Visual comparison of clustering gene ontology with different similarity measures

Michał Kozielski, Aleksandra Gruca


The work presents comparison of four Gene Ontology term similarity measures combined with two methods calculating gene similarity on the basis of terms similarity. Visual comparison of clustering results, where different clustering methods were applied, indicates the best combination of similarity methods that can be utilised in a clustering process.


gene similarity; gene ontology; clustering process

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Al Mubaid H., Nagar A.: Comparison of four similarity measures based on GO annotations for Gene Clustering, IEEE Symposium on Computers and Communications, ISCC 2008, 2008, p. 531÷536.

Ankerst M., Breunig M., Kriegel H. P., Sander J.: OPTICS: ordering points to identify the clustering structure, SIGMOD Rec., 1999, Vol. 28, No 2, p. 49÷60.

Azuaje F., Wang H., Bodenreider O.: Ontology-driven similarity approaches to supporting gene functional assessment In Proc. Of The Eighth Annual Bio-Ontologies Meeting, 2005.

Eisen M. B., Spellman P. T., Brown P. O., Botstein D.: Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA, Vol. 95, 1998, p. 14863÷14868.

Gruca A., Kozielski M., Sikora M.: Fuzzy Clustering and Gene Ontology Based Decision Rules for Identification and Description of Gene Groups, AISC, Vol. 59, 2009, p. 141÷149.

Han J., Kamber M.: Data Mining: Concepts and Techniques. Morgan Kaufmann Publishers, Academic Press, San Francisco 2001.

Iyer V. R., Eisen M. B., Ross D. T., Schuler G., Moore T., Lee J. C., Trent J. M., Staudt L. M., Hudson J., Boguski M. S., Lashkari D., Shalon D., Botstein D., Brown P. O.: The transcriptional program in the response of human fibroblasts to serum. Science, Vol. 283, 1999, p. 83÷87.

Jiang J. J., Conrath D. W.: Semantic similarity based on corpus statistics and lexical ontology In Proc. on Int. Conference on Research in Computational Linguistics, 1997, p. 19÷33.

Lin D.: An information-theoretic definition of similarity In Proc. of the 15th Int'l Conference on Machine Learning, 1998, p. 296÷304.

Resnik P.: Semantic Similarity in a Taxonomy: An Information-Based Measure and its Application to Problems of Ambiguity in Natural Language J. Artif. Intell. Res. (JAIR), Vol. 11, 1999, p. 95÷130.

Sikora M., Gruca A.: Induction and selection of the most interesting Gene Ontology based multiattribute rules for descriptions of gene groups. Pattern Recogn. Letters, Vol. 32, 2011, p. 258÷269.

Sikora M., Gruca A.: Quality improvement of rules based gene groups descriptions using information about GO terms importance occurring in premises of determined rules. Int. Journal of Applied Mathematics & Computer Science. Vol. 20, No.3, 2010, p. 555÷570.

Wang H., Azuaje F., Bodenreider O., Dopazo J.: Gene expression correlation and gene ontology-based similarity: an assessment of quantitative relationships. In Proc. of the 2004 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology CIBCB’04, 2004, p. 25÷31.