GenomicInteractions: An R/Bioconductor package for manipulating and investigating chromatin interaction data.

Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164 (Electronic) Linking ISSN: 14712164 NLM ISO Abbreviation: BMC Genomics Subsets: MEDLINE

Original Publication: London : BioMed Central, [2000-

Software*; Chromatin/*genetics ; Genomics/*methods; Animals ; Computer Graphics ; Databases, Genetic ; Humans ; K562 Cells ; Mice ; Molecular Sequence Annotation ; Thymocytes/metabolism

Background: Precise quantitative and spatiotemporal control of gene expression is necessary to ensure proper cellular differentiation and the maintenance of homeostasis. The relationship between gene expression and the spatial organisation of chromatin is highly complex, interdependent and not completely understood. The development of experimental techniques to interrogate both the higher-order structure of chromatin and the interactions between regulatory elements has recently lead to important insights on how gene expression is controlled. The ability to gain these and future insights is critically dependent on computational tools for the analysis and visualisation of data produced by these techniques.
Results and Conclusion: We have developed GenomicInteractions, a freely available R/Bioconductor package designed for processing, analysis and visualisation of data generated from various types of chromosome conformation capture experiments. The package allows the easy annotation and summarisation of large genome-wide datasets at both the level of individual interactions and sets of genomic features, and provides several different methods for interrogating and visualising this type of data. We demonstrate this package's utility by showing example analyses performed on interaction datasets generated using Hi-C and ChIA-PET.

Science. 2002 Feb 15;295(5558):1306-11. (PMID: 11847345)
Genes Dev. 2004 May 15;18(10):1119-30. (PMID: 15155579)
Cancer Cell. 2004 Jun;5(6):587-96. (PMID: 15193261)
Genome Biol. 2004;5(10):R80. (PMID: 15461798)
Genome Res. 2006 Oct;16(10):1299-309. (PMID: 16954542)
Nat Genet. 2006 Nov;38(11):1348-54. (PMID: 17033623)
Nature. 2008 Jun 12;453(7197):948-51. (PMID: 18463634)
Dev Cell. 2009 Jan;16(1):47-57. (PMID: 19097946)
Genome Biol. 2009;10(3):R25. (PMID: 19261174)
Science. 2009 Oct 9;326(5950):289-93. (PMID: 19815776)
Nature. 2009 Nov 5;462(7269):58-64. (PMID: 19890323)
Nat Genet. 2010 Jan;42(1):53-61. (PMID: 20010836)
J Neurosci. 2009 Dec 16;29(50):15923-32. (PMID: 20016108)
Genome Biol. 2010;11(2):R22. (PMID: 20181287)
Mol Cell. 2010 May 28;38(4):576-89. (PMID: 20513432)
Nucleic Acids Res. 2010 Nov;38(21):7410-21. (PMID: 20675721)
Blood. 2011 Mar 3;117(9):2681-90. (PMID: 21205929)
Nat Commun. 2011;2:269. (PMID: 21468021)
EMBO J. 2012 Feb 15;31(4):986-99. (PMID: 22157820)
Cell. 2012 Jan 20;148(1-2):84-98. (PMID: 22265404)
Cell Res. 2012 Mar;22(3):490-503. (PMID: 22270183)
Nature. 2012 Apr 11;485(7398):376-80. (PMID: 22495300)
Methods. 2012 Nov;58(3):268-76. (PMID: 22652625)
Cell. 2012 Jun 8;149(6):1233-44. (PMID: 22682246)
Nature. 2012 Aug 2;488(7409):116-20. (PMID: 22763441)
Bioinformatics. 2012 Nov 1;28(21):2843-4. (PMID: 22923296)
Nat Methods. 2012 Oct;9(10):999-1003. (PMID: 22941365)
Nature. 2012 Sep 6;489(7414):109-13. (PMID: 22955621)
Nat Immunol. 2012 Dec;13(12):1196-204. (PMID: 23064439)
Nucleic Acids Res. 2013 Jan;41(2):827-41. (PMID: 23221638)
World J Gastroenterol. 2012 Dec 21;18(47):6865-73. (PMID: 23322982)
Mol Cell. 2013 Mar 7;49(5):773-82. (PMID: 23473598)
Nat Rev Genet. 2013 Jun;14(6):390-403. (PMID: 23657480)
Nucleic Acids Res. 2013 Jul;41(13):e132. (PMID: 23671339)
Cell. 2013 Jun 6;153(6):1281-95. (PMID: 23706625)
Mol Cell. 2013 May 23;50(4):461-74. (PMID: 23706817)
Nucleic Acids Res. 2013 Aug;41(15):7185-99. (PMID: 23766291)
PLoS Comput Biol. 2013;9(8):e1003118. (PMID: 23950696)
Genome Res. 2013 Dec;23(12):2066-77. (PMID: 24002784)
Blood. 2013 Oct 31;122(18):3169-77. (PMID: 24047651)
Nature. 2013 Nov 14;503(7475):290-4. (PMID: 24141950)
Nature. 2013 Dec 12;504(7479):306-310. (PMID: 24213634)
Nucleic Acids Res. 2014 Jan;42(Database issue):D764-70. (PMID: 24270787)
Nat Genet. 2014 Feb;46(2):205-12. (PMID: 24413732)
Genome Res. 2014 Jun;24(6):999-1011. (PMID: 24501021)
Nat Rev Genet. 2014 Apr;15(4):272-86. (PMID: 24614317)
Mol Cancer Ther. 2014 May;13(5):1231-45. (PMID: 24659821)
Nature. 2014 Mar 27;507(7493):462-70. (PMID: 24670764)
Epigenetics Chromatin. 2014 Jun 16;7:10. (PMID: 25031611)
Bioinformatics. 2014 Nov 15;30(22):3268-9. (PMID: 25078398)
Nucleic Acids Res. 2014 Oct;42(18):e143. (PMID: 25114054)
PLoS One. 2014 Sep 10;9(9):e107497. (PMID: 25208325)
Genome Res. 2014 Dec;24(12):1905-17. (PMID: 25228660)
Bioinformatics. 2015 Oct 1;31(19):3092-8. (PMID: 26034063)
Bioinformatics. 2015 Oct 1;31(19):3085-91. (PMID: 26034064)
BMC Bioinformatics. 2015 Aug 19;16:258. (PMID: 26283514)
Genome Biol. 2015 Sep 02;16:183. (PMID: 26328929)
PLoS One. 2017 Apr 5;12(4):e0174744. (PMID: 28379994)
Int J Hematol. 1994 Apr;59(3):211-8. (PMID: 8011990)
Leukemia. 1994 Jul;8(7):1176-80. (PMID: 8035609)
Blood. 1997 Mar 15;89(6):2048-59. (PMID: 9058727)
Biochim Biophys Acta. 1997 Mar 20;1351(1-2):181-91. (PMID: 9116032)

MC_UP_1102/1 United Kingdom MRC_ Medical Research Council

0 (Chromatin)

Date Created: 20151119 Date Completed: 20160829 Latest Revision: 20220129

20250114

PMC4650858

10.1186/s12864-015-2140-x

26576536