Table 3.
User-friendly computational tools for inferring gene regulatory networks.
| Tool | Description | Platform | Type of data | Reference/URL | |
|---|---|---|---|---|---|
| Expression | Promoter | ||||
| ARACNe | Creates a network based on Mutual Information | Multi | ✓ | http://apps.cytoscape.org/apps/aracne; (Floratos et al., 2010) | |
| CyGenexpi | A toolset for identifying regulons and validating gene regulatory networks using time-course expression data | Multi | ✓ | https://apps.cytoscape.org/apps/cygenexpi; (Modrák and Vohradský, 2018) | |
| CyNetworkBMA | Infers gene regulatory networks from expression measurements using Bayesian Model Averaging | Multi | ✓ | https://apps.cytoscape.org/apps/cynetworkbma; (Fronczuk et al., 2015) | |
| GRNCOP2 | Model-free combinatorial optimization algorithm to infer time-delayed gene regulatory networks from genome-wide time series datasets | Multi | ✓ | https://apps.cytoscape.org/apps/grncop2; (Gallo et al., 2011) | |
| iRegulon | Allows identification of regulons using motif and track discovery in an existing network | Multi | ✓ | https://apps.cytoscape.org/apps/iregulon; (Janky et al., 2014) | |
| NetworkAnalyst | Allows establishing TF-target genes and miRNAs-target genes associations. | Webserver | ✓ | http://www.networkanalyst.ca; (Zhou et al., 2019) | |
| TRRUST | TFs and target genes interactions, and TFs cis-regulatory elements | Webserver | ✓ | ✓ | https://www.grnpedia.org/trrust/Network_search_form.php; (Han et al., 2018) |
| RegNetwork | Genic regulations by TFs and microRNAs | Webserver | ✓ | http://www.regnetworkweb.org/search.jsp; (Liu et al., 2015) | |
| ORegAnno | Regulatory regions, transcription factor binding sites, etc. | Webserver | ✓ | http://www.oreganno.org/; (Lesurf et al., 2016) | |
| rSNPBase | Harbors curated information on regulatory SNPs | Webserver | ✓ | http://rsnp.psych.ac.cn/; (Guo and Wang, 2018) | |
| MEME | Sequence analysis tools for motifs discovery | Webserver | ✓ | http://meme-suite.org/ (Bailey et al., 2009) | |