For this purpose, three microarray datasets were considered.
The recurrence of a co-expression link in all three microarray datasets was considered to increase the reliability of the inference.
HOCTARdb contains a substantial improvement over these preliminary data in terms of number of miRNAs analyzed (n = 290), number of expression datasets considered for the meta-analysis (217 microarray datasets), and number of putative target genes analyzed for each miRNA.
Microarray based gene expression dataset considered for the present study consists of a total of 39 samples of the same WT condition, with 3923 genes in each sample [ 37].
Besides, Asfar et al. [ 46] utilized the network modeling based on the Ingenuity Pathway Anallysis (IPA) Software which considers the microarray datasets at different time points to understand central synergy mechanisms for the combination of MI219 and oxaliplatin.
However, several important challenges need to be considered when integrating microarray datasets for meta-analysis.
29 microarray datasets that corresponded to 809 chips were considered in this study.
Considering PC1, the microarray datasets in which light conditions were altered (turquoise), comprise the closest cluster to the microwave dataset.
Furthermore, we propose that our model selection approach can be extended to discover DE and DV genes from microarray datasets with discrete class labels, by considering different quantile regression models.
Our analysis predicts 86% (31/36) of the connections as significant based on the microarray dataset; however, four are considered inhibitory interactions instead of activations, suggesting possible feedback loops between Pax6 and Ngn1, between Satb2, Ngn2 and Nhlh1, as well as between NeuroD and Etv1 (Additional file 6).
