Graphical Visualization Of Motif Words From Chip-Seq As A Network Cloud

Question

[Biostar User]

Starting from a few tens of thousands of ChIP-seq peaks that contain transcription factor recognition sequences identifiable with a motif search program, how can one represent each of these words as a network cloud where every node would represent every word found in a peak, the size of the nodes would represent the number of times the word is found, and the edges represent the DNA sequence distance (mismatches) between two words. Is there any software to produce that network?

Word length I am expecting would be typical of TFs as found on Jaspar, for example, say, 10-mers.

[Ying W]

how long would your words be? typically you generate these motifs either de novo by comparing ~100mers under every peak summit or use a pre-existing db of motifs (ie jasper). the motifs themselves are not very long <10bp and in the db of motifs stored as position weight matricies (pwm) so then would your edges be a measure of differences between these pwm? or diff between 100mers?

Answer 1

[Malachi Griffith]

Perhaps Cytoscape could be used to generate such visualizations...

Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization. Cytoscape core distribution provides a basic set of features for data integration, analysis, and visualization. Additional features are available as Apps (formerly called Plugins). Apps are available for network and molecular profiling analyses, new layouts, additional file format support, scripting, and connection with databases. They may be developed by anyone using the Cytoscape open API based on Java™ technology and App community development is encouraged. Most of the Apps are freely available from Cytoscape App Store.