The compendium of crop Proteins with Annotated Locations (cropPAL) version 2020

  • Cornelia Hooper (Creator)
  • Ian Castleden (Data Manager)
  • Nader Aryamanesh Precision Medicine Theme, South Australian Health and Medical Research Institute, University of Adelaide (Data Collector)
  • Kylie Black (Contributor)
  • Sally Grasso (Data Collector)
  • Harvey Millar (Creator)

Dataset

Description

The compendium of crop Proteins with Annotated Locations (cropPAL) is a comprehensive collection of subcellular location annotation for crop proteins. Crops included are banana (musa acuminata), barley (hordeum vulgare), canola (brassica napus), field mustard (brassica rapa), maize (zea mays), potato (solanum tuberosum), rice (oryza sativa), sorghum (sorghum bicolor), soybean (glycine max), tomato (solanum lycopersicum), wheat (triticum aestivum) and wine grape (vitis vinifera). The location annotations are derived from published experimental localization studies and precompiled bioinformatic predictions. A protein-protein interaction list was compiled using homology linking of experimental Arabidopsis protein-protein interactions. A user-friendly search interface is provided on the http://crop-pal.org/ web server that allows filtering for species, location, methods, study parameters as well as allows to blast sequences to find localisations for the closest crop match.
Date made availableJan 2020
PublisherThe University of Western Australia
Temporal coverage1989 - 2019
Date of data productionAug 2020

Keywords

  • crop
  • subcellular location
  • proteomics
  • barley
  • hordeum vulgare
  • banana
  • musa acuminata
  • wheat
  • triticum aestivum
  • corn
  • maize
  • zea mays
  • rice
  • oryza sativa
  • GFP
  • protein location
  • fusion protein
  • fluorescent protein
  • brassica napus
  • canola
  • brassica rapa
  • field mustard
  • potato
  • solanum tuberosum
  • sorghum
  • sorghum bicolor
  • soybean
  • glycine max
  • tomato
  • solanum lycopersicum
  • grape
  • vitis vinifera
  • systems biology
  • molecular breeding
  • subcellulomes
  • organelles
  • compartment
  • plant cell
  • agriculture
  • metabolic modelling

Field of Research (FoR)

  • 060702 Plant Cell and Molecular Biology
  • 060114 Systems Biology
  • 060799 Plant Biology not elsewhere classified
  • 080403 Data Structures
  • 080704 Information Retrieval and Web Search

Research Output

  • 3 Article
  • 1 Conference paper

CropPAL for discovering protein subcellular location divergence in crops to support strategies for molecular crop breeding

Hooper, C. M., Castleden, I. R., Aryamanesh, N., Black, K., Grasso, S. V. & Millar, A. H., 11 Aug 2020, In : The Plant Journal.

Research output: Contribution to journalArticle

  • cropPAL2: Creating Ongoing, Mutually Beneficial Collaboration Between Biological Scientists and Librarians

    Black, K., Hooper, C., Gedeon, A. K., Toufexis, K., Albatis, M., Nicholls, S. & Millar, A., 2017, eResearch Australasia 2017, Brisbane, Australia.

    Research output: Chapter in Book/Conference paperConference paper

    SUBA4: The interactive data analysis centre for Arabidopsis subcellular protein locations

    Hooper, C. M., Castleden, I. R., Tanz, S. K., Aryamanesh, N. & Millar, A. H., 4 Jan 2017, In : Nucleic Acids Research. 45, D1, p. D1064-D1074

    Research output: Contribution to journalArticle

    Open Access
  • 97 Citations (Scopus)

    Projects

    Datasets

    The compendium of crop Proteins with Annotated Locations (cropPAL) version 2

    Hooper, C. (Creator), Millar, H. (Creator), Castleden, I. (Creator), Aryamanesh, N. (Contributor), Jacoby, R. (Data Collector) & Grasso, S. (Data Collector), The University of Western Australia, 1 Jun 2017

    Dataset

    File

    Subcellular Localisation database for Arabidopsis proteins version 4

    Hooper, C. (Creator) & Castleden, I. (Creator), The University of Western Australia, 26 Oct 2016

    Dataset

    File

    The compendium of crop Proteins with Annotated Locations (cropPAL) version 1

    Hooper, C. (Creator), Castleden, I. (Creator), Aryamanesh, N. (Creator), Jacoby, R. (Creator) & Millar, H. (Creator), The University of Western Australia, 2 Jun 2015

    Dataset

    File

    Cite this

    Hooper, C. (Creator), Millar, H. (Creator) (Jan 2020). The compendium of crop Proteins with Annotated Locations (cropPAL) version 2020. The University of Western Australia. cropPAL2020_Arabidopsis_WTA_18_8_20(.csv), cropPAL2020_Arabidopsis_WTA_18_8_20(.sql), cropPAL2020_inferredPPI_18_8_20(.sql), cropPAL2020_localisations_18_8_20(.csv), cropPAL2020_localisations_18_8_20(.sql), cropPAL2020_inferredPPI_18_8_20(.csv), cropPAL2020_predictors_18_8_20(.csv), cropPAL2020_taxa_legend_18_8_20(.csv), cropPAL2020_taxa_legend_18_8_20(.sql), cropPAL2020_predictors_18_8_20(.sql). 10.26182/5f3b83f9c3229