Hi, Does anybody knows that genes expression are linear or non-linear ? I want to find out co-expressed genes in microarry study data and people usually use correlation to find out co-expressed genes. I wounder, whether genes expression with identical TF are linear or non-linear ? (cuz, correlation just detect linear relationship between two variables)
There are some studies on which measure to use to correlate genes or patient samples, for instance:
Pablo A. Jaskowiak, Ricardo J. G. B. Campello, Ivan G. Costa Filho, "Proximity Measures for Clustering Gene Expression Microarray Data: A Validation Methodology and a Comparative Analysis," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 99, no. PrePrints, p. 1, , 2013
Note that Pearson only detects linear correlations, but if you use, for instance, Spearman, you can catch some non linear correlations as well.
Hope it helps, Cheers