TRNInfer

[…] izedthem into one of them. For instance, REVEAL also employs mutual information technique beyond Boolean network, so it can also belong to correlation-based methods. In (Table ), some methods such as TRNInfer [] and Inferelator [] reconstruct the four levels of transcriptional regulatory relationships, while others such as PCA-CMI [] and WGCNA [] generally identify gene regulations without directi […]

[…] ational programs were developed to integrate selected genes or proteins into the knowledge-based networks via the combination of genomics, proteomics and bioinformatics, such as GRNInfer , MDCinfer , TRNInfer , Samo , MNAligner , PTG , PRNA , NOA , differential dependency network (DDN) , WGCNA , SurvNet or DiME , each of them has its own advantages and strength on basis of scientific needs and in […]

[…] ince larger networks generally need more samples to gain inference accuracy comparable to smaller ones. Second, we apply DEI to datasets generated by GeneSim to infer the networks. Since the DEI tool TRNinfer does not accept large datasets (with many time points), here we use smaller datasets than the previous group of experiments with at most 75 time points. For each setup, experiments with diffe […]