A vector space model approach to identify genetically related diseases.
OBJECTIVE
The relationship between diseases and their causative genes can be complex, especially in the case of polygenic diseases. Further exacerbating the challenges in their study is that many genes may be causally related to multiple diseases. This study explored the relationship between diseases through the adaptation of an approach pioneered in the context of information retrieval: vector space models.


METHODS
A vector space model approach was developed that bridges gene disease knowledge inferred across three knowledge bases: Online Mendelian Inheritance in Man, GenBank, and Medline. The approach was then used to identify potentially related diseases for two target diseases: Alzheimer disease and Prader-Willi Syndrome.


RESULTS
In the case of both Alzheimer Disease and Prader-Willi Syndrome, a set of plausible diseases were identified that may warrant further exploration.


CONCLUSIONS
This study furthers seminal work by Swanson, et al. that demonstrated the potential for mining literature for putative correlations. Using a vector space modeling approach, information from both biomedical literature and genomic resources (like GenBank) can be combined towards identification of putative correlations of interest. To this end, the relevance of the predicted diseases of interest in this study using the vector space modeling approach were validated based on supporting literature.


CONCLUSIONS
The results of this study suggest that a vector space model approach may be a useful means to identify potential relationships between complex diseases, and thereby enable the coordination of gene-based findings across multiple complex diseases.
Center for Clinical and Translational Science, University of Vermont, Burlington, Vermont 05405, USA. neil.sarkar@uvm.edu
Indra Neil
IN
Sarkar
D000544:Alzheimer Disease / Q000235:genetics*; D030561:Databases, Nucleic Acid; D006801:Humans; D016239:MEDLINE; D055641:Mathematical Concepts; D011218:Prader-Willi Syndrome / Q000235:genetics*; D060388:Support Vector Machine