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

Naim Matasci, Ling Hong Hung, Zhixiang Yan, Eric J. Carpenter, Norman J. Wickett, Siavash Mirarab, Nam Nguyen, Tandy Warnow, Saravanaraj Ayyampalayam, Michael S Barker, J. G. Burleigh, Matthew A. Gitzendanner, Eric Wafula, Joshua P. Der, Claude W. dePamphilis, Béatrice Roure, Hervé Philippe, Brad R. Ruhfel, Nicholas W. Miles, Sean W. Graham & 24 others Sarah Mathews, Barbara Surek, Michael Melkonian, Douglas E. Soltis, Pamela S. Soltis, Carl Rothfels, Lisa Pokorny, Jonathan A. Shaw, Lisa DeGironimo, Dennis W. Stevenson, Juan C. Villarreal, Tao Chen, Toni M. Kutchan, Megan Rolf, Regina S. Baucom, Michael K. Deyholos, Ram Samudrala, Zhijian Tian, Xiaolei Wu, Xiao Sun, Yong Zhang, Jun Wang, Jim Leebens-Mack, Gane Ka Shu Wong

Research output: Contribution to journalArticle

241 Citations (Scopus)

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.

Original languageEnglish (US)
Article number17
JournalGigaScience
Volume3
Issue number1
DOIs
StatePublished - Oct 27 2014

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Viridiplantae
Proteins
Transcriptome
Visualization
Pipelines
Genes
Datasets

Keywords

  • Biodiversity
  • Interactions
  • Pathways
  • Phylogenomics
  • Transcriptomes
  • Viridiplantae

ASJC Scopus subject areas

  • Health Informatics
  • Computer Science Applications

Cite this

Matasci, N., Hung, L. H., Yan, Z., Carpenter, E. J., Wickett, N. J., Mirarab, S., ... Wong, G. K. S. (2014). Data access for the 1,000 Plants (1KP) project. GigaScience, 3(1), [17]. https://doi.org/10.1186/2047-217X-3-17

Data access for the 1,000 Plants (1KP) project. / Matasci, Naim; Hung, Ling Hong; Yan, Zhixiang; Carpenter, Eric J.; Wickett, Norman J.; Mirarab, Siavash; Nguyen, Nam; Warnow, Tandy; Ayyampalayam, Saravanaraj; Barker, Michael S; 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 Ka Shu.

In: GigaScience, Vol. 3, No. 1, 17, 27.10.2014.

Research output: Contribution to journalArticle

Matasci, N, Hung, LH, Yan, Z, Carpenter, EJ, Wickett, NJ, Mirarab, S, Nguyen, N, Warnow, T, Ayyampalayam, S, Barker, MS, Burleigh, JG, Gitzendanner, MA, Wafula, E, Der, JP, dePamphilis, CW, Roure, B, Philippe, H, Ruhfel, BR, Miles, NW, Graham, SW, Mathews, S, Surek, B, Melkonian, M, Soltis, DE, Soltis, PS, Rothfels, C, Pokorny, L, Shaw, JA, DeGironimo, L, Stevenson, DW, Villarreal, JC, Chen, T, Kutchan, TM, Rolf, M, Baucom, RS, Deyholos, MK, Samudrala, R, Tian, Z, Wu, X, Sun, X, Zhang, Y, Wang, J, Leebens-Mack, J & Wong, GKS 2014, 'Data access for the 1,000 Plants (1KP) project', GigaScience, vol. 3, no. 1, 17. https://doi.org/10.1186/2047-217X-3-17
Matasci N, Hung LH, Yan Z, Carpenter EJ, Wickett NJ, Mirarab S et al. Data access for the 1,000 Plants (1KP) project. GigaScience. 2014 Oct 27;3(1). 17. https://doi.org/10.1186/2047-217X-3-17
Matasci, Naim ; Hung, Ling Hong ; Yan, Zhixiang ; Carpenter, Eric J. ; Wickett, Norman J. ; Mirarab, Siavash ; Nguyen, Nam ; Warnow, Tandy ; Ayyampalayam, Saravanaraj ; Barker, Michael S ; 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 Ka Shu. / Data access for the 1,000 Plants (1KP) project. In: GigaScience. 2014 ; Vol. 3, No. 1.
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AU - Hung, Ling Hong

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AU - Mirarab, Siavash

AU - Nguyen, Nam

AU - Warnow, Tandy

AU - Ayyampalayam, Saravanaraj

AU - Barker, Michael S

AU - Burleigh, J. G.

AU - Gitzendanner, Matthew A.

AU - Wafula, Eric

AU - Der, Joshua P.

AU - dePamphilis, Claude W.

AU - Roure, Béatrice

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AU - Miles, Nicholas W.

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AU - Shaw, Jonathan A.

AU - DeGironimo, Lisa

AU - Stevenson, Dennis W.

AU - Villarreal, Juan C.

AU - Chen, Tao

AU - Kutchan, Toni M.

AU - Rolf, Megan

AU - Baucom, Regina S.

AU - Deyholos, Michael K.

AU - Samudrala, Ram

AU - Tian, Zhijian

AU - Wu, Xiaolei

AU - Sun, Xiao

AU - Zhang, Yong

AU - Wang, Jun

AU - Leebens-Mack, Jim

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