Scholars@Duke publication: Data access for the 1,000 Plants (1KP) project.

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

Publication , Journal Article

Matasci, N; Hung, L-H; Yan, Z; Carpenter, EJ; Wickett, NJ; Mirarab, S; Nguyen, N; Warnow, T; Ayyampalayam, S; Barker, M; Burleigh, JG; Der, JP ...

Published in: GigaScience

January 2014

Published version (DOI)

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.

Duke Scholars

Author A. Jonathan Shaw Biology

Altmetric Attention Stats

Dimensions Citation Stats

Published In

GigaScience

DOI

10.1186/2047-217x-3-17

EISSN

2047-217X

ISSN

2047-217X

Publication Date

January 2014

Volume

Start / End Page

Citation

APA

Chicago

ICMJE

MLA

NLM

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

Matasci, Naim, Ling-Hong Hung, Zhixiang Yan, Eric J. Carpenter, Norman J. Wickett, Siavash Mirarab, Nam Nguyen, et al. “Data access for the 1,000 Plants (1KP) project.” GigaScience 3 (January 2014): 17. https://doi.org/10.1186/2047-217x-3-17.

Matasci N, Hung L-H, Yan Z, Carpenter EJ, Wickett NJ, Mirarab S, et al. Data access for the 1,000 Plants (1KP) project. GigaScience. 2014 Jan;3:17.

Matasci, Naim, et al. “Data access for the 1,000 Plants (1KP) project.” GigaScience, vol. 3, Jan. 2014, p. 17. Epmc, doi:10.1186/2047-217x-3-17.

Matasci N, Hung L-H, Yan Z, Carpenter EJ, Wickett NJ, Mirarab S, Nguyen N, Warnow T, Ayyampalayam S, Barker M, 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 GK-S. Data access for the 1,000 Plants (1KP) project. GigaScience. 2014 Jan;3:17.

Published In

GigaScience

DOI

10.1186/2047-217x-3-17

EISSN

2047-217X

ISSN

2047-217X

Publication Date

January 2014