Matasci, Naim ORCID: 0000-0003-4416-048X, Hung, Ling-Hong, Yan, Zhixiang, Carpenter, Eric J., Wickett, Norman J., Mirarab, Siavash ORCID: 0000-0001-5410-1518, Warnow, Tandy, Ayyampalayam, Saravanaraj, Barker, Michael, Burleigh, J. Gordon, Gitzendanner, Matthew A., Wafula, Eric, Der, Joshua P., dePamphilis, Claude W., Roure, Beatrice, Philippe, Herve, Ruhfel, Brad R., Miles, Nicholas W., Graham, Sean W., Mathews, Sarah ORCID: 0000-0002-5518-7541, Surek, Barbara, Melkonian, Michael, Soltis, Douglas E., Soltis, Pamela S., Rothfels, Carl, Pokorny, Lisa ORCID: 0000-0002-2478-8555, Shaw, Jonathan A., DeGironimo, Lisa, Stevenson, Dennis W., Villarreal, Juan Carlos, Chen, Tao, Kutchan, Toni M., Rolf, Megan, Baucom, Regina S., Deyholos, Michael K., Samudrala, Ram, Tian, Zhijian, Wu, Xiaolei, Sun, Xiao, Zhang, Yong, Wang, Jun ORCID: 0000-0002-8540-8931, Leebens-Mack, Jim and Wong, Gane Ka-Shu (2014). Data access for the 1,000 Plants (1KP) project. GigaScience, 3. LONDON: BIOMED CENTRAL LTD. ISSN 2047-217X

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Abstract

The 1,000 plants (1KP) project is an international multi-disciplinary consortium that has generated transcriptome data from over 1,000 plant species, with exemplars for all of the major lineages across the Viridiplantae (green plants) clade. Here, we describe how to access the data used in a phylogenomics analysis of the first 85 species, and how to visualize our gene and species trees. Users can develop computational pipelines to analyse these data, in conjunction with data of their own that they can upload. Computationally estimated protein-protein interactions and biochemical pathways can be visualized at another site. Finally, we comment on our future plans and how they fit within this scalable system for the dissemination, visualization, and analysis of large multi-species data sets.

Item Type: Journal Article
Creators:
CreatorsEmailORCIDORCID Put Code
Matasci, NaimUNSPECIFIEDorcid.org/0000-0003-4416-048XUNSPECIFIED
Hung, Ling-HongUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Yan, ZhixiangUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Carpenter, Eric J.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Wickett, Norman J.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Mirarab, SiavashUNSPECIFIEDorcid.org/0000-0001-5410-1518UNSPECIFIED
Warnow, TandyUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Ayyampalayam, SaravanarajUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Barker, MichaelUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Burleigh, J. GordonUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Gitzendanner, Matthew A.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Wafula, EricUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Der, Joshua P.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
dePamphilis, Claude W.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Roure, BeatriceUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Philippe, HerveUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Ruhfel, Brad R.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Miles, Nicholas W.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Graham, Sean W.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Mathews, SarahUNSPECIFIEDorcid.org/0000-0002-5518-7541UNSPECIFIED
Surek, BarbaraUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Melkonian, MichaelUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Soltis, Douglas E.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Soltis, Pamela S.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Rothfels, CarlUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Pokorny, LisaUNSPECIFIEDorcid.org/0000-0002-2478-8555UNSPECIFIED
Shaw, Jonathan A.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
DeGironimo, LisaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Stevenson, Dennis W.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Villarreal, Juan CarlosUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Chen, TaoUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Kutchan, Toni M.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Rolf, MeganUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Baucom, Regina S.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Deyholos, Michael K.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Samudrala, RamUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Tian, ZhijianUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Wu, XiaoleiUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Sun, XiaoUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Zhang, YongUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Wang, JunUNSPECIFIEDorcid.org/0000-0002-8540-8931UNSPECIFIED
Leebens-Mack, JimUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Wong, Gane Ka-ShuUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
URN: urn:nbn:de:hbz:38-425526
DOI: 10.1186/2047-217X-3-17
Journal or Publication Title: GigaScience
Volume: 3
Date: 2014
Publisher: BIOMED CENTRAL LTD
Place of Publication: LONDON
ISSN: 2047-217X
Language: English
Faculty: Unspecified
Divisions: Unspecified
Subjects: no entry
Uncontrolled Keywords:
KeywordsLanguage
Biology; Multidisciplinary SciencesMultiple languages
URI: http://kups.ub.uni-koeln.de/id/eprint/42552

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