Protein networks: A basis for large-scale data mining
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This document discusses protein networks and how they can be used for large-scale data mining. It describes three phases: 1) constructing association networks using different data types like genomic context and protein interactions, 2) building signaling networks using phosphoproteomics and sequence motifs, and 3) analyzing dynamic networks on the temporal level using microarray time courses and evolutionary flexibility of individual genes and protein complexes. The overall goal is to integrate different data sources to generate specific predictions and gain systems-level properties and insights.
Protein networks: A basis for large-scale data mining
- 1. Protein networks A basis for large-scale data mining Lars Juhl Jensen
- 7. who?
- 9. STRING
- 10. Jensen, Kuhn et al., Nucleic Acids Research, 2009
- 11. genomic context
- 12. Korbel et al., Nature Biotechnology, 2004
- 16. Jensen & Bork, Science, 2008
- 18. Letunic & Bork, Trends in Biochemical Sciences, 2008
- 20. Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology, 2009
- 22. von Mering et al., Nucleic Acids Research, 2005
- 25. Frishman et al., Modern Genome Annotation, 2009
- 27. what?
- 30. signaling events
- 31. sequence motifs
- 32. Miller, Jensen et al., Science Signaling, 2008
- 33. NetPhorest
- 34. Miller, Jensen et al., Science Signaling, 2008
- 36. NetworKIN
- 37. Linding, Jensen, Ostheimer et al., Cell, 2007
- 38. benchmarking
- 39. Linding, Jensen, Ostheimer et al., Cell, 2007
- 41. use cases
- 43. Linding, Jensen, Ostheimer et al., Cell, 2007
- 45. Olsen, Vermeulen, Santamaria, Kumar et al., Science Signaling, 2010
- 47. when?
- 51. Gauthier et al., Nucleic Acids Research, 2007
- 53. temporal network
- 54. de Lichtenberg, Jensen et al., Science, 2005
- 55. de Lichtenberg, Jensen et al., Science, 2005
- 57. de Lichtenberg, Jensen et al., Cell Cycle, 2007
- 59. individual genes
- 60. Jensen, Jensen, de Lichtenberg et al., Nature, 2006
- 62. Jensen, Jensen, de Lichtenberg et al., Nature, 2006
- 63. phosphorylation
- 64. co-evolution
- 65. Jensen, Jensen, de Lichtenberg et al., Nature, 2006
- 66. summary
- 67. networks
- 68. data integration
- 72. thank you!
- 73. Acknowledgments NetPhorest.info – Rune Linding – Martin Lee Miller – Francesca Diella – Claus Jørgensen – Michele Tinti – Lei Li – Marilyn Hsiung – Sirlester A. Parker – Jennifer Bordeaux – Thomas Sicheritz-Pontén – Marina Olhovsky – Adrian Pasculescu – Jes Alexander – Stefan Knapp – Nikolaj Blom – Peer Bork – Shawn Li – Gianni Cesareni – Tony Pawson – Benjamin E. Turk – Michael B. Yaffe – Søren Brunak STRING-DB.org – Christian von Mering – Damian Szklarczyk – Michael Kuhn – Manuel Stark – Samuel Chaffron – Chris Creevey – Jean Muller – Tobias Doerks – Philippe Julien – Alexander Roth – Milan Simonovic – Jan Korbel – Berend Snel – Martijn Huynen – Peer Bork Cyclebase.org – Ulrik de Lichtenberg – Thomas Skøt Jensen – Nicholas Paul Gauthier – Rasmus Wernersson – Søren Brunak NetworKIN.info – Rune Linding – Heiko Horn – Gerard Ostheimer – Martin Lee Miller – Francesca Diella – Karen Colwill – Jing Jin – Pavel Metalnikov – Vivian Nguyen – Adrian Pasculescu – Jin Gyoon Park – Leona D. Samson – Rob Russell – Peer Bork – Michael Yaffe – Tony Pawson
- 74. larsjuhljensen