QuIN: A Web Server for Querying and Visualizing Chromatin Interaction Networks
Fig 3
A breast cancer case study with QuIN.
(A) Workflow of the case study analysis. (1) Upload the DNASE-Seq and Interaction data into QuIN, constructing an MCF-7 interaction network where each node represents an open chromatin site. (2) Annotate the network with Non-Coding Variants (NCVs) in MCF-7 and cancer associated gene lists. (3) Perform target discovery between NCVs (source) and promoters and cancer gene lists (targets) and find all direct and indirect associations between NCVs and their gene targets. (B) A simplified network example showing the interactions between a node harboring an NCV (shown in purple) and known oncogenes (green), genes associated with poor prognosis in breast cancer (red), and tumor suppressor genes (blue). Nodes shown were selected based on their overlap with an annotation or if the node is necessary to connect the NCV to the annotated node. Width of the edges correspond to the relative number of paired end tags supporting the edge.