In silico and Text-Based Analysis of Cellular Networks
This document discusses in silico and text-based analysis of cellular networks. It describes using computational predictions from over 2000 genomes and experimental data to build protein interaction networks in databases like STRING. It also discusses challenges like different data sources using different formats and identifiers. The document outlines using natural language processing techniques like named entity recognition to extract and normalize biomolecular identifiers. It proposes using co-mentioning of entities within texts to assign confidence scores to interactions for building integrated interaction networks. Finally it acknowledges contributions to building networks describing protein interactions, chemical interactions, subcellular localization, tissue expression, cell cycle expression, and disease associations.
In silico and Text-Based Analysis of Cellular Networks
- 1. In Silico and Text-Based Analysis of Cellular Networks Lars Juhl Jensen
- 6. STRING
- 9. gene fusion
- 10. Korbel et al., Nature Biotechnology, 2004
- 12. Korbel et al., Nature Biotechnology, 2004
- 17. Jensen & Bork, Science, 2008
- 19. pathways
- 20. Letunic & Bork, Trends in Biochemical Sciences, 2008
- 21. many databases
- 24. variable quality
- 25. not comparable
- 26. hard work
- 27. parsers
- 28. mapping files
- 29. quality scores
- 30. von Mering et al., Nucleic Acids Research, 2005
- 32. gold standard
- 33. von Mering et al., Nucleic Acids Research, 2005
- 34. common scale
- 35. missing most of the data
- 36. >10 km
- 37. too much to read
- 38. computer
- 39. as smart as a dog
- 40. teach it specific tricks
- 45. cyclin dependent kinase 1
- 46. CDC2
- 49. cyclin dependent kinase 1
- 52. CDC2
- 53. hCdc2
- 54. “black list”
- 55. SDS
- 56. co-mentioning
- 57. within documents
- 59. within sentences
- 60. quality score
- 61. protein networks
- 62. Szklarczyk et al., Nucleic Acids Research, 2015string-db.org
- 63. general approach
- 65. Kuhn et al., Nucleic Acids Research, 2014stitch-db.org
- 66. space
- 68. Binder et al., Database, 2014compartments.jensenlab.org
- 70. tissues.jensenlab.org Santos et al., submitted, 2015
- 71. time
- 73. Santos et al., Nucleic Acids Research, 2015cyclebase.org
- 75. diseases.jensenlab.org Frankild et al., Methods, 2015
- 76. Acknowledgments Molecular networks Michael Kuhn Damian Szklarczyk Andrea Franceschini Milan Simonovic Alexander Roth Sune Pletscher-Frankild Jianyi Lin Pablo Minguez Christian von Mering Peer Bork Time and space Alberto Santos Sune Pletscher-Frankild Janos Binder Kalliopi Tsafou Christian Stolte Albert Palleja Heiko Horn Rasmus Wernersson Reinhardt Schneider Sean O’ Donoghue