Abstract
Mining of biomedical data increasingly relies on utility of knowledge repositories. In gene expression analysis, these are often used for gene labeling with an assumption that similarly annotated genes have similar expression profiles. In the paper we use this assumption to craft a method with which we scored six different annotation sources (e.g., Gene Ontology, PubMed, and MeSH annotations) for their utility in gene expression data analysis. Experiments show that the sources that include manual curation perform well and, for instance, score better than automatic annotation from gene-related PubMed abstracts. We also show that there is no clear winner, pointing at the need for methods that could successfully integrate annotations from different sources.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Subramanian, A., Tamayo, P., Mootha, V.K., Mukherjee, S., Ebert, B.L., Gillette, M.A., Paulovich, A., Pomeroy, S.L., Golub, T.R., Lander, E.S., Mesirov, J.P.: Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci., USA 102(43), 15545–15550 (2005)
Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T., Harris, M.A., Hill, D.P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J.C., Richardson, J.E., Ringwald, M., Rubin, G.M., Sherlock, G.: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25(1), 25–29 (2000)
Petrovic, S., Kolar, M., Saric, F., Demsar, J., Dalbelo Basic, B., Zupan, B.: orngTxt, Orange data mining tool, Add-On for Text mining (2008), http://www.ailab.si/orange/downloads.asp
Demsar, J.: Statistical Comparisons of Classifiers over Multiple Data Sets. J. Mach. Learn. Res. 7, 1–30 (2006)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Mulas, F., Curk, T., Bellazzi, R., Zupan, B. (2009). On Quality of Different Annotation Sources for Gene Expression Analysis. In: Combi, C., Shahar, Y., Abu-Hanna, A. (eds) Artificial Intelligence in Medicine. AIME 2009. Lecture Notes in Computer Science(), vol 5651. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-02976-9_60
Download citation
DOI: https://doi.org/10.1007/978-3-642-02976-9_60
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-02975-2
Online ISBN: 978-3-642-02976-9
eBook Packages: Computer ScienceComputer Science (R0)