Download - Data Integration and Systems Biology
![Page 1: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/1.jpg)
Lars Juhl Jensen
Data Integration and Systems Biology
![Page 2: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/2.jpg)
Lars Juhl Jensen
Data Integration and Systems Biology
![Page 3: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/3.jpg)
what went wrong?
![Page 4: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/4.jpg)
a good problem
![Page 5: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/5.jpg)
a good idea
![Page 6: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/6.jpg)
cell-cycle regulation
![Page 7: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/7.jpg)
microarray data
![Page 8: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/8.jpg)
interaction network
![Page 9: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/9.jpg)
de Lichtenberg, Jensen, et al., Science, 2005
![Page 10: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/10.jpg)
new uses for old drugs
![Page 11: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/11.jpg)
chemical similarity
![Page 12: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/12.jpg)
side effects
![Page 13: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/13.jpg)
![Page 14: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/14.jpg)
![Page 15: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/15.jpg)
![Page 16: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/16.jpg)
the problem
![Page 17: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/17.jpg)
phosphorylation networks
![Page 18: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/18.jpg)
mass spectrometry
![Page 19: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/19.jpg)
Linding, Jensen, Ostheimer et al., Cell, 2007
![Page 20: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/20.jpg)
phosphorylation sites
![Page 21: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/21.jpg)
in vivo
![Page 22: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/22.jpg)
kinases are unknown
![Page 23: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/23.jpg)
peptide assays
![Page 24: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/24.jpg)
Miller, Jensen et al., Science Signaling, 2008
![Page 25: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/25.jpg)
sequence specificity
![Page 26: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/26.jpg)
kinase-specific
![Page 27: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/27.jpg)
in vitro
![Page 28: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/28.jpg)
no context
![Page 29: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/29.jpg)
what a kinase could do
![Page 30: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/30.jpg)
not what it actually does
![Page 31: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/31.jpg)
computational methods
![Page 32: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/32.jpg)
sequence specificity
![Page 33: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/33.jpg)
Miller, Jensen et al., Science Signaling, 2008
![Page 34: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/34.jpg)
kinase-specific
![Page 35: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/35.jpg)
no context
![Page 36: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/36.jpg)
what a kinase could do
![Page 37: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/37.jpg)
not what it actually does
![Page 38: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/38.jpg)
in vitro
![Page 39: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/39.jpg)
in vivo
![Page 40: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/40.jpg)
context
![Page 41: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/41.jpg)
co-activators
![Page 42: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/42.jpg)
scaffolders
![Page 43: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/43.jpg)
expression
![Page 44: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/44.jpg)
association networks
![Page 45: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/45.jpg)
Linding, Jensen, Ostheimer et al., Cell, 2007
![Page 46: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/46.jpg)
the idea
![Page 47: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/47.jpg)
mass spectrometry
![Page 48: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/48.jpg)
phosphorylation sites
![Page 49: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/49.jpg)
sequence motifs
![Page 50: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/50.jpg)
sequence specificity
![Page 51: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/51.jpg)
association network
![Page 52: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/52.jpg)
context
![Page 53: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/53.jpg)
in vitro
![Page 54: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/54.jpg)
in vivo
![Page 55: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/55.jpg)
Linding, Jensen, Ostheimer et al., Cell, 2007
![Page 56: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/56.jpg)
the sequence motifs
![Page 57: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/57.jpg)
NetPhorest
![Page 58: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/58.jpg)
Miller, Jensen et al., Science Signaling, 2008
![Page 59: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/59.jpg)
pipeline
![Page 60: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/60.jpg)
data organization
![Page 61: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/61.jpg)
Miller, Jensen et al., Science Signaling, 2008
![Page 62: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/62.jpg)
compilation of datasets
![Page 63: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/63.jpg)
Miller, Jensen et al., Science Signaling, 2008
![Page 64: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/64.jpg)
redundancy reduction
![Page 65: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/65.jpg)
Miller, Jensen et al., Science Signaling, 2008
![Page 66: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/66.jpg)
cross-validation partitioning
![Page 67: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/67.jpg)
Miller, Jensen et al., Science Signaling, 2008
![Page 68: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/68.jpg)
training and evaluation
![Page 69: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/69.jpg)
classifier selection
![Page 70: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/70.jpg)
Miller, Jensen et al., Science Signaling, 2008
![Page 71: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/71.jpg)
motif atlas
![Page 72: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/72.jpg)
![Page 73: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/73.jpg)
179 kinases
![Page 74: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/74.jpg)
93 SH2 domains
![Page 75: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/75.jpg)
8 PTB domains
![Page 76: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/76.jpg)
BRCT domains
![Page 77: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/77.jpg)
WW domains
![Page 78: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/78.jpg)
14-3-3 proteins
![Page 79: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/79.jpg)
benchmarking
![Page 80: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/80.jpg)
Miller, Jensen et al., Science Signaling, 2008
![Page 81: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/81.jpg)
low-specificity kinases
![Page 82: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/82.jpg)
disease-related kinases
![Page 83: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/83.jpg)
Miller, Jensen et al., Science Signaling, 2008
![Page 84: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/84.jpg)
docking domains
![Page 85: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/85.jpg)
Miller, Jensen et al., Science Signaling, 2008
![Page 86: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/86.jpg)
the context network
![Page 87: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/87.jpg)
STRING
![Page 88: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/88.jpg)
functional associations
![Page 89: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/89.jpg)
373 genomes
![Page 90: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/90.jpg)
Jensen et al., Nucleic Acids Research, 2008
![Page 91: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/91.jpg)
genomic context methods
![Page 92: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/92.jpg)
gene fusion
![Page 93: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/93.jpg)
Korbel et al., Nature Biotechnology, 2004
![Page 94: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/94.jpg)
conserved neighborhood
![Page 95: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/95.jpg)
Korbel et al., Nature Biotechnology, 2004
![Page 96: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/96.jpg)
phylogenetic profiles
![Page 97: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/97.jpg)
Korbel et al., Nature Biotechnology, 2004
![Page 98: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/98.jpg)
primary experimental data
![Page 99: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/99.jpg)
protein interactions
![Page 100: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/100.jpg)
Jensen & Bork, Science, 2008
![Page 101: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/101.jpg)
gene coexpression
![Page 102: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/102.jpg)
![Page 103: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/103.jpg)
literature mining
![Page 104: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/104.jpg)
![Page 105: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/105.jpg)
curated knowledge
![Page 106: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/106.jpg)
Letunic & Bork, Trends in Biochemical Sciences, 2008
![Page 107: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/107.jpg)
different formats
![Page 108: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/108.jpg)
parsers
![Page 109: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/109.jpg)
different gene identifiers
![Page 110: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/110.jpg)
thesaurus
![Page 111: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/111.jpg)
redundancy
![Page 112: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/112.jpg)
bookkeeping
![Page 113: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/113.jpg)
variable reliability
![Page 114: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/114.jpg)
benchmarking
![Page 115: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/115.jpg)
von Mering et al., Nucleic Acids Research, 2005
![Page 116: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/116.jpg)
spread over many species
![Page 117: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/117.jpg)
transfer by orthology
![Page 118: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/118.jpg)
von Mering et al., Nucleic Acids Research, 2005
![Page 119: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/119.jpg)
combine all evidence
![Page 120: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/120.jpg)
Linding, Jensen, Ostheimer et al., Cell, 2007
![Page 121: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/121.jpg)
the results
![Page 122: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/122.jpg)
NetworKIN
![Page 123: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/123.jpg)
123 kinases
![Page 124: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/124.jpg)
5515 substrates
![Page 125: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/125.jpg)
21,702 sites
![Page 126: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/126.jpg)
benchmarking
![Page 127: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/127.jpg)
Phospho.ELM
![Page 128: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/128.jpg)
Linding, Jensen, Ostheimer et al., Cell, 2007
![Page 129: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/129.jpg)
2.5-fold better accuracy
![Page 130: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/130.jpg)
context is crucial
![Page 131: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/131.jpg)
ATM signaling
![Page 132: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/132.jpg)
Linding, Jensen, Ostheimer et al., Cell, 2007
![Page 133: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/133.jpg)
Linding, Jensen, Ostheimer et al., Cell, 2007
![Page 134: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/134.jpg)
small-scale validation
![Page 135: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/135.jpg)
ATM phosphorylates Rad50
![Page 136: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/136.jpg)
Linding, Jensen, Ostheimer et al., Cell, 2007
![Page 137: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/137.jpg)
high-throughput validation
![Page 138: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/138.jpg)
multiple reaction monitoring
![Page 139: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/139.jpg)
Linding, Jensen, Ostheimer et al., Cell, 2007
![Page 140: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/140.jpg)
systematic validation
![Page 141: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/141.jpg)
kinase inhibitor matrix
![Page 142: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/142.jpg)
Fedorov et al., PNAS, 2007
![Page 143: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/143.jpg)
design optimal experiments
![Page 144: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/144.jpg)
Acknowledgments
NetworKIN.info– Rune Linding– Gerard Ostheimer– 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
NetPhorest.info– 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.embl.de– Christian von Mering– Michael Kuhn– Manuel Stark– Samuel Chaffron– Philippe Julien– Tobias Doerks– Jan Korbel– Berend Snel– Martijn Huynen– Peer Bork
![Page 145: Data Integration and Systems Biology](https://reader031.vdocument.in/reader031/viewer/2022020101/554e8aedb4c905fc368b48c8/html5/thumbnails/145.jpg)
http://larsjuhljensen.wordpress.com