Exploiting the Functional and Taxonomic Structure of Genomic Data by Probabilistic Topic Modeling

• Published in: IEEE/ACM transactions on computational biology and bioinformatics Vol. 9; no. 4; pp. 980 - 991
• Main Authors: Xin Chen, Xiaohua Hu, Lim, T. Y., Xiajiong Shen, Park, E. K., Rosen, G. L.
• Format: Journal Article
• Language: English
• Published: United States IEEE 01.07.2012; The Institute of Electrical and Electronics Engineers, Inc. (IEEE)
• Subjects: Bacteria - genetics; Bioinformatics; bioinformatics (genome or protein) databases; Computational Biology - methods; Data mining; Data Mining - methods; Data models; Databases, Genetic; DNA; Gastrointestinal Tract - microbiology; Genome, Bacterial; Genomes; Genomics; Humans; Inflammatory Bowel Diseases - microbiology; Integrated circuit modeling; language models; metagenomics; Metagenomics - methods; Models, Genetic; Models, Statistical; Strain; Studies
• ISSN: 1545-5963; 1557-9964
• DOI: 10.1109/TCBB.2011.113

In this paper, we present a method that enable both homology-based approach and composition-based approach to further study the functional core (i.e., microbial core and gene core, correspondingly). In the proposed method, the identification of major functionality groups is achieved by generative topic modeling, which is able to extract useful information from unlabeled data. We first show that generative topic model can be used to model the taxon abundance information obtained by homology-based approach and study the microbial core. The model considers each sample as a "document," which has a mixture of functional groups, while each functional group (also known as a "latent topic") is a weight mixture of species. Therefore, estimating the generative topic model for taxon abundance data will uncover the distribution over latent functions (latent topic) in each sample. Second, we show that, generative topic model can also be used to study the genome-level composition of "N-mer" features (DNA subreads obtained by composition-based approaches). The model consider each genome as a mixture of latten genetic patterns (latent topics), while each functional pattern is a weighted mixture of the "N-mer" features, thus the existence of core genomes can be indicated by a set of common N-mer features. After studying the mutual information between latent topics and gene regions, we provide an explanation of the functional roles of uncovered latten genetic patterns. The experimental results demonstrate the effectiveness of proposed method.