The best CoMFA and CoMSIA models had a cross-validated coefficient q2 of 0.733 and 0.738, respectively, which showed high correlative and predictive abilities on both the test set and training set.
The gene expression data of both the test set (n = 32) and validation set 1 (n = 140) for the 359 genes identified by ACE-it is available at the Array Express database (www.ebi.ac.uk/aerep/login, accession number Array design: A-MEXP-749, Experiment data: E-TABM-270).
To minimize the influence of preanalytical biases on the classification approach, urine samples of patients with diabetic nephropathy collected in three distinct nephrology units were evenly distributed in both the training and the testing set.
There were single-EC entries and multiple-EC entries in both the training set and the testing set.
Moreover, the RT-qPCR results of several genes from both the training set and the testing set displayed good consistency with the results obtained from gene expression microarray, further indicating the accuracy and reliability of this technology (Fig. 4, 5).
It is important to note that in this and all experiments in this article, when we split the data set into training and testing sets for cross-validation, all of the regions and cells belonging to the same protein were in either the training or the testing set (i.e. the same protein cannot be in both the training the testing sets simultaneously).
We compared the quality of the tested EEM parameter set on both the test set and the extended test set.
These classification results were consistent in both the test set and the leave-one-out cross-validation.
Plots of observed versus predicted estimates at each decile for the validation set were produced, and the root mean square error (RMSE) was calculated for both the test set and validation set using the model generated from the test set.
Our test set has 16 compounds, which were randomly kept with bias given to both chemical and biological diversity in both the training set and the test set molecules, as shown in Tables 6.
