This validates that the generated data set can be useful for predicting activity for novel compounds and for benchmarking studies.
They were originally designed for substructure search and typically show a low performance level for virtual screening, thus they are often used as baseline fingerprint for benchmarking studies.
In the framework of the TOXDROP STREP consortium (http://toxdrop.vitamib.com/) hsp22 and hsp70-EGFP DNA vector constructs were thus introduced in HepG2 cell line which is considered a suitable liver model for toxicity testing [10], [14], [15] and has been used for benchmarking studies [16].
It appears that all methods of network generation via some measure of correlation is able to return some measure of high impact result; suggesting the power of the correlation network and additionally a possible future need for benchmarking studies to investigate which measure is the most appropriate for which domain.
For benchmark study, we generated test datasets having several samples from relatively large datasets.
"Experimental setup" presents the experimental setup for benchmark studies, including general settings, performance indicators, and software platform.
The lessons learned through the development of clinical applications of microarrays, such as the need for benchmark studies such as those conducted by the MAQC project, should help accelerate the process of incorporating high-throughput sequencing into the clinic.
It is important to mention that the composition of the simulated data sets was explicitly intended as an example for a benchmarking study, not for modelling real ecological environments.
Different parameters are considered for the benchmarking study.
13321_2013_478_MOESM1_ESM.docx Additional file 1: Table S1: Physicochemical properties of amino acids residues, setup of all software tools used for the benchmarking study.
