Hi-C contact map

Introduction

This extension provides nodes that allow the processing and depicting of data from high-throughput chromosome conformation capture (Hi-C). By constructing spatial proximity maps (or contact maps) of a genome with Hi-C the structure of chromosomes can be explored.

So far, this extension contains a 'Hi-C contact map'-node to create and visually explore contact maps. The example workflow below demonstrates the analysis of Hi-C data by creating a Hi-C contact map.

Installation instructions

The Hi-C extension is still in a experimental state and, hence, is only available via the nightly build update site. This nightly build update site (http://tech.knime.org/update/community-contributions/trunk) needs to be added manually to the list of Available Update Sites (see here for instructions). Then the extension will be available for installation and the newly installed nodes will appear in KNIME in the "Hi-C" category of the community nodes.

Example workflow

The attached example workflow below demonstrates the analysis of Hi-C data by preparing the data and finally creating a Hi-C contact map. Further documentation can be found within the workflow. The example workflow requires the installation of the following extensions: 'KNIME Math Expression (JEP)', 'KNIME Virtual Nodes' and 'KNIME Nodes to create KNIME Quick Forms'. Optionally for an alternative contact map visualization the extensions 'KNIME JFreeChart' and 'KNIME R Statistics Integration' might be of interest, too.

Selected references

[1] Lieberman-Aiden, E.; van Berkum, N. L.; Williams, L.; Imakaev, M.; Ragoczy, T.; Telling, A.; Amit, I.; Lajoie, B. R.; Sabo, P. J.; Dorschner, M. O.; Sandstrom, R.; Bernstein, B.; Bender, M. A.; Groudine, M.; Gnirke, A.; Stamatoyannopoulos, J.; Mirny, L. A.; Lander, E. S. & Dekker, J. Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome Science, 2009, 326, 289-293

[2] Imakaev, M.; Fudenberg, G.; McCord, R. P.; Naumova, N.; Goloborodko, A.; Lajoie, B. R.; Dekker, J. & Mirny, L. A. Iterative correction of Hi-C data reveals hallmarks of chromosome organization Nat Meth, Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved., 2012, 9, 999-1003

[3]  Jon-Matthew Belton, Rachel Patton McCord, Johan Harmen Gibcus, Natalia Naumova, Ye Zhan, Job Dekker, Hi–C: A comprehensive technique to capture the conformation of genomes, Methods, Volume 58, Issue 3, November 2012, Pages 268-276

[3] Le, T. B. K.; Imakaev, M. V.; Mirny, L. A. & Laub, M. T. High-Resolution Mapping of the Spatial Organization of a Bacterial Chromosome Science, 2013, 342, 731-734

 

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