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Predicting protein-protein interactions in Arabidopsis thaliana through integration of orthology, gene ontology and co-expression

By Stefanie De Bodt, Sebastian Proost, Klaas Vandepoele, Pierre Rouzé and Yves Van de Peer
Topics: Research Article
Publisher: BioMed Central
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Provided by: PubMed Central

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  1. (2000). A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature
  2. (2005). A human protein-protein interaction network: a resource for annotating the proteome. Cell
  3. (2004). A map of the interactome network of the metazoan C. elegans. Science
  4. (2007). A predicted interactome for Arabidopsis. Plant Physiol
  5. (1999). A: Identification and analysis of the Arabidopsis thaliana BSH gene, a member of the SNF5 gene family. Nucleic Acids Res
  6. (2004). AG: A first-draft human protein-interaction map. Genome Biol
  7. (2003). Amasino RM: PIE1, an ISWI family gene, is required for FLC activation and floral repression in Arabidopsis. Plant Cell
  8. (2004). Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res
  9. (2005). Assessing the limits of genomic data integration for predicting protein networks. Genome Res
  10. AtPID: Arabidopsis thaliana protein interactome database – an integrative platform for plant systems biology.
  11. (2005). Barkai N: Computational verification of protein-protein interactions by orthologous co-expression.
  12. (2008). Breusegem F: Hydrogen peroxide-induced gene expression across kingdoms: a comparative analysis. Mol Biol Evol
  13. Cesareni G: MINT: the Molecular INTeraction database.
  14. (2006). Characterization and prediction of protein-protein interactions within and between complexes.
  15. (2005). Chinnaiyan AM: Probabilistic model of the human protein-protein interaction network. Nat Biotechnol
  16. (1999). Clustering gene expression patterns.
  17. (2006). Co-evolution of transcriptional and post-translational cell-cycle regulation. Nature
  18. (2002). Comparative assessment of large-scale data sets of protein-protein interactions.
  19. (2007). Computational analysis of human protein interaction networks. Proteomics
  20. (2003). Computational methods of analysis of protein-protein interactions.
  21. (2001). Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nat Genet
  22. (2004). D: The Database of Interacting Proteins:
  23. (2005). De Veylder L: Genome-wide identification of potential plant E2F target genes. Plant Physiol
  24. (2006). Different Polycomb group complexes regulate common target genes in Arabidopsis. EMBO Rep
  25. (2008). et al.: High-Quality Binary Protein Interaction Map of the Yeast Interactome Network. Science
  26. (2002). et al.: Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature
  27. (2005). et al.: Towards a proteome-scale map of the human protein-protein interaction network. Nature
  28. (2008). F: Retinoblastoma and its binding partner MSI1 control imprinting in Arabidopsis. PLoS Biol
  29. (2005). Filtering high-throughput protein-protein interaction data using a combination of genomic features.
  30. (2003). FP: Assessing experimentally derived interactions in a small world. Proc Natl Acad Sci USA
  31. (2002). Functional organization of the yeast proteome by systematic analysis of protein complexes.
  32. (2000). Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet
  33. (2008). Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics. Science
  34. (2002). Holstege FC: Protein interaction verification and functional annotation by integrated analysis of genome-scale data. Mol Cell
  35. (2006). How complete are current yeast and human protein-interaction networks? Genome Biol
  36. (2003). How reliable are experimental protein-protein interaction data?
  37. (2006). Human protein reference database –
  38. (2001). Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or "interologs". Genome Res
  39. (2004). Information assessment on predicting protein-protein interactions.
  40. IntAct: an open source molecular interaction database.
  41. (2002). Interaction generality, a measurement to assess the reliability of a protein-protein interaction. Nucleic Acids Res
  42. (2007). Jurisica I: Unequal evolutionary conservation of human protein interactions in interologous networks.
  43. (2005). Lengauer T: Confirmation of human protein interaction data by human expression data.
  44. (1990). Lipman DJ: Basic local alignment search tool.
  45. Millar AH: SUBA: the Arabidopsis Subcellular Database.
  46. (2007). Panchenko AR: Deciphering Protein-Protein Interactions. Part I. Experimental Techniques and Databases. PLoS Comput Biol
  47. (2007). Panchenko AR: Deciphering protein-protein interactions. Part II. Computational methods to predict protein and domain interaction partners. PLoS Comput Biol
  48. (2007). Probabilistic prediction and ranking of human protein-protein interactions.
  49. (2000). Protein interaction mapping in C. elegans using proteins involved in vulval development. Science
  50. (2005). Protein interaction mapping: a Drosophila case study. Genome Res
  51. (2004). Protein interaction networks from yeast to human. Curr Opin Struct Biol
  52. (2006). Protein-protein interactions more conserved within species than across species. PLoS Comput Biol
  53. (2007). Reconstruction of human protein interolog network using evolutionary conserved network. BMC Bioinformatics
  54. (2002). Relating whole-genome expression data with protein-protein interactions. Genome Res
  55. (2003). Roos DS: OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res
  56. Roos DS: querying a comprehensive multi-species collection of ortholog groups.
  57. S: NASCArrays: a repository for microarray data generated by NASC's transcriptomics service.
  58. (2000). Sakaki Y: Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. Proc Natl Acad Sci USA
  59. Sonnhammer EL: Inparanoid: a comprehensive database of eukaryotic orthologs.
  60. (2003). Speed TP: Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics
  61. (2003). Speed TP: Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res
  62. (2003). The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Res
  63. The Gene Ontology (GO) database and informatics resource.
  64. (2006). Tikuisis AP, et al.: Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature
  65. Tyers M: a general repository for interaction datasets.
  66. (2007). Unique, shared, and redundant roles for the Arabidopsis SWI/SNF chromatin remodeling ATPases BRAHMA and SPLAYED. Plant Cell
  67. V: MPact: the MIPS protein interaction resource on yeast.
  68. (2005). WS: Kernel methods for predicting proteinprotein interactions. Bioinformatics

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