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

Matasci N, Hung LH, 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 - Gigascience (2014)

Bottom Line: 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: iPlant Collaborative, Tucson 85721, AZ, USA ; Department of Ecology and Evolutionary Biology, University of Arizona, Tucson 85721, AZ, USA.

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.

No MeSH data available.


iPlant DE data window.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC4306014&req=5

Figure 1: iPlant DE data window.

Mentions: For access to the 1KP files, users should visit [9] and search for a folder called Community Data/onekp_pilot Figure 1.


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

Matasci N, Hung LH, 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 - Gigascience (2014)

iPlant DE data window.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4306014&req=5

Figure 1: iPlant DE data window.
Mentions: For access to the 1KP files, users should visit [9] and search for a folder called Community Data/onekp_pilot Figure 1.

Bottom Line: 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: iPlant Collaborative, Tucson 85721, AZ, USA ; Department of Ecology and Evolutionary Biology, University of Arizona, Tucson 85721, AZ, USA.

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.

No MeSH data available.