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. 2017 Nov 16;18(1):495.
doi: 10.1186/s12859-017-1932-1.

ANAT 2.0: reconstructing functional protein subnetworks

Yomtov Almozlino  1 , Nir Atias  1 , Dana Silverbush  1 , Roded Sharan  2
Affiliations

ANAT 2.0: reconstructing functional protein subnetworks

Yomtov Almozlino et al. BMC Bioinformatics. .

Abstract

Background: ANAT is a graphical, Cytoscape-based tool for the inference of protein networks that underlie a process of interest. The ANAT tool allows the user to perform network reconstruction under several scenarios in a number of organisms including yeast and human.

Results: Here we report on a new version of the tool, ANAT 2.0, which introduces substantial code and database updates as well as several new network reconstruction algorithms that greatly extend the applicability of the tool to biological data sets.

Conclusions: ANAT 2.0 is an up-to-date network reconstruction tool that addresses several reconstruction challenges across multiple species.

Keywords: Cytoscape plugin; Network inference; Protein-protein interaction network; Subnetwork reconstruction.

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Competing interests

The authors declare that they have no competing interests.

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Figures

Fig. 1
Fig. 1
a The anchored network parameter dialog box. iPoint can be selected as an alternative “sub-algorithm” in the “Advanced” section, while anchor prediction and transcription factor prediction are available as additional options. b The network solution (left panel) and the network solution with “predict transcription factors” (right panel). The “predict transcription factors” reveals key transcription factors on a breast cancer dataset such as HIF1α and PARP1. The network shows the predicted pathways connecting the anchors (green) via connecting proteins (pink) and predicted transcription factors (salmon) to the terminals (red). Undirected edges correspond to PPIs and directed edges depict PDIs
See this image and copyright information in PMC

References

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