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    Data access for the 1,000 Plants (1KP) project

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    13742_2014_Article_69.pdf (1.519Mb)
    Date
    2014-10-27
    Author
    Matasci, Naim
    Hung, Ling-Hong
    Yan, Zhixiang
    Carpenter, Eric J
    Wickett, Norman J
    Mirarab, Siavash
    Nguyen, Nam
    Warnow, Tandy
    Ayyampalayam, Saravanaraj
    Barker, Michael
    Burleigh, J G
    Gitzendanner, Matthew A
    Wafula, Eric
    Der, Joshua P
    dePamphilis, Claude W
    Roure, Béatrice
    Philippe, Hervé
    Ruhfel, Brad R
    Miles, Nicholas W
    Graham, Sean W
    Mathews, Sarah
    Surek, Barbara
    Melkonian, Michael
    Soltis, Douglas E
    Soltis, Pamela S
    Rothfels, Carl
    Pokorny, Lisa
    Shaw, Jonathan A
    DeGironimo, Lisa
    Stevenson, Dennis W
    Villarreal, Juan C
    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
    Leebens-Mack, Jim
    Wong, Gane K
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    Abstract
    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.
    URI
    http://dx.doi.org/10.1186/2047-217X-3-17
    http://hdl.handle.net/10724/32628
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