STRING - Modeling of biological systems through cross-species data integration
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The document discusses the STRING database, which integrates data from diverse sources to predict protein-protein interactions and functional associations. It summarizes different lines of evidence used by STRING, including genomic context, co-expression, co-mentioning in articles, and transfer of functional annotations between orthologs. The document also briefly outlines how STRING scores and benchmarks different predictive methods and defines functional modules to model biological systems.
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STRING - Modeling of biological systems through cross-species data integration
- 1. STRING Modeling of biological systems through cross-species data integration
- 6. Jensen et al., Bioinformatics, 2000
- 8. Pedersen et al., Journal of Molecular Biology, 2000
- 13. STRING
- 17. Bork et al., Current Opinion in Structural Biology, 2005
- 18. 179 proteomes
- 29. Morett et al., Nature Biotechnology, 2003
- 34. Korbel et al., Nature Biotechnology, 2004
- 35. gene fusion
- 37. evolution
- 40. statistics
- 45. sum of intergenic distances
- 47. many types of evidence
- 49. calibrate vs. gold standard
- 52. KEGG Kyoto Encyclopedia of Genes and Genomes
- 53. STKE Signal Transduction Knowledge Environment
- 54. Reactome
- 55. MIPS Munich Information center for Protein Sequences
- 57. Jensen et al., Drug Discovery Today: Targets, 2004
- 59. GEO Gene Expression Omnibus
- 61. BIND Biomolecular Interaction Network Database
- 62. MINT Molecular Interactions Database
- 63. GRID General Repository for Interaction Datasets
- 64. DIP Database of Interacting Proteins
- 65. HPRD Human Protein Reference Database
- 66. von Mering et al., Nucleic Acids Research, 2005
- 68. M EDLINE
- 69. SGD Saccharomyces Genome Database
- 71. OMIM Online Mendelian Inheritance in Man
- 72. co-mentioning
- 75. NLP Natural Language Processing
- 76. Gene and protein names Cue words for entity recognition Verbs for relation extraction [ nxgene The GAL4 gene ] [ nxexpr T he expression of [ nxgene the cytochrome genes [ nxpg CYC1 and CYC7 ]]] is controlled by [ nxpg HAP1 ]
- 77. Jensen et al., Nature Reviews Genetics, 2006
- 79. na ïve Bayesian scheme
- 80. spread over many species
- 82. ? Source species Target species
- 95. RCCs
- 96. predicting “mode of action”
- 97. Jensen et al., Drug Discovery Today: Targets, 2004
- 98. Jensen et al., Drug Discovery Today: Targets, 2004
- 99. Acknowledgments The STRING team (EMBL) Christian von Mering Berend Snel Martijn Huynen Sean Hooper Mathilde Foglierini Julien Lagarde Peer Bork Literature mining project (EML Research) Jasmin Saric Rossitza Ouzounova Isabel Rojas New genomic context methods (EMBL) Jan Korbel Peer Bork Modeling of yeast mitochondria (EMBL) Fabiana Perocchi Lars Steinmetz Inspiration for presentation Dick Clarence Hardt Anders Gorm Pedersen
- 100. Thank you!