Publication:

• Official reference of COXPRESdb
  • Please cite this reference when you refer to COXPRESdb.
  • Obayashi T, Hayashi S, Shibaoka M, Saeki M, Ohta H, Kinoshita K. COXPRESdb: a database of coexpressed gene networks in mammals. Nucleic Acids Res. 36, D77-D82. [PubMed] [PDF]
    
    
• Other technical papers to construct COXPRESdb;
  • For MR.
    • Obayashi T, Kinoshita K. (2009) Rank of correlation coefficient as a comparable measure for biological significance of gene coexpression. DNA Res., 16, 249-60. [PubMed] [PDF]
      
  • For stability of coexpression provided in CoexViewer.
    • Kinoshita K, Obayashi T. (2009) Multi-dimensional correlations for gene coexpression and application to the large-scale data of Arabidopsis. Bioinformatics., 25, 2677-84. [PubMed] [PDF]
      
  • Coexpression database for plants.
    • Obayashi T, Hayashi S, Saeki M, Ohta H, Kinoshita K. (2009) ATTED-II provides coexpressed gene networks for Arabidopsis. Nucleic Acids Res., 37, D987-91. [PubMed] [PDF]
      
      
• Acknowledgements;
  • Computation time is provided by the Super Computer System, Human Genome Center, Institute of Medical Science, The University of Tokyo.

Examples to use COXPRESdb to discuss functions of paralogous genes

• Vos MJ et al. (2009) HSPB7 is a SC35 speckle resident small heat shock protein. Biochim Biophys Acta. [PubMed]
• Vicinanza M et al. (2008) Function and dysfunction of the PI system in membrane trafficking. EMBO J. [PubMed]

Examples to analyze COXPRESdb bulk-downloadable data

• Agarwal S et al. (2010) Revisiting date and party hubs: novel approaches to role assignment in protein interaction networks. PLoS Comput Biol [PubMed]
• Lachmann A, Ma'ayan A. (2010) Lists2Networks: integrated analysis of gene/protein lists. BMC Bioinformatics [PubMed]