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Normalization of Chromosome Contact Maps: Matrix Balancing and Visualization

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Hi-C Data Analysis

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2301))

Abstract

Over the last decade, genomic proximity ligation approaches have reshaped our vision of chromosomes 3D organizations, from bacteria nucleoids to larger eukaryotic genomes. The different protocols (3Cseq, Hi-C, TCC, MicroC [XL], Hi-CO, etc.) rely on common steps (chemical fixation digestion, ligation…) to detect pairs of genomic positions in close proximity. The most common way to represent these data is a matrix, or contact map, which allows visualizing the different chromatin structures (compartments, loops, etc.) that can be associated to other signals such as transcription, protein occupancy, etc. as well as, in some instances, to biological functions.

In this chapter we present and discuss the filtering of the events recovered in proximity ligation experiments as well as the application of the balancing normalization procedure on the resulting contact map. We also describe a computational tool for visualizing normalized contact data dubbed Scalogram.

The different processes described here are illustrated and supported by the laboratory custom-made scripts pooled into “hicstuff,” an open-access python package accessible on github (https://github.com/koszullab/hicstuff).

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Acknowledgments

All members of the Régulation Spatiale des Génomes laboratory are thanked for the daily exchanges and feedbacks.

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Authors and Affiliations

  1. Institut Pasteur, Unité Régulation Spatiale des Génomes, Paris, France

    Cyril Matthey-Doret, Lyam Baudry, Shogofa Mortaza, Pierrick Moreau, Romain Koszul & Axel Cournac

  2. Sorbonne Université, Collège Doctoral, Paris, France

    Cyril Matthey-Doret & Lyam Baudry

Authors
  1. Cyril Matthey-Doret
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  2. Lyam Baudry
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  3. Shogofa Mortaza
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  4. Pierrick Moreau
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  5. Romain Koszul
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  6. Axel Cournac
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Corresponding author

Correspondence to Axel Cournac .

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Editors and Affiliations

  1. Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy

    Silvio Bicciato

  2. IFOM, The FIRC Institute of Molecular Oncology, Milan, Italy

    Francesco Ferrari

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Matthey-Doret, C., Baudry, L., Mortaza, S., Moreau, P., Koszul, R., Cournac, A. (2022). Normalization of Chromosome Contact Maps: Matrix Balancing and Visualization. In: Bicciato, S., Ferrari, F. (eds) Hi-C Data Analysis. Methods in Molecular Biology, vol 2301. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1390-0_1

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  • DOI: https://doi.org/10.1007/978-1-0716-1390-0_1

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1389-4

  • Online ISBN: 978-1-0716-1390-0

  • eBook Packages: Springer Protocols

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