Academic Commons

Articles

Identifying functional relationships among human genes by systematic analysis of biological literature

Tao, Yong-Chuan; Leibel, Rudolph L.

Background: The availability of biomedical literature in electronic format has made it possible to implement automatic text processing methods to expose implicit relationships among different documents, and more importantly, the functional relationships among the molecules and processes that these documents describe. Results: A computational strategy that identifies functionally related human genes by detecting the implicit relationships among the publications cited under each gene in the Online Mendelian Inheritance in Man (OMIM) was implemented. The implementation was based on a substantially modified version of the kernel document method. The improvements include assigning a calculated weight for a document to indicate its importance in establishing the relationship between two documents, and using multiple kernel documents to reflect the multiple functions of the same gene. An example of using this strategy to identify genes related to the apoptosis pathway in human was given. Conclusions: The results showed that this method can indeed produce meaningful results when applied to human genes.

Files

Also Published In

Title
BMC Bioinformatics
DOI
https://doi.org/10.1186/1471-2105-3-16

More About This Work

Academic Units
Pediatrics
Publisher
BioMed Central
Published Here
September 9, 2014
Academic Commons provides global access to research and scholarship produced at Columbia University, Barnard College, Teachers College, Union Theological Seminary and Jewish Theological Seminary. Academic Commons is managed by the Columbia University Libraries.