TABLE 1.
List of the genomic regions enrichment analysis tools mentioned in this study. We report each tool’s name, its statistical methods for the p-value calculation, its distinctive traits, its web URL, its year, its reference, a field stating whether it is available as web tool, and a field indicating the name of its standalone software package. FDR: false discovery rate. α: The LOLA web server is called LOLAweb (Nagraj et al., 2018). g:SCS is the statistical method for adjusted p-value calculation employed by g:Profiler g:GOSt by default (g:Profiler g:GOSt, 2022). The article by Raudvere et al. (2019) refers to the latest update of g:Profiler; its original release and previous updates were described in past studies (Reimand et al., 2007, 2011, 2016; Kolberg et al., 2020). The bottom table contains the lists of the supported organisms of the data for each tool.
| tool | Statistical methods | Distinctive traits | Web tool |
|---|---|---|---|
| BEHST | g:SCS of g:Profiler g:GOSt | Inclusion of long-range chromatin interactions | Yes |
| g:Profiler g:GOSt | g:SCS, Bonferroni correction | Fast execution, easy web interface and publication-ready visualization results | Yes |
| or Benjamini-Hochberg FDR | |||
| GREAT | Binomial and hypergeometric tests | Inclusion of distal genomic sites of binding events | Yes |
| LOLA | Fisher’s exact test with FDR correction |
Inclusion of transcription factors, histone modifications and DNase hypersensitivity annotations | Yes α |
| Poly-Enrich | Likelihood ratio test | Optimized for narrow genomic regions and accounting for the strength of binding sites’ peaks | Yes |
| ReactomePA | Hyper-geometric tests | Inclusion of molecular reactions and their pathways | No |
| tool | Web URL | References | softwarepackage |
| BEHST | https://behst.hoffmanlab.org | Chicco et al. (2019) | behst |
| g:Profiler g:GOSt | https://biit.cs.ut.ee/gprofiler/gost | Raudvere et al. (2019) | gprofiler2 |
| GREAT | http://great.stanford.edu | McLean et al. (2010) | rGREAT |
| LOLA | http://lola.computational-epigenetics.org | Sheffield and Bock (2016) | LOLA |
| Poly-Enrich | http://chip-enrich.med.umich.edu | Lee et al. (2020) | chipenrich |
| ReactomePA | http://bioconductor.org/packages/ReactomePA | Yu and He (2016) | ReactomePA |
| tool | Supported organisms | ||
| BEHST | Human | ||
| g:Profiler g:GOSt | Human and 757 other species | ||
| GREAT | Human, mouse | ||
| LOLA | Human, mouse | ||
| Poly-Enrich | Human, mouse, rat, D. melanogaster, D. zebrafish | ||
| ReactomePA | Human, celegans, fly, mouse, rat, yeast, zebrafish |