A comprehensive review and benchmark of differential analysis tools for Hi-C data.

IF 6.8 2区生物学 Q1 BIOCHEMICAL RESEARCH METHODS

Briefings in bioinformatics Pub Date : 2025-03-04 DOI:10.1093/bib/bbaf074

Elise Jorge, Sylvain Foissac, Pierre Neuvial, Matthias Zytnicki, Nathalie Vialaneix

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引用次数: 0

Abstract

Motivation: The 3D organization of the genome plays a crucial role in various biological processes. Hi-C technology is widely used to investigate chromosome structures by quantifying 3D proximity between genomic regions. While numerous computational tools exist for detecting differences in Hi-C data between conditions, a comprehensive review and benchmark comparing their effectiveness is lacking.

Results: This study offers a comprehensive review and benchmark of 10 generic tools for differential analysis of Hi-C matrices at the interaction count level. The benchmark assesses the statistical methods, usability, and performance (in terms of precision and power) of these tools, using both real and simulated Hi-C data. Results reveal a striking variability in performance among the tools, highlighting the substantial impact of preprocessing filters and the difficulty all tools encounter in effectively controlling the false discovery rate across varying resolutions and chromosome sizes.

Availability: The complete benchmark is available at https://forgemia.inra.fr/scales/replication-chrocodiff using processed data deposited at https://doi.org/10.57745/LR0W9R.

Contact: nathalie.vialaneix@inrae.fr.

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来源期刊

Briefings in bioinformatics 生物-生化研究方法

CiteScore

13.20

自引率

13.70%

发文量

549

审稿时长

6 months

期刊介绍： Briefings in Bioinformatics is an international journal serving as a platform for researchers and educators in the life sciences. It also appeals to mathematicians, statisticians, and computer scientists applying their expertise to biological challenges. The journal focuses on reviews tailored for users of databases and analytical tools in contemporary genetics, molecular and systems biology. It stands out by offering practical assistance and guidance to non-specialists in computerized methodologies. Covering a wide range from introductory concepts to specific protocols and analyses, the papers address bacterial, plant, fungal, animal, and human data. The journal's detailed subject areas include genetic studies of phenotypes and genotypes, mapping, DNA sequencing, expression profiling, gene expression studies, microarrays, alignment methods, protein profiles and HMMs, lipids, metabolic and signaling pathways, structure determination and function prediction, phylogenetic studies, and education and training.