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:


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,

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


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:

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.

Get help

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