Dataset Information

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.

SUBMITTER: Matasci N

PROVIDER: S-EPMC4306014 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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Publications

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

Matasci Naim N Hung Ling-Hong LH Yan Zhixiang Z Carpenter Eric J EJ Wickett Norman J NJ Mirarab Siavash S Nguyen Nam N Warnow Tandy T Ayyampalayam Saravanaraj S Barker Michael M Burleigh J Gordon JG Gitzendanner Matthew A MA Wafula Eric E Der Joshua P JP dePamphilis Claude W CW Roure Béatrice B Philippe Hervé H Ruhfel Brad R BR Miles Nicholas W NW Graham Sean W SW Mathews Sarah S Surek Barbara B Melkonian Michael M Soltis Douglas E DE Soltis Pamela S PS Rothfels Carl C Pokorny Lisa L Shaw Jonathan A JA DeGironimo Lisa L Stevenson Dennis W DW Villarreal Juan Carlos JC Chen Tao T Kutchan Toni M TM Rolf Megan M Baucom Regina S RS Deyholos Michael K MK Samudrala Ram R Tian Zhijian Z Wu Xiaolei X Sun Xiao X Zhang Yong Y Wang Jun J Wang Jun J Leebens-Mack Jim J Wong Gane Ka-Shu GK

GigaScience 20141027

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 th ...[more]

PMID: 25625010

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Project description:BackgroundElectromagnetic navigation bronchoscopy (ENB) is an image-guided, minimally invasive approach that uses a flexible catheter to access pulmonary lesions.MethodsNAVIGATE is a prospective, multicenter study of the superDimension™ navigation system. A prespecified 1-month interim analysis of the first 1,000 primary cohort subjects enrolled at 29 sites in the United States and Europe is described. Enrollment and 24-month follow-up are ongoing.ResultsENB index procedures were conducted for lung lesion biopsy (n = 964), fiducial marker placement (n = 210), pleural dye marking (n = 17), and/or lymph node biopsy (n = 334; primarily endobronchial ultrasound-guided). Lesions were in the peripheral/middle lung thirds in 92.7%, 49.7% were <20 mm, and 48.4% had a bronchus sign. Radial EBUS was used in 54.3% (543/1,000 subjects) and general anesthesia in 79.7% (797/1,000). Among the 964 subjects (1,129 lesions) undergoing lung lesion biopsy, navigation was completed and tissue was obtained in 94.4% (910/964). Based on final pathology results, ENB-aided samples were read as malignant in 417/910 (45.8%) subjects and non-malignant in 372/910 (40.9%) subjects. An additional 121/910 (13.3%) were read as inconclusive. One-month follow-up in this interim analysis is not sufficient to calculate the true negative rate or diagnostic yield. Tissue adequacy for genetic testing was 80.0% (56 of 70 lesions sent for testing). The ENB-related pneumothorax rate was 4.9% (49/1,000) overall and 3.2% (32/1,000) CTCAE Grade ≥2 (primary endpoint). The ENB-related Grade ≥2 bronchopulmonary hemorrhage and Grade ≥4 respiratory failure rates were 1.0 and 0.6%, respectively.ConclusionsOne-month results of the first 1,000 subjects enrolled demonstrate low adverse event rates in a generalizable population across diverse practice settings. Continued enrollment and follow-up are required to calculate the true negative rate and delineate the patient, lesion, and procedural factors contributing to diagnostic yield.Trial registrationClinicalTrials.gov NCT02410837 . Registered 31 March 2015.

Dataset Information

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

Publications

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

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