivation: Staining the mRNA of a gene via in situ hybridization (ISH) during the development of a Drosophila melanogaster embryo delivers the detailed spatio-temporal patterns of the gene expression. Many related biological problems such as the detection of co-expressed genes, co-regulated genes and transcription factor binding motifs rely heavily on the analysis of these image patterns. To provide the text-based pattern searching for facilitating related biological studies, the images in the Berkeley Drosophila Genome Project (BDGP) study are annotated with developmental stage term and anatomical ontology terms manually by domain experts. Due to the rapid increase in the number of such images and the inevitable bias annotations by human curators, it is necessary to develop an automatic method to recognize the developmental stage and annotate anatomical terms. Results: In this article, we propose a novel computational model for jointly stage classification and anatomical terms annotation of Drosophila gene expression patterns. We propose a novel Tri-Relational Graph (TG) model that comprises the data graph, anatomical term graph, developmental stage term graph, and connect them by two additional graphs induced from stage or annotation label assignments. Upon the TG model, we introduce a Preferential Random Walk (PRW) method to jointly recognize developmental stage and annotate anatomical terms by utilizing the interrelations between two tasks. The experimental results on two refined BDGP datasets demonstrate that our joint learning method can achieve superior prediction results on both tasks than the state-of-the-art methods.


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Cai, Xiao, et al. "Joint stage recognition and anatomical annotation of Drosophila gene expression patterns." Bioinformatics 28.12 (2012): i16-i24.
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  title={Joint stage recognition and anatomical annotation of Drosophila gene expression patterns},
  author={Cai, Xiao and Wang, Hua and Huang, Heng and Ding, Chris},
  publisher={Oxford University Press}