Mining heterogeneous data: Understanding systems at the level of complexes and networks
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The document discusses understanding biological systems at the level of complexes and networks. It mentions that the cell cycle consists of four phases (G1, S, G2, M) involving growth and DNA replication. Gene expression and protein complexes are regulated through phosphorylation and degradation. The author and colleagues have studied the cell cycle across species including S. cerevisiae using microarray time courses. They developed scoring schemes to analyze cycling genes and protein complexes. Their work has provided insights into just-in-time assembly of complexes and temporal networks as well as cross-species comparisons of orthologous genes. Reanalysis and integration of high-throughput data can provide new biological understanding.
Mining heterogeneous data: Understanding systems at the level of complexes and networks
- 1. Mining heterogeneous data Understanding systems at the level of complexes and networks Lars Juhl Jensen
- 4. one cell
- 5. two cells
- 6. four phases
- 7. G 1 phase
- 8. growth
- 9. S phase
- 10. DNA replication
- 11. G 2 phase
- 12. growth
- 13. M phase
- 14. cell division
- 16. regulation
- 17. gene expression
- 19. phosphorylation
- 21. gene expression
- 22. cell cultures
- 23. S. cerevisiae
- 25. synchronization
- 26. microarrays
- 28. time courses
- 29. Gauthier et al., Nucleic Acids Research , 2007
- 30. cycling genes
- 31. scoring scheme
- 32. shape
- 33. magnitude
- 34. benchmarking
- 35. Gauthier et al., Nucleic Acids Research , 2007
- 37. interaction data
- 38. Jensen & Bork, Science , 2008
- 39. high error rate
- 40. scoring scheme
- 41. von Mering et al., Nucleic Acids Research , 2005
- 42. von Mering et al., Nucleic Acids Research , 2005
- 44. time of peak mRNA level
- 45. temporal network
- 46. de Lichtenberg, Jensen et al., Science , 2005
- 47. hypothesis
- 49. de Lichtenberg, Jensen et al., Cell Cycle , 2007
- 50. how can we test it?
- 51. evolution
- 53. S. pombe
- 54. H. sapiens
- 55. A. thaliana
- 59. Jensen, Jensen, de Lichtenberg et al., Nature , 2006
- 62. Jensen, Jensen, de Lichtenberg et al., Nature , 2006
- 63. time of peak mRNA level
- 64. time of action
- 66. pathways
- 71. phenotypes
- 72. H. sapiens
- 73. siRNA screen
- 76. summary
- 77. reanalysis
- 78. integration
- 81. Acknowledgments Thomas Skøt Jensen Ulrik de Lichtenberg Søren Brunak Peer Bork
- 82. larsjuhljensen