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 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; 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

doi:10.1186/2047-217X-3-17

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 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. GrahamSarah 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 journal › Review article › peer-review

453 Scopus citations

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 language	English (US)
Article number	17
Journal	GigaScience
Volume	3
Issue number	1
DOIs	https://doi.org/10.1186/2047-217X-3-17
State	Published - Oct 27 2014

Keywords

Biodiversity
Interactions
Pathways
Phylogenomics
Transcriptomes
Viridiplantae

ASJC Scopus subject areas

General Medicine

Access to Document

10.1186/2047-217X-3-17

Cite this

Matasci, N., Hung, L. H., Yan, Z., Carpenter, E. J., Wickett, N. J., Mirarab, S., Nguyen, N., Warnow, T., Ayyampalayam, S., Barker, M., Burleigh, J. G., Gitzendanner, M. A., Wafula, E., Der, J. P., dePamphilis, C. W., Roure, B., Philippe, H., Ruhfel, B. R., Miles, N. W., ... Wong, G. K. S. (2014). Data access for the 1,000 Plants (1KP) project. GigaScience, 3(1), Article 17. https://doi.org/10.1186/2047-217X-3-17

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, 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

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

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.",

keywords = "Biodiversity, Interactions, Pathways, Phylogenomics, Transcriptomes, Viridiplantae",

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

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AU - Matasci, Naim

AU - Hung, Ling Hong

AU - Yan, Zhixiang

AU - Carpenter, Eric J.

AU - Wickett, Norman J.

AU - Mirarab, Siavash

AU - Nguyen, Nam

AU - Warnow, Tandy

AU - Ayyampalayam, Saravanaraj

AU - Barker, Michael

AU - Burleigh, J. G.

AU - Gitzendanner, Matthew A.

AU - Wafula, Eric

AU - Der, Joshua P.

AU - dePamphilis, Claude W.

AU - Roure, Béatrice

AU - Philippe, Hervé

AU - Ruhfel, Brad R.

AU - Miles, Nicholas W.

AU - Graham, Sean W.

AU - Mathews, Sarah

AU - Surek, Barbara

AU - Melkonian, Michael

AU - Soltis, Douglas E.

AU - Soltis, Pamela S.

AU - Rothfels, Carl

AU - Pokorny, Lisa

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

AU - Wong, Gane Ka Shu

PY - 2014/10/27

Y1 - 2014/10/27

N2 - 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.

AB - 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.

KW - Biodiversity

KW - Interactions

KW - Pathways

KW - Phylogenomics

KW - Transcriptomes

KW - Viridiplantae

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U2 - 10.1186/2047-217X-3-17

DO - 10.1186/2047-217X-3-17

M3 - Review article

AN - SCOPUS:84909590553

SN - 2047-217X

VL - 3

JO - GigaScience

JF - GigaScience

IS - 1

M1 - 17

ER -

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

Abstract

Keywords

ASJC Scopus subject areas

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