Arabidopsis thaliana 7TMR Mining

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Moriyama, E. N., Strope, P. K., Opiyo, S. O., Chen, Z. and Jones, A. M. (2006)
"Mining the Arabidopsis thaliana genome for highly-divergent seven transmembrane receptors." Genome Biology 7: R96.

— Lists of 7-transmembrane putative receptor (7TMpR) candidiates —

• 394 Arabidopsis thaliana 7TMpR candidates (Additional Data File 1 of Genome Biology paper)
  • Open the table with links (Download the Excel file)
  • Download the sequences
• 54 Arabidopsis thaliana 7TMpR candidates (Additional Data File 2 of Genome Biology paper)
  • Open the table with links (Download the PDF file)
  • Download the sequences

— Tools —

Hierarchical Mining Web-server — do your own hierarchical mining

• Get AA/dipeptide composition from your sequences
• Convert amino acid sequences to 5 PC scores
  (12 physico-chemical property table, 5 PC score table)
• ACC - Mean transformation
• Kim's 4 variables for DA analysis

— Methods used —

• Profile hidden Markov models using SAM
  • SAM model file, SAM model library file (how to use these model files)
  • An example fasta format file
  • Sequence Alignment and Modeling System (SAM) at UCSC (academic license required for local installation)
• Support Vector Machines (SVMs)
  • SVM-AA model (SVM-AA model for v5), SVM-di model (SVM-di model for v5) (how to use these model files)
  • Example input files: amino acid composition, dipeptide composition
  • SVM-light by Thorsten Joachims
• Partial Least Squares Regression (PLS)
  • PLS-ACC model (how to use these model files)
  • Example input files: 5 PC score data, ACC data
  • pls/CRAN by Ron Wehrens & Bjorn-Helge Mevik (installation of R is required)
• Discriminant function analyses (DAs) using S-PLUS
  • Splus binary object files: LDA model, QDA model (how to use these model files)
    training data, training data label [required only for KNN]
  • Example input files: 19 aa composition, 3 periodicity variables
  • S-PLUS statiscial package from Insightful Corporation
• Transmembrane prediction methods
  • HMMTOP v2.0 by Tusnady (academic license required for local installation)

— Arabidopsis thaliana protein data used —

• Originally obtained from TIGR Arabidopsis thaliana Database Release 5 (06/10/04):
  Direct ftp site @ TIGR
• Download the entire protein sequences (28,952 proteins, 7.6MB gzip file)

— Training datasets used —

• 500 positive samples: Entry list with lengths, Sequences (FASTA format)
• 500 negative samples: Entry list with length, Sequences (FASTA format)

— Related links —

• TAIR: The Arabidopsis Information Resource
• GPCRDB: Information system for G protein-coupled receptors (GPCRs)
• E. Moriyama Lab at University of Nebraska-Lincoln
• Jones Lab at University of North Carolina at Chapel Hill

— Other related publications —

Johnston, C. A., Temple, B. R., Chen, J.-G., Gao, Y., Moriyama, E. N., Jones, A. M., Siderovski, D. P. and Willard, F. S. (2007)
Comment on "A G protein-coupled receptor is a plasma membrane receptor for the plant hormone abscisic acid". Science 318: 914.

Opiyo, S. O. and Moriyama, E. N. (2007)
"Protein family classification with partial least squares." J Proteome Res 6: 846-853.

Strope, P. K. and Moriyama, E. N. (2007)
"Simple alignment-free methods for protein classification: a case study from G-protein coupled receptors." Genomics 89: 602-612.

The Arabidopsis image was reproduced with permission from: The Arabidopsis Information Resource (TAIR), www.arabidopsis.org/portals/education/aboutarabidopsis.html, Sep 11, 2006.

[Last updated: 12/25/2007]