## ANANSE: ANalysis Algorithm for Networks Specified by Enhancers

### What is ANANSE?

ANANSE is a computational approach to infer enhancer-based gene regulatory networks (GRNs) and to identify key transcription factors between two GRNs. You can use it to study transcription regulation during development and differentiation, or to generate a shortlist of transcription factors for trans-differentiation experiments.

ANANSE is written in Python and comes with a command-line interface that includes the following commands:

Command Function
ananse binding predict transcription factor binding profiles
ananse network infer a gene regulatory network
ananse influence infer key transcription factors between two networks
ananse plot plot influence results in a dotplot and optionally a GRN of the Top TFs
ananse view inspect the output of ananse binding

All functionality is also available through a Python API.

ANANSE is free and open source research software. If you find it useful please cite it:

Citation

Quan Xu, Georgios Georgiou, Siebren Frölich, Maarten van der Sande, Gert Jan C Veenstra, Huiqing Zhou, Simon J van Heeringen, ANANSE: an enhancer network-based computational approach for predicting key transcription factors in cell fate determination, Nucleic Acids Research, Volume 49, Issue 14, 20 August 2021, Pages 7966–7985, https://doi.org/10.1093/nar/gkab598

ANANSE can also be useful when using CAGE-seq data. If you used this tool with CAGE-seq data, please cite:

Citation

Heuts BMH, Arza-Apalategi S, Frölich S, Bergevoet SM, van den Oever SN, van Heeringen SJ, et al. Identification of transcription factors dictating blood cell development using a bidirectional transcription network-based computational framework. Scientific Reports 2022 12:1 [Internet]. 2022 Nov 4 [cited 2022 Dec 6];12(1):1–12. Available from: https://www.nature.com/articles/s41598-022-21148-w

### Getting started

• Install ANANSE on Linux or Mac, see the Installation page for details.
• Have a look at these simple examples to get a taste of what is possible.
• Check out the command-line reference to get going with your own data.