Proceedings of the 13th ACM SIGKDD international conference on Knowledge discovery and data mining
PRIB '08 Proceedings of the Third IAPR International Conference on Pattern Recognition in Bioinformatics
Association Analysis Techniques for Bioinformatics Problems
BICoB '09 Proceedings of the 1st International Conference on Bioinformatics and Computational Biology
Subspace sums for extracting non-random data from massive noise
Knowledge and Information Systems
Data mining of vector–item patterns using neighborhood histograms
Knowledge and Information Systems
Independent component analysis: Mining microarray data for fundamental human gene expression modules
Journal of Biomedical Informatics
Multivariate hypergeometric similarity measure
Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine
Multivariate Hypergeometric Similarity Measure
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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It is commonly accepted that genes with similar expression profiles are functionally related. However, there are many ways one can measure the similarity of expression profiles, and it is not clear a priori what is the most effective one. Moreover, so far no clear distinction has been made as for the type of the functional link between genes as suggested by microarray data. Similarly expressed genes can be part of the same complex as interacting partners; they can participate in the same pathway without interacting directly; they can perform similar functions; or they can simply have similar regulatory sequences. Here we conduct a study of the notion of functional link as implied from expression data. We analyze different similarity measures of gene expression profiles and assess their usefulness and robustness in detecting biological relationships by comparing the similarity scores with results obtained from databases of interacting proteins, promoter signals and cellular pathways, as well as through sequence comparisons. We also introduce variations on similarity measures that are based on statistical analysis and better discriminate genes which are functionally nearby and faraway. Our tools can be used to assess other similarity measures for expression profiles, and are accessible at biozon.org/tools/expression/ Contact: golan@cs.technion.ac.il Supplementary information: Supplementary data are available at Bioinformatics online.