Computer vision for pattern detection in chromosome contact maps.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
16 11 2020
16 11 2020
Historique:
received:
12
06
2020
accepted:
16
10
2020
entrez:
17
11
2020
pubmed:
18
11
2020
medline:
26
11
2020
Statut:
epublish
Résumé
Chromosomes of all species studied so far display a variety of higher-order organisational features, such as self-interacting domains or loops. These structures, which are often associated to biological functions, form distinct, visible patterns on genome-wide contact maps generated by chromosome conformation capture approaches such as Hi-C. Here we present Chromosight, an algorithm inspired from computer vision that can detect patterns in contact maps. Chromosight has greater sensitivity than existing methods on synthetic simulated data, while being faster and applicable to any type of genomes, including bacteria, viruses, yeasts and mammals. Our method does not require any prior training dataset and works well with default parameters on data generated with various protocols.
Identifiants
pubmed: 33199682
doi: 10.1038/s41467-020-19562-7
pii: 10.1038/s41467-020-19562-7
pmc: PMC7670471
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
5795Références
FEBS Lett. 2015 Oct 7;589(20 Pt A):2975-86
pubmed: 26096785
Cell. 2009 May 15;137(4):685-96
pubmed: 19450516
Nat Cell Biol. 2019 Nov;21(11):1393-1402
pubmed: 31685986
Mol Cell. 2015 Aug 20;59(4):588-602
pubmed: 26295962
Nature. 2012 Apr 11;485(7398):381-5
pubmed: 22495304
PLoS Comput Biol. 2019 Aug 21;15(8):e1007273
pubmed: 31433799
Elife. 2014 Dec 17;3:e03318
pubmed: 25517076
Science. 2017 Feb 3;355(6324):524-527
pubmed: 28154080
Science. 2009 Oct 9;326(5950):289-93
pubmed: 19815776
Nat Methods. 2017 Jul;14(7):679-685
pubmed: 28604721
BMC Bioinformatics. 2015 Aug 19;16:258
pubmed: 26283514
Sci Adv. 2017 Feb 17;3(2):e1602105
pubmed: 28232956
Cell. 2018 Feb 8;172(4):771-783.e18
pubmed: 29358050
Bioinformatics. 2020 Feb 1;36(3):666-675
pubmed: 31504161
Nature. 2017 Sep 13;549(7671):219-226
pubmed: 28905911
Science. 2013 Nov 8;342(6159):731-4
pubmed: 24158908
Curr Opin Cell Biol. 2020 Jun;64:124-138
pubmed: 32534241
Cell. 2018 Sep 6;174(6):1522-1536.e22
pubmed: 30146161
BMC Genomics. 2012 Aug 30;13:436
pubmed: 22935139
Nat Commun. 2018 Jan 15;9(1):189
pubmed: 29335486
Cell. 2014 Dec 18;159(7):1665-80
pubmed: 25497547
Science. 2017 Apr 7;356(6333):92-95
pubmed: 28336562
Cell Syst. 2016 Jul;3(1):95-8
pubmed: 27467249
PLoS Genet. 2016 Sep 23;12(9):e1006317
pubmed: 27662467
Cell. 2018 Jul 26;174(3):744-757.e24
pubmed: 29887377
Cell Host Microbe. 2012 Aug 16;12(2):233-45
pubmed: 22901543
Nat Methods. 2016 Nov;13(11):919-922
pubmed: 27643841
Cell Rep. 2016 May 31;15(9):2038-49
pubmed: 27210764
Bioinformatics. 2014 Aug 1;30(15):2105-13
pubmed: 24711652
Nat Struct Mol Biol. 2017 Nov;24(11):965-976
pubmed: 28991264
Nat Protoc. 2020 Mar;15(3):991-1012
pubmed: 31980751
Nat Struct Mol Biol. 2019 Oct;26(10):970-979
pubmed: 31582854
FEBS Lett. 2015 Oct 7;589(20 Pt A):2966-74
pubmed: 25935414
Nucleic Acids Res. 2017 Apr 7;45(6):2994-3005
pubmed: 28334773
Annu Rev Genet. 2009;43:525-58
pubmed: 19886810
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D493-6
pubmed: 14681465
Nat Protoc. 2017 May;12(5):899-915
pubmed: 28358394
Genome Biol. 2020 Jun 18;21(1):148
pubmed: 32552806
Proc Natl Acad Sci U S A. 2019 Oct 8;116(41):20489-20499
pubmed: 31548377
Mol Cell. 2010 May 28;38(4):576-89
pubmed: 20513432
Nature. 2009 Nov 5;462(7269):58-64
pubmed: 19890323
Nucleic Acids Res. 2015 Nov 16;43(20):e132
pubmed: 26130708
Bioinformatics. 2020 Jan 1;36(1):311-316
pubmed: 31290943
Nature. 2012 Apr 11;485(7398):376-80
pubmed: 22495300
Nat Rev Immunol. 2003 Oct;3(10):801-12
pubmed: 14523386
Bioinformatics. 2014 Sep 1;30(17):i386-92
pubmed: 25161224
Science. 2002 Feb 15;295(5558):1306-11
pubmed: 11847345
Cell. 2015 Dec 17;163(7):1611-27
pubmed: 26686651
Mol Syst Biol. 2018 Jul 16;14(7):e8293
pubmed: 30012718
Mol Cell. 2020 Mar 19;77(6):1279-1293.e4
pubmed: 32032532
Mol Cell. 2020 May 7;78(3):554-565.e7
pubmed: 32213324
Cell. 2017 Oct 19;171(3):557-572.e24
pubmed: 29053968
Mol Cell. 2011 Oct 21;44(2):252-64
pubmed: 22017872
Nat Methods. 2012 Oct;9(10):999-1003
pubmed: 22941365
Science. 2013 Nov 22;342(6161):948-53
pubmed: 24200812