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Lars Juhl Jensen
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Journée Thematique Biologie des Systèmes, INRA, Jouy-en-Josas, France, February 2, 2006
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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
2.
Lars Juhl Jensen
3.
4.
5.
promoter analysis
6.
Jensen et al.,
Bioinformatics, 2000
7.
genome visualization
8.
Pedersen et al.,
Journal of Molecular Biology, 2000
9.
protein function prediction
10.
11.
12.
13.
STRING
14.
15.
integrate diverse evidence
16.
functional interactions
17.
Bork et al.,
Current Opinion in Structural Biology, 2005
18.
179 proteomes
19.
genomic context methods
20.
phylogenetic profiles
21.
22.
23.
24.
25.
Cell Cellulosomes Cellulose
26.
anti-correlated profiles
27.
28.
analogous enzymes
29.
Morett et al.,
Nature Biotechnology, 2003
30.
gene neighborhood
31.
32.
bidirectional promoters
33.
34.
Korbel et al.,
Nature Biotechnology, 2004
35.
gene fusion
36.
37.
evolution
38.
39.
40.
statistics
41.
(the original sin)
42.
scoring and benchmarking
43.
raw quality scores
44.
gene neighborhood
45.
sum of intergenic
distances
46.
47.
many types of
evidence
48.
not directly comparable
49.
calibrate vs. gold
standard
50.
51.
curated knowledge
52.
KEGG Kyoto Encyclopedia
of Genes and Genomes
53.
STKE Signal Transduction
Knowledge Environment
54.
Reactome
55.
MIPS Munich Information
center for Protein Sequences
56.
primary experimental data
57.
Jensen et al.,
Drug Discovery Today: Targets, 2004
58.
microarray expression data
59.
GEO Gene Expression
Omnibus
60.
physical protein interactions
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
67.
literature mining
68.
M EDLINE
69.
SGD Saccharomyces Genome
Database
70.
The Interactive Fly
71.
OMIM Online Mendelian
Inheritance in Man
72.
co-mentioning
73.
different gene names
74.
curated synonyms lists
75.
NLP Natural Language
Processing
76.
77.
Jensen et al.,
Nature Reviews Genetics, 2006
78.
combine all evidence
79.
na ïve Bayesian
scheme
80.
spread over many
species
81.
transfer based orthology
82.
? Source species
Target species
83.
84.
85.
86.
87.
88.
89.
defining functional modules
90.
91.
92.
qualitative modeling
93.
the mitochondrial system
94.
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.
100.
Thank you!
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