ChromNetMotif: a Python tool to extract chromatin-sate marked motifs in a chromatin interaction network

Abstract

Motivation: Analysis of network motifs is crucial to studying the robustness, stability, and functions of complex networks. Genome organization can be viewed as a biological network that consists of interactions between different chromatin regions. These interacting regions are also marked by epigenetic or chromatin states which can contribute to the overall organization of the chromatin and proper genome function. Therefore, it is crucial to integrate the chromatin states of the nodes when performing motif analysis in chromatin interaction networks. Even though there has been increasing production of chromatin interaction and genome-wide epigenetic modification data, there is a lack of publicly available tools to extract chromatin state-marked motifs from genome organization data.

Results: We develop a Python tool, ChromNetMotif, offering an easy-to-use command line interface to extract chromatin-state-marked motifs from a chromatin interaction network. The tool can extract occurrences, frequencies, and statistical enrichment of the chromatin state-marked motifs. Visualization files are also generated which allow the user to interpret the motifs easily. ChromNetMotif also allows the user to leverage the features of a multicore processor environment to reduce computation time for larger networks. The output files generated can be used to perform further downstream analysis. ChromNetMotif aims to serve as an important tool to comprehend the interplay between epigenetics and genome organization.

Availability and implementation: ChromNetMotif is available at https://github.com/lncRNAAddict/ChromNetworkMotif.

Figure 1.

Chromatin state-marked network motifs. (a) An example chromatin state-marked chromatin interaction network file. Each row is an interaction with participating regions indicated in the first and second columns and their chromatin states in the third and fourth columns. (b) Possible network motifs of size 3 and (c) size 4 without considering the chromatin states of the nodes. Seven different possible chromatin state-marked Type I motif (size = 3) are shown in (d). Four possible chromatin states are considered. Participating nodes: A, B, and C can be marked as one of the four example chromatin states: “active,” “repressed,” “poised,” and “weak.”

Figure 2.

Chromatin state-marked motifs. The figure shows visualizations of examples of different chromatin state-marked motifs (of sizes 3 and 4) in the HeLa cell line. There are four possible chromatin states (“active,” “weak,” “poised,” and “repressed”) indicated by color codes. For example, in Type I of the motif of size 3, there are nine enriched different chromatin state-marked motifs as shown by the heatmap. In Type II of the motif of size 3, there are only two enriched different chromatin state-marked motifs as shown by the heatmap. The heatmaps for the motifs of size 4 are also shown.