Protein-Protein Interactions, Networks and Pathways - Chagall

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Computational ChallengesI:Data description• The identity of the interacting proteins is notalways clear. Gene names, differentIdentifiers, alternative splicing, experimentalconstructs - a major resource expend.• Post translational modification. Not easy todescribe and can be very complex (e.g.glycosylation).• Conditions and context are often missing. Invitro experiments may lack the time/spatialcomponents of interactions.
Computational Challenges II:Data quality• Different experiments provide differentinformation: functional assays, site-directedmutagenesis, Y2H, IP-MS, IP-Western.• Different levels of details: Structuralcomplexes provide detailed atomicinformation. IP-MS provide proteincomplexes.• Incomplete coverage: not all cellularcomponents and events are covered equally.For example, membrane proteins are missedby Y2H. Impacts PPI predictions.
Page 1 and 2: Protein-Protein Interactions,Networ
Page 3 and 4: David S. Goodsell, http://mgl.scrip
Page 5 and 6: http://www.biocarta.com/pathfiles/h
Page 7 and 8: Protein Interactions• A geometric
Page 9 and 10: Yeast-two-hybrid• Widely used for
Page 11 and 12: Graph TheoryVertex (node)CycleEdge-
Page 13: Yeast Protein Linkage Map Project
Page 17 and 18: www.pathguide.org
Page 23 and 24: Data standards• There are none cu
Page 25 and 26: CellMap.org
Page 27 and 28: PATIKA.org
Page 29 and 30: Rual JF, et al. Nature, (2005), 437
Page 31 and 32: Yeast protein complexesKrogan NJ.,
Page 33 and 34: Many ways to draw the samethingsLe
Page 35: Cytoscape• Open source platform f
Page 43 and 44: Osprey
Page 45 and 46: Cerami, et al. PLoS One, (2010), 5,
Page 47 and 48: Cerami, et al. PLoS One, (2010), 5,
Page 49 and 50: How to assess reliability?• Repea
Page 51 and 52: Human PPI (2006)Gandhi TKB. et al.,
Page 53 and 54: Milo R., et al., Science, 298:824-8
Page 55 and 56: Zhang LV., et al., J Biol. 2005;4(2
Page 57 and 58: Barabasi AL, et al., Nat Rev Genet.
Page 59: Gene Fusion
Page 64 and 65:
Domain-Domain Interactions• Many
Page 66 and 67:
SH3 domain
Page 68 and 69:
Learning the motifsRhoGAPPPI source
Page 70 and 71:
Converting a motif to a profile
Page 73:
Verified PredictionsBetel D. et al.
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Protein-Protein Interactions, Networks and Pathways - Chagall

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