Effective similarity measures for expression profiles.
ABSTRACT 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/
Full-textDOI: · Available from: Golan Yona, Jun 10, 2015
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ABSTRACT: Combination therapies have recently been shown to be more effective than monotherapies that may provide synergistic effects in the treatment of stroke, but its selective mechanism still remains unclear. Based on the median-effect method, the combination therapy of jasminoidin and ursodeoxycholic acid had a synergic effect on reducing the infarct volume. The numbers of up- or down-regulated genes by at least 1.5-fold in the vehicle, jasminoidin, ursodeoxycholic acid, and the combination of jasminoidin and ursodeoxycholic acid treatment groups were 228, 95, 136, and 101, respectively. According to clustering and principal component analysis, the pattern of gene expression in the combination group was similar to that of jasminoidin group rather than ursodeoxycholic acid group. Based on these nine top sequences in the combination group excluding four overlapping pathways (MAPK-ERK, Kitlg, Icam1-Ap1, and prolactin), the jasminoidin group had four (PRLR-STAT1, AcvR2-AcvR1B, ACVR1/2A-SMAD1, GHR-NF-κB) contributing pathways, and the ursodeoxycholic acid group had one (IL-6) contributing pathway. Based on the multiple-pathway-dependent comparison analysis (MPDCA), it may lead to the conclusion that jasminoidin possibly contributes more important pharmacological effect in the combined treatment as jasminoidin regulated 80% of the pathways that the combination group mediated. The study reveals a horizontal synergistic effect by optimizing the fusion of more pathways from the compounds with more contribution to the combination therapy. Rather than selecting compounds only based on experience in the past, this study would give a new insight into the systematic strategies for designing synergistic combination therapies.European journal of pharmacology 06/2011; 667(1-3):278-86. DOI:10.1016/j.ejphar.2011.05.046 · 2.68 Impact Factor