Using unsupervised patterns to extract gene regulation relationships for network construction

Abstract

Background: The gene expression is usually described in the literature as a transcription factor X that regulates the target gene Y. Previously, some studies discovered gene regulations by using information from the biomedical literature and most of them require effort of human annotators to build the training dataset. Moreover, the large amount of textual knowledge recorded in the biomedical literature grows very rapidly, and the creation of manual patterns from literatures becomes more difficult. There is an increasing need to automate the process of establishing patterns.

Methodology/principal findings: In this article, we describe an unsupervised pattern generation method called AutoPat. It is a gene expression mining system that can generate unsupervised patterns automatically from a given set of seed patterns. The high scalability and low maintenance cost of the unsupervised patterns could help our system to extract gene expression from PubMed abstracts more precisely and effectively.

Conclusions/significance: Experiments on several regulators show reasonable precision and recall rates which validate AutoPat's practical applicability. The conducted regulation networks could also be built precisely and effectively. The system in this study is available at http://ikmbio.csie.ncku.edu.tw/AutoPat/.

Figure 1. The overall architecture of AutoPat.

Figure 2. Example of combined weight of extracted sentences.

Figure 3. The frequency distribution of unsupervised patterns.

Figure 4. The extraction precision of different thresholds.

Figure 5. The precision of the Top N ranking results for unsupervised patterns.

Figure 6. Examples of the homonym and abbreviation issues.

Figure 7. The global network of HIF-1 TF.

Figure 8. The example of an indirect relationship between HIF-1 and p53.