HiCdat: A fast and easy-to-use Hi-C data analysis tool

BMC Bioinformatics

Volumn 16, Issue 1, 2015, Pages

  Schmid, Marc W ^a,b   Grob, Stefan ^a,b   Grossniklaus, Ueli ^a,b  

^a UNIVERSITY OF ZURICH   (Switzerland)

^b Botanical Institute of the University of Basel   (Switzerland)

Author keywords

Chromosome Conformation Capture (3C); Correlation to (epi )genome; Data analysis; Hi C; Nuclear architecture; Sample comparison; Structural domains

Indexed keywords

CHROMOSOMES; DATA REDUCTION; GENES; GRAPHICAL USER INTERFACES; INFORMATION ANALYSIS; USER INTERFACES;

CHROMOSOME CONFORMATION CAPTURE (3C); COMPARATIVE STUDIES; DATA PREPROCESSING; GENETIC BACKGROUNDS; HI-C; NUCLEAR ARCHITECTURE; STRUCTURAL DOMAINS; STRUCTURAL FEATURE;

DATA HANDLING;

RNA;

CHROMOSOME; GENETICS; GENOMICS; HUMAN; PROCEDURES; SOFTWARE; STATISTICS;

CHROMOSOMES; GENOMICS; HUMANS; RNA; SOFTWARE; STATISTICS AS TOPIC;

EID: 84940472481     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/s12859-015-0678-x     Document Type: Article

References (30)

1. Dekker J, Marti-Renom MA, Mirny LA. Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. Nat Rev Genet. 2013; 14:390-403.
2. Duan Z, Andronescu M, Schutz K, McIlwain S, Kim YJ, Lee C, et al. A three-dimensional model of the yeast genome. Nature. 2010; 465:363-7.
3. Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012; 485:376-80.
4. Moissiard G, Cokus SJ, Cary J, Feng S, Billi AC, Stroud H, et al. MORC family ATPases required for heterochromatin condensation and gene silencing. Science. 2012; 336(6087):1448-51.
5. Grob S, Schmid MW, Grossniklaus U. Hi-C analysis in Arabidopsis identifies the KNOT, a structure with similarities to the flamenco locus of Drosophila. Mol Cell. 2014; 55(5):678-93.
6. Feng S, Cokus SJ, Schubert V, Zhai J, Pellegrini M, Jacobsen SE. Genome-wide Hi-C analyses in wild-type and mutants reveal high-resolution chromatin interactions in Arabidopsis. Mol Cell. 2014; 55(5):694-707.
7. HiCUP. http://www.bioinformatics.babraham.ac.uk/projects/hicup/ .
8. Phanstiel DH, Boyle AP, Araya CL, Snyder MP. Sushi.r: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures. Bioinformatics. 2014; 30(19):2808-10.
9. Servant N, Lajoie BR, Nora EP, Giorgetti L, Chen C, Heard E, et al. HiTC : exploration of high-throughput 'C' experiments. Bioinformatics. 2012; 28(21):2843-4.
10. Lévy-Leduc C, Delattre M, Mary-Huard T, Robin S. Two-dimensional segmentation for analyzing Hi-C data. Bioinformatics. 2014; 30:386-92.
11. Shavit Y, Lio P. Combining a wavelet change point and the Bayes factor for analysing chromosomal interaction data. Mol Biosyst. 2014; 10(6):1576-85.
12. Yaffe E, Tanay A. Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture. Nat Genet. 2011; 43(11):1059-65.
13. Hu M, Deng K, Selvaraj S, Qin ZS, Ren B, Liu JS. HiCNorm: removing biases in Hi-C data via Poisson regression. Bioinformatics. 2012; 28(23):3131-3.
14. Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell. 2010; 38(4):576-89.
15. Imakaev M, Fudenberg G, McCord RP, Naumova N, Goloborodko A, Lajoie BR, et al. Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nat Methods. 2012; 9(10):999-1003.
16. Paulsen J, Sandve GK, Gundersen S, Lien TG, Trengereid K, Hovig E. HiBrowse: multi-purpose statistical analysis of genome-wide chromatin 3D organization. Bioinformatics. 2014; 30(11):1620-22.
17. R-Project. http://www.r-project.org/ .
18. Liao Y, Smyth GK, Shi W. The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote. Nucleic Acids Res. 2013; 41(10):108.
19. Jin F, Li Y, Dixon JR, Selvaraj S, Ye Z, Lee AY, et al. A high-resolution map of the three-dimensional chromatin interactome in human cells. Nature. 2013; 503:290-4.
20. Liebermann-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009; 326(5950):289-93.
21. Zhang Y, McCord RP, Ho YJ, Lajoie BR, Hildebrand DG, Simon AC, et al. Spatial organization of the mouse genome and its role in recurrent chromosomal translocations. Cell. 2012; 148(5):908-21.
22. Grob S, Schmid MW, Grossniklaus U. Characterization of chromosomal architecture in Arabidopsis by chromosome conformation capture. Genome Biol. 2013; 14:129.
23. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009; 10:25.
24. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012; 9(4):357-9.
25. Kasschau KD, Fahlgren N, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, et al. Genome-wide profiling and analysis of Arabidopsis siRNAs. PLoS Biol. 2007; 5(3):57.
26. Gregory BD, O'Malley RC, Lister R, Urich MA, Tonti-Filippini J, Chen H, et al. A link between RNA metabolism and silencing affecting Arabidopsis development. Dev Cell. 2008; 14(6):854-66.
27. Lister R, O'Malley RC, Tonti-Filippini J, Gregory BG, Berry CC, Millar AH, et al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell. 2008; 133(3):523-36.
28. Jacob Y, Stroud H, LeBlanc C, Feng S, Zhuo L, Caro E, et al. Regulation of heterochromatic DNA replication by histone H3 lysine 27 methyltransferases. Nature. 2010; 466:987-1.
29. Luo C, Sidote DJ, Zhang Y, Kerstetter RA, Michael TP, Lam E. Integrative analysis of chromatin states in Arabidopsis identified potential regulatory mechanisms for natural antisense transcript production. Plant J. 2013; 73:77-90.
30. Stroud H, Greenberg MVC, Feng S, Bernatavichute YV, Jacobsen SE. Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome. Cell. 2013; 152(1-2):352-64.