Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

. 2020 Feb;30(2):227–238. doi: 10.1101/gr.250316.119

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

© 2020 Tian et al.; Published by Cold Spring Harbor Laboratory Press

This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.

PMC Copyright notice

Figure 1. — Workflow of our MOCHI algorithm and output examples of HIMs. The network has both gene–gene spatial proximity and TF–gene regulation relationships. (A) A four-node motif M represents the smallest HIM. Here a directed interaction represents a TF–gene regulation relationship, and an undirected interaction represents that the two genes are spatially more proximal to each other than expected. (B) Given a heterogeneous network G, we find HIMs by minimizing the motif conductance (see Equation 2). (C) We compute the subgraph adjacency matrix W_M, with [W_M]_ij being the number of occurrences of M that have both nodes i and j. (D) The weighted network G_M is defined from adjacency matrix W_M. (E) Spectral clustering will find clusters in G_M. We recursively apply the method to find multiple HIMs and overlapping HIMs. (F,G) Two HIMs as examples in GM12878. (H) Example of two overlapping HIMs in GM12878 sharing seven TFs (the group with pink nodes in the middle). TFs in orange and pink nodes form one HIM with their target genes (bottom left). TFs in pink and blue nodes form another HIM with their target genes (bottom right). Note that the directed interactions from TFs to their target genes are bundled.