دورية أكاديمية
أعرض في EDS

Accelerating structure-function mapping using the ViVa webtool to mine natural variation.

التفاصيل البيبلوغرافية
العنوان: Accelerating structure-function mapping using the ViVa webtool to mine natural variation.
المؤلفون: Hamm MO; Department of Biology University of Washington Seattle Washington., Moss BL; Department of Biology Whitman College Walla Walla Washington., Leydon AR; Department of Biology University of Washington Seattle Washington., Gala HP; Department of Biology University of Washington Seattle Washington., Lanctot A; Department of Biology University of Washington Seattle Washington., Ramos R; Department of Biology University of Washington Seattle Washington., Klaeser H; Department of Biology Whitman College Walla Walla Washington., Lemmex AC; Department of Biology University of Washington Seattle Washington., Zahler ML; Department of Biology University of Washington Seattle Washington., Nemhauser JL; Department of Biology University of Washington Seattle Washington., Wright RC; Biological Systems Engineering Virginia Tech Blacksburg Virginia.
المصدر: Plant direct [Plant Direct] 2019 Jul 26; Vol. 3 (7), pp. e00147. Date of Electronic Publication: 2019 Jul 26 (Print Publication: 2019).
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: John Wiley & Sons Ltd Country of Publication: England NLM ID: 101716131 Publication Model: eCollection Cited Medium: Internet ISSN: 2475-4455 (Electronic) Linking ISSN: 24754455 NLM ISO Abbreviation: Plant Direct Subsets: PubMed not MEDLINE
أسماء مطبوعة: Original Publication: [Oxford, U.K.] : John Wiley & Sons Ltd., [2017]-
مستخلص: Thousands of sequenced genomes are now publicly available capturing a significant amount of natural variation within plant species; yet, much of these data remain inaccessible to researchers without significant bioinformatics experience. Here, we present a webtool called ViVa (Visualizing Variation) which aims to empower any researcher to take advantage of the amazing genetic resource collected in the Arabidopsis thaliana 1001 Genomes Project (http://1001genomes.org). ViVa facilitates data mining on the gene, gene family, or gene network level. To test the utility and accessibility of ViVa, we assembled a team with a range of expertise within biology and bioinformatics to analyze the natural variation within the well-studied nuclear auxin signaling pathway. Our analysis has provided further confirmation of existing knowledge and has also helped generate new hypotheses regarding this well-studied pathway. These results highlight how natural variation could be used to generate and test hypotheses about less-studied gene families and networks, especially when paired with biochemical and genetic characterization. ViVa is also readily extensible to databases of interspecific genetic variation in plants as well as other organisms, such as the 3,000 Rice Genomes Project ( http://snp-seek.irri.org/) and human genetic variation ( https://www.ncbi.nlm.nih.gov/clinvar/).
Competing Interests: The authors declare no conflict of interest associated with the work described in this manuscript.
References: Proc Natl Acad Sci U S A. 2007 Jul 17;104(29):12057-62. (PMID: 17626786)
Bioinformatics. 2015 Nov 15;31(22):3709-11. (PMID: 26227143)
Proc Natl Acad Sci U S A. 2009 Dec 29;106(52):22540-5. (PMID: 20018756)
Plant Direct. 2019 Jul 26;3(7):e00147. (PMID: 31372596)
Nat Commun. 2017 Jun 07;8:15706. (PMID: 28589936)
Proc Natl Acad Sci U S A. 2014 Apr 8;111(14):5427-32. (PMID: 24706860)
Plant Physiol. 2004 Jul;135(3):1738-52. (PMID: 15247399)
Am J Hum Genet. 2017 Sep 7;101(3):315-325. (PMID: 28886340)
Nat Genet. 2013 Aug;45(8):884-890. (PMID: 23793030)
G3 (Bethesda). 2016 May 03;6(5):1383-90. (PMID: 26976444)
Plant Cell. 1997 Nov;9(11):1963-71. (PMID: 9401121)
Nature. 2010 Jun 3;465(7298):627-31. (PMID: 20336072)
Curr Opin Plant Biol. 2005 Apr;8(2):122-8. (PMID: 15752990)
Plant Cell. 2017 Aug;29(8):1806-1821. (PMID: 28808136)
Nature. 2000 Dec 14;408(6814):796-815. (PMID: 11130711)
Proc Natl Acad Sci U S A. 1979 Oct;76(10):5269-73. (PMID: 291943)
Methods Mol Biol. 2012;819:29-42. (PMID: 22183528)
Nat Protoc. 2016 Oct;11(10):1782-7. (PMID: 27583640)
Curr Opin Plant Biol. 2007 Oct;10(5):453-60. (PMID: 17900969)
Cell. 2014 Jan 30;156(3):577-89. (PMID: 24485461)
Nat Commun. 2014 Apr 07;5:3617. (PMID: 24710426)
Plant Cell. 2003 Feb;15(2):533-43. (PMID: 12566590)
Development. 2005 Oct;132(20):4563-74. (PMID: 16176952)
Genetics. 2017 Oct;207(2):583-591. (PMID: 28760746)
Plant Physiol. 2012 Sep;160(1):135-42. (PMID: 22843664)
Elife. 2015 Oct 13;4:e09269. (PMID: 26460543)
Nature. 2018 May;557(7703):43-49. (PMID: 29695866)
Bioinformatics. 2012 May 15;28(10):1303-6. (PMID: 22451271)
Annu Rev Plant Biol. 2019 Apr 29;70:667-697. (PMID: 30835493)
Sci Adv. 2015 Jul 24;1(6):e1500107. (PMID: 26601214)
Elife. 2018 Mar 27;7:. (PMID: 29580381)
Nucleic Acids Res. 2017 Jun 20;45(11):e102. (PMID: 28335006)
Nucleic Acids Res. 2013 Aug;41(15):7420-8. (PMID: 23754851)
BMC Bioinformatics. 2015 Oct 06;16:322. (PMID: 26445311)
Nat Chem Biol. 2012 Apr 01;8(5):477-85. (PMID: 22466420)
Nat Biotechnol. 2015 Apr;33(4):408-14. (PMID: 25643055)
Nature. 2001 Nov 15;414(6861):271-6. (PMID: 11713520)
Trends Genet. 2014 Nov;30(11):504-12. (PMID: 25182195)
Nat Commun. 2018 Feb 7;9(1):541. (PMID: 29416032)
PLoS Genet. 2015 May 28;11(5):e1005207. (PMID: 26020649)
Sci Adv. 2017 Jun 02;3(6):e1601217. (PMID: 28630893)
Front Zool. 2010 Mar 31;7:10. (PMID: 20356385)
PLoS Genet. 2016 Sep 12;12(9):e1006301. (PMID: 27618443)
Plant Sci. 2012 Jul;190:82-8. (PMID: 22608522)
Nat Plants. 2015 Mar;1(3):. (PMID: 26236497)
Plant Cell. 2004 Feb;16(2):533-43. (PMID: 14742873)
Plant J. 2017 Feb;89(4):789-804. (PMID: 27862469)
PLoS Genet. 2015 Feb 11;11(2):e1004918. (PMID: 25671604)
PLoS Biol. 2005 Jul;3(7):e196. (PMID: 15907155)
Bioinformatics. 2003 Aug 12;19(12):1572-4. (PMID: 12912839)
PLoS One. 2008 Mar 19;3(3):e1838. (PMID: 18350173)
Development. 2015 Mar 1;142(5):905-9. (PMID: 25633353)
Proc Natl Acad Sci U S A. 2017 Jul 25;114(30):8107-8112. (PMID: 28698367)
Proc Natl Acad Sci U S A. 2016 Oct 4;113(40):11354-11359. (PMID: 27647902)
Proc Natl Acad Sci U S A. 2016 Jun 7;113(23):6562-7. (PMID: 27217573)
Proc Natl Acad Sci U S A. 2000 Mar 28;97(7):3319-23. (PMID: 10725351)
Genome Biol. 2009;10(5):107. (PMID: 19519932)
Science. 1977 Jun 10;196(4295):1161-6. (PMID: 860134)
Curr Opin Plant Biol. 2016 Apr;30:101-7. (PMID: 26950251)
Dev Cell. 2005 Jul;9(1):109-19. (PMID: 15992545)
Mol Biol Evol. 2017 Apr 1;35(4):837-854. (PMID: 29272536)
Plant J. 2013 Mar;73(6):941-51. (PMID: 23216999)
Science. 2007 Jul 20;317(5836):338-42. (PMID: 17641193)
Plant Cell. 2005 Dec;17(12):3282-300. (PMID: 16284307)
Proc Natl Acad Sci U S A. 2001 Sep 25;98(20):11795-800. (PMID: 11573012)
Genetics. 2017 Aug;206(4):2105-2117. (PMID: 28550014)
Science. 2006 Jun 9;312(5779):1520-3. (PMID: 16763149)
Nature. 2007 Apr 5;446(7136):640-5. (PMID: 17410169)
Science. 2008 Mar 7;319(5868):1384-6. (PMID: 18258861)
BMC Bioinformatics. 2018 Aug 14;19(1):300. (PMID: 30107777)
Plant Cell. 2010 Jul;22(7):2184-200. (PMID: 20622145)
Dev Cell. 2012 Jan 17;22(1):211-22. (PMID: 22264733)
Nat Biotechnol. 2012 May 27;30(6):543-8. (PMID: 22634563)
Biochim Biophys Acta. 2011 Oct;1810(10):959-66. (PMID: 21320572)
معلومات مُعتمدة: R01 GM107084 United States GM NIGMS NIH HHS
فهرسة مساهمة: Keywords: Arabidopsis thaliana; accessibility; genome diversity; genotype‐phenotype; natural variation; structure‐function
تواريخ الأحداث: Date Created: 20190803 Latest Revision: 20231013
رمز التحديث: 20231215
مُعرف محوري في PubMed: PMC6658840
DOI: 10.1002/pld3.147
PMID: 31372596
قاعدة البيانات: MEDLINE
الوصف
تدمد:2475-4455
DOI:10.1002/pld3.147