Molecular Basis for G Protein Control of the Prokaryotic ATP
Protein networks: A basis for large-scale data mining
-
Upload
lars-juhl-jensen -
Category
Technology
-
view
485 -
download
0
Transcript of Protein networks: A basis for large-scale data mining
![Page 1: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/1.jpg)
Protein networksA basis for large-scale data mining
Lars Juhl Jensen
![Page 2: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/2.jpg)
![Page 3: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/3.jpg)
![Page 4: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/4.jpg)
![Page 5: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/5.jpg)
![Page 6: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/6.jpg)
Phase 1association networks
![Page 7: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/7.jpg)
who?
![Page 8: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/8.jpg)
![Page 9: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/9.jpg)
STRING
![Page 10: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/10.jpg)
Jensen, Kuhn et al., Nucleic Acids Research, 2009
![Page 11: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/11.jpg)
genomic context
![Page 12: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/12.jpg)
gene fusion
![Page 13: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/13.jpg)
Korbel et al., Nature Biotechnology, 2004
![Page 14: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/14.jpg)
conserved neighborhood
![Page 15: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/15.jpg)
Korbel et al., Nature Biotechnology, 2004
![Page 16: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/16.jpg)
phylogenetic profiles
![Page 17: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/17.jpg)
Korbel et al., Nature Biotechnology, 2004
![Page 18: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/18.jpg)
gene coexpression
![Page 19: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/19.jpg)
![Page 20: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/20.jpg)
protein interactions
![Page 21: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/21.jpg)
Jensen & Bork, Science, 2008
![Page 22: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/22.jpg)
genetic interactions
![Page 23: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/23.jpg)
Beyer et al., Nature Reviews Genetics, 2007
![Page 24: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/24.jpg)
curated knowledge
![Page 25: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/25.jpg)
Letunic & Bork, Trends in Biochemical Sciences, 2008
![Page 26: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/26.jpg)
literature mining
![Page 27: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/27.jpg)
>10 km
![Page 28: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/28.jpg)
co-mentioning
![Page 29: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/29.jpg)
NLPNatural Language Processing
![Page 30: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/30.jpg)
Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology, 2009
![Page 31: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/31.jpg)
confidence scores
![Page 32: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/32.jpg)
von Mering et al., Nucleic Acids Research, 2005
![Page 33: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/33.jpg)
transfer by orthology
![Page 34: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/34.jpg)
probabilistic integration
![Page 35: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/35.jpg)
Frishman et al., Modern Genome Annotation, 2009
![Page 36: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/36.jpg)
Phase 2signaling networks
![Page 37: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/37.jpg)
what?
![Page 38: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/38.jpg)
phosphoproteomics
![Page 39: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/39.jpg)
![Page 40: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/40.jpg)
signaling events
![Page 41: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/41.jpg)
sequence motifs
![Page 42: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/42.jpg)
Miller, Jensen et al., Science Signaling, 2008
![Page 43: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/43.jpg)
NetPhorest
![Page 44: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/44.jpg)
Miller, Jensen et al., Science Signaling, 2008
![Page 45: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/45.jpg)
![Page 46: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/46.jpg)
NetworKIN
![Page 47: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/47.jpg)
Linding, Jensen, Ostheimer et al., Cell, 2007
![Page 48: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/48.jpg)
benchmarking
![Page 49: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/49.jpg)
Linding, Jensen, Ostheimer et al., Cell, 2007
![Page 50: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/50.jpg)
context is crucial
![Page 51: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/51.jpg)
use cases
![Page 52: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/52.jpg)
DNA damage response
![Page 53: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/53.jpg)
Linding, Jensen, Ostheimer et al., Cell, 2007
![Page 54: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/54.jpg)
cell-cycle kinases
![Page 55: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/55.jpg)
Olsen, Vermeulen, Santamaria, Kumar et al., Science Signaling, 2010
![Page 56: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/56.jpg)
Phase 3dynamic networks
![Page 57: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/57.jpg)
when?
![Page 58: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/58.jpg)
cell-cycle regulation
![Page 59: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/59.jpg)
![Page 60: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/60.jpg)
microarray time courses
![Page 61: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/61.jpg)
Gauthier et al., Nucleic Acids Research, 2007
![Page 62: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/62.jpg)
protein interactions
![Page 63: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/63.jpg)
temporal network
![Page 64: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/64.jpg)
de Lichtenberg, Jensen et al., Science, 2005
![Page 65: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/65.jpg)
de Lichtenberg, Jensen et al., Science, 2005
![Page 66: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/66.jpg)
just-in-time assembly
![Page 67: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/67.jpg)
de Lichtenberg, Jensen et al., Cell Cycle, 2007
![Page 68: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/68.jpg)
evolutionary flexibility
![Page 69: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/69.jpg)
individual genes
![Page 70: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/70.jpg)
Jensen, Jensen, de Lichtenberg et al., Nature, 2006
![Page 71: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/71.jpg)
protein complexes
![Page 72: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/72.jpg)
Jensen, Jensen, de Lichtenberg et al., Nature, 2006
![Page 73: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/73.jpg)
phosphorylation
![Page 74: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/74.jpg)
co-evolution
![Page 75: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/75.jpg)
Jensen, Jensen, de Lichtenberg et al., Nature, 2006
![Page 76: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/76.jpg)
summary
![Page 77: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/77.jpg)
networks
![Page 78: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/78.jpg)
data integration
![Page 79: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/79.jpg)
specific predictions
![Page 80: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/80.jpg)
systems properties
![Page 81: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/81.jpg)
![Page 82: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/82.jpg)
thank you!
![Page 83: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/83.jpg)
AcknowledgmentsNetPhorest.info
– Rune Linding– 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-DB.org– Christian von Mering– Damian Szklarczyk– Michael Kuhn– Manuel Stark– Samuel Chaffron– Chris Creevey– Jean Muller– Tobias Doerks– Philippe Julien– Alexander Roth– Milan Simonovic– Jan Korbel– Berend Snel– Martijn Huynen– Peer Bork
Cyclebase.org– Ulrik de Lichtenberg– Thomas Skøt Jensen– Nicholas Paul Gauthier– Rasmus Wernersson– Søren Brunak
NetworKIN.info– Rune Linding– Heiko Horn– Gerard Ostheimer– Martin Lee Miller– 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
![Page 84: Protein networks: A basis for large-scale data mining](https://reader036.fdocuments.us/reader036/viewer/2022062512/55495301b4c905e94e8b4be7/html5/thumbnails/84.jpg)
larsjuhljensen