florencio pazos (cnb-csic)€¦ · •gavin, a.c., et al. (2002) functional organisation of the...
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BIOINFORMÁTICA Y BIOLOGÍA COMPUTACIONAL
Curso de la Escuela Complutense de Verano 2007
Florencio Pazos (CNB-CSIC)
Redes de Interacciones entre Proteínas
Florencio Pazos CabaleiroComputational Systems Biology GroupCentro Nacional de Biotecnología (CNB-CSIC)[email protected]://pdg.cnb.uam.es
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Redes de Interacciones entre Proteínas
- El Interactoma- Determinación experimental masiva del interactoma- Estudios globales del interactoma
- Características topológicas- Nodos (proteínas) importantes topologicamente- Origen de la topología- Motivos topológicos- Características funcionales- Resumen
- Calidad de los datos masivos de interacciones- Métodos computacionales para predicción de interacciones
- Conservación de cercanía genómica- Fusión génica- Perfiles filogenéticos- Similitud de árboles filogenéticos
- Repositorios on-line de interacciones- Bibliografía
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Biología de SistemasCaracterización masiva de componentes moleculares
y sus relaciones
- Genome sequencing (“genome”).- Transcript characterization (mRNA) (“transcriptome”)- Characteristics of the protein repertory (“proteome”)- Cellular localization of the components (“localizome”)- Gene regulation network (“regulome”)- Protein interaction network (“interactome”)- Massive gene-phenotype studies (“fenoma”)- Metabolic networks (“metabolome”)- ......
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Interactoma
Walhout, A. J. & Vidal, M. (2001). Protein interaction maps for model organisms. Nat Rev Mol Cell Biol 2(1), 55-62.
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Determinación Experimental Masiva del Interactoma
Y2H TAP/MShttp://pubs.acs.org/hotartcl/mdd/00/sep/edwards.html
Uetz, P. and Finley, R.L., Jr. (2005) From protein networks to biological systems. FEBS Lett, 579, 1821-1827.
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Determinación Experimental Masiva del Interactoma
TAP/MS Y2H
A.Valencia
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Interactomas determinados experimentalmente (high throughput)
•Rain, J.C., Selig, L., De Reuse, H., et al. (2001) The protein-protein interaction map of Helicobacter pylori. Nature, 409, 211-215.•Gavin, A.C., et al. (2002) Functional organisation of the yeast proteome by systematic analysis of protein complexes. Nature, 415, 141-147.•Ho, Y., et al. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature, 415, 180-183.•Ito, T., et al. (2000) Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. Proc Natl Acad Sci USA, 97, 1143-1147.•Uetz, P., et al. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature, 403, 623-631.•Giot, L., Bader, J.S., Brouwer, et al. (2003) A protein interaction map of Drosophila melanogaster. Science, 302, 1727-1736.•Li, S., Armstrong, C.M., Bertin, N., et al. (2004) A map of the interactome network of the metazoan C. elegans. Science, 303, 540-543.•Butland, G., Peregrin-Alvarez, J.M., Li, J., et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature, 433, 531-537. • Rual, J.F., Venkatesan, K., Hao, T., Hirozane-Kishikawa, T., Dricot, A., Li, N., Berriz, G.F., Gibbons, F.D., Dreze, M., Ayivi-Guedehoussou, N., et al. (2005) Towards a proteome-scale map of the human protein-protein interaction network. Nature., 437, 1173-1178.• LaCount, D.J., Vignali, M., Chettier, R., Phansalkar, A., Bell, R., Hesselberth, J.R., Schoenfeld, L.W., Ota, I., Sahasrabudhe, S., Kurschner, C., et al. (2005) A protein interaction network of the malaria parasite Plasmodium falciparum. Nature., 438, 103-107.• Uetz, P., Dong, Y.A., Zeretzke, C., Atzler, C., Baiker, A., Berger, B., Rajagopala, S.V., Roupelieva, M., Rose, D., Fossum, E., et al. (2006) Herpesviral protein networks and their interaction with the human proteome. Science., 311, 239-242.
A.Valencia
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Diseño del experimentoSelección de Anzuelos (Baits)
Lappe, M. and Holm, L. (2004) Unraveling protein interaction networks with near-optimal efficiency. Nat Biotechnol, 22, 98-103.
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Propiedades Topologicas Globales del InteractomaParámetros Topológicos
Zhu, X., Gerstein, M. and Snyder, M. (2007) Getting connected: analysis and principles of biological networks. Genes Dev., 21, 1010-1024.
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Propiedades Topologicas Globales del Interactoma
Barabasi, A.L. and Oltvai, Z.N. (2004) Network biology: understanding the cell's functional organization. Nat Rev Genet, 5, 101-113.
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Propiedades topologicas globales del interactomaRed Scale-Free/Jerarquica
Jeong, H., Mason, S. P., Barabasi, A. L. & Oltvai, Z. N. (2001). Lethality and centrality in protein networks. Nature 411, 41-42.
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Fraser, H.B., Hirsh, A.E., Steinmetz, L.M., Scharfe, C. and Feldman, M.W. (2002) Evolutionary rate in the protein interaction network. Science, 296, 750-752.
Nodos Importantes
hub
Hubs
- conserved- lethal- important- ...
Bottlenecks
Yu, H., Kim, P.M., Sprecher, E., Trifonov, V. and Gerstein, M. (2007) The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comput Biol., 3, e59
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Añadiendo Información Dinámica
RandomHubsPartyDate
Han, J.D., Bertin, N., Hao, T., Goldberg, D.S., Berriz, G.F., Zhang, L.V., Dupuy, D., Walhout, A.J., Cusick, M.E., Roth, F.P. and Vidal, M. (2004) Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature, 430, 88-93. Epub 2004 Jun 2009.
de Lichtenberg U, Jensen LJ, Brunak S, Bork P. (2005). Dynamic complex formation during the yeast cell cycle. Science. 307(5710):724-727.
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Aparición de la Estructura Scale-Free
Barabasi, A.L. and Oltvai, Z.N. (2004) Network biology: understanding the cell's functional organization. Nat Rev Genet, 5, 101-113.
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¿Artefactos debido al muestreo (sampling)?
Stumpf, M.P., Wiuf, C. and May, R.M. (2005) Subnets of scale-free networks are not scale-free: Sampling properties of networks. Proc Natl Acad Sci U S A, 102, 4221-4224.
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¿Otros Artefactos?
Deeds, E.J., Ashenberg, O. and Shakhnovich, E.I. (2006) A simple physical model for scaling in protein-protein interaction networks. Proc Natl Acad Sci U S A., 103, 311-316.
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Motivos en la Red de Interacciones
Wuchty, S., Oltvai, Z.N. & Barabasi, A.L. (2003) Evolutionary conservation of motif constituents in the yeast protein interaction network. Nat Genet, 35, 176-179.
Kelley, B.P., et al. (2003) Conserved pathways within bacteria and yeast as revealed by global protein network alignment. Proc Natl Acad Sci U S A, 100, 11394-11399.
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Predicción de Función Basada en el Contexto de Interacciones
Sharan, R., Ulitsky, I. and Shamir, R. (2007) Network-based prediction of protein function. Mol Syst Biol., 3, 88.
Schwikowski, B., Uetz, P. & Fields, S. (2002). A network of protein-protein interactions in yeast. Nature Biotech 18, 1257-1261.
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Estudios globales de la red de interacciones - Resumen
- scale-free / jerarquica=> resistente a fallos aleatorios; caminos cortosTopología scale-free explicable por duplicaciones
- hubs: esenciales/conservados(date/party)
- modulos topológicos <> modulos funcionales
- motivos (pequeños) funcionales conservados
Barabasi, A.L. and Oltvai, Z.N. (2004) Network biology: understanding the cell's functional organization. Nat Rev Genet, 5, 101-113.
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Calidad de los datos de interacciones high throughput
Overlap:6 int !
Estimation (yeast): 12.000-40000 (6000)
Uetz, P. and Finley, R.L., Jr. (2005) From protein networks to biological systems. FEBS Lett, 579, 1821-1827.
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von Mering, C., Krause, R., Snel, B., Cornell, M., Oliver, S.G., Fields, S. and Bork, P. (2002) Comparative assessment of large scale data sets of protein-protein interactions. Nature, 417, 399-403.
Calidad de los datos de interacciones high throughput
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Calidad de los datos de interacciones high throughput
Hoffmann R, Valencia A. (2003). Protein interaction: same network, different hubs. Trends Genet. 19(12):681-683.
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Combinación con Otras Fuentes de Información para Aumentar Fiabilidad
Lee, I., Date, S.V., Adai, A.T. and Marcotte, E.M. (2004) A probabilistic functional network of yeast genes. Science, 306, 1555-1558.
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Predicción Computacional de Interacciones entre Proteínasc) gene fusion
d) similarity of phylogenetic trees
proteindistancematrices
d1
d2
a) phylogenetic profiles
org. 1org. 2org. 3
prot. a prot. b prot. c prot. d
b) conservation of gene neighbouring
org. 4prot. a prot. cprot. a prot. c
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prot. a
prot. b
prot. c
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org. 2
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prot. ab
prot. a prot. borg. 1
org. 1org. 2 org. 2org. 3 org. 3org. 4
org. 4org. 5
org. 5
r: similaritybetweena and b trees
multiple sequence alignments(MSA)
reducedMSAs& implicittrees
Caa Cbb Cab
0.0
+1.0
correlation values distributions
e) correlated mutations
intra-protein inter-protein
intra- and inter-protein correlatedmutations
interaction index between a and b
reducedMSAs
prot. a prot. b prot. a prot. bprot. a prot. b
•Huynen, M., Snel, B., Lathe, W. & Bork, P. (2000) Predicting protein function by genomic context: quantitative evaluation and qualitative inferences. Genome Res, 10, 1204-1210.•Valencia, A. & Pazos, F. (2002) Computational methods for the prediction of protein interactions. Curr Opin Struct Biol, 12, 368-373.•Salwinski, L. & Eisenberg, D. (2003). Computational methods of analysis of protein-protein interactions. Curr Opin Struct Biol. 13, 377-382.
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Conservación de Cercanía Genómica
Dandekar, T., Snel, B., Huynen, M. & Bork, P. (1998). Conservation of gene order: a fingerprint of proteins thatphysicaly interact. Trends Biochem Sci. 23, 324-328.
Overbeek, R., Fonstein, M., D'Souza, M., Pusch, G. D. &Maltsev, N. (1999). Use of contiguity on the chromosome to predict functional coupling. In Silico Biol. 1, 93-108.
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Enright, A. J., Iliopoulos, I., Kyrpides, N. C. & Ouzounis, C. A. (1999). Protein interaction maps for complete genomes based on gene fusion events. Nature. 402, 86-90.
Fusion Génica
Marcotte, E. M., Pellegrini, M., Ho-Leung, N., Rice, D. W.,Yeates, T. O. & Eisenberg, D. (1999). Detecting protein function and protein-protein interactions from genome sequences. Science. 285, 751-753.
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Perfiles Filogenéticos
•Pellegrini, M., Marcotte, E. M., Thompson, M. J., Eisenberg, D. & Yeates, T. O. (1999). Assigning protein functions by comparative genome analysis: Protein pylogenetic profiles. Proc Natl Acad Sci USA. 96, 4285-4288.
•Date, S. V. & Marcotte, E. M. (2003). Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages. NatBiotechnol. 21, 1055-1062.
H(A) = - Σp(a) ln p(a)
pij = -1/logEij
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Perfiles Filogenéticos
• Zhou, Y., Wang, R., Li, L., Xia, X. and Sun, Z. (2006) Inferring functional linkages between proteins from evolutionary scenarios. J Mol Biol., 359, 1150-1159.• Barker, D., Meade, A. and Pagel, M. (2007) Constrained models of evolution lead to improved prediction of functional linkage from correlated gain and loss of genes. Bioinformatics., 23, 14-20.
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Perfiles Filogenéticos
• Bowers, P.M., Cokus, S.J., Eisenberg, D. and Yeates, T.O. (2004) Use of logic relationships to decipher protein network organization. Science, 306, 2246-2249.
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Similitud de Árboles Filogenéticos - MirrorTree
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Goh, C.-S., Bogan, A.A., Joachimiak, M., Walther, D. and Cohen, F.E. (2000) Co-evolution of Proteins with their Interaction Partners.J Mol Biol, 299, 283-293.
Pazos, F. and Valencia, A. (2001) Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Eng, 14, 609-614.
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2c2c_2-4mt2_2 0,9599pap_1-9pap_2 * 0,9072c2c_1-4mt2_2 0,9013pgk_1-3pgk_2 * 0,9014mt2_1-4mt2_2 * 0,8983trx_1-3trx_2 * 0,8944tms_1-4tms_2 * 0,8542c2c_2-4mt2_1 0,8491rnd_1-1rnd_2 * 0,8172c2c_1-4mt2_1 0,8131alc_1-1alc_2 * 0,8014tnc_1-4tnc_2 * 0,7942c2c_1-2c2c_2 * 0,7733pgk_1-4tms_1 0,7563pgk_1-4tms_2 0,7312c2c_1-3adk_1 0,7263pgk_2-4tms_1 0,7232c2c_2-3pgk_1 0,7151alc_1-1rnd_1 0,7122c2c_2-3pgk_2 0,6981alc_2-1rnd_1 0,6971sgt_1-1sgt_2 * 0,6933pgk_2-4tms_2 0,6913adk_2-3dfr_2 0,6751sgt_2-2pf2_2 0,6733dfr_1-3dfr_2 * 0,6722c2c_2-9pap_1 0,6582c2c_1-3pgk_1 0,6483trx_2-9pap_1 0,6461sgt_1-2pf2_2 0,6462c2c_2-3adk_1 0,6313trx_1-9pap_1 0,6272c2c_2-1alc_2 0,6262c2c_1-3pgk_2 0,6203trx_2-9pap_2 0,6201rnd_2-4mt2_1 0,6191alc_2-1rnd_2 0,6071rnd_2-4mt2_2 0,6063blm_1-3blm_2 * 0,6031alc_1-1rnd_2 0,5993trx_1-3pgk_1 0,5953trx_1-9pap_2 0,5891alc_2-4mt2_1 0,5882c2c_1-1alc_2 0,5872c2c_1-9pap_1 0,5813trx_1-3pgk_2 0,5774tnc_1-4mt2_1 0,5563adk_1-3pgk_1 0,554
4tnc_1-4mt2_2 0,4489pap_2-4tnc_1 0,4461alc_2-4mt2_2 0,4461sgt_2-4mt2_1 0,4333adk_1-4tnc_2 0,4211rnd_1-4mt2_2 0,4054tnc_2-4mt2_2 0,4052c2c_1-3adk_2 0,4011sgt_2-2c2c_1 0,3994tms_2-3dfr_2 0,3943adk_1-3dfr_1 0,3901sgt_2-2c2c_2 0,3813adk_2-3dfr_1 0,3721sgt_2-1alc_1 0,3714tms_1-3dfr_2 0,3581sgt_1-4mt2_1 0,3431sgt_1-4mt2_2 0,3369pap_2-4tnc_2 0,3314tms_1-3dfr_1 0,3273trx_1-2c2c_2 0,3193trx_1-2c2c_1 0,3121sgt_1-1alc_1 0,3123trx_2-2c2c_2 0,2873trx_2-2c2c_1 0,2811sgt_1-2c2c_2 0,2701alc_1-4mt2_2 0,2681sgt_1-2c2c_1 0,2682c2c_1-1rnd_1 0,2639pap_1-3adk_2 0,2542c2c_2-3adk_2 0,2543adk_2-3pgk_1 0,2511sgt_1-1rnd_1 0,2383adk_2-3pgk_2 0,2389pap_2-3adk_2 0,2211sgt_2-1alc_2 0,2192c2c_2-1alc_1 0,2039pap_1-4tnc_1 0,2021sgt_2-1rnd_1 0,1911sgt_1-1alc_2 0,1783trx_2-3adk_2 0,1751sgt_1-1rnd_2 0,1682pf2_2-1alc_1 0,1602c2c_1-1alc_1 0,1559pap_1-4tnc_2 0,1492c2c_2-1rnd_2 0,1464tms_2-3dfr_1 0,1303trx_1-3adk_2 0,1282c2c_2-1rnd_1 0,1252c2c_1-1rnd_2 0,113
MirrorTree
Pazos, F. and Valencia, A. (2001) Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Eng, 14, 609-614.
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MirrorTree
Pazos, F. and Valencia, A. (2001) Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Eng, 14, 609-614.
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MirrorTree - Variaciones
Gertz, J., Elfond, G., Shustrova, A., Weisinger, M., Pellegrini, M., Cokus, S. and Rothschild, B. (2003) Inferring protein interactions from phylogenetic distance matrices. Bioinformatics, 19, 2039-2045.
Goh, C.S. and Cohen, F.E. (2002) Co-evolutionary analysis reveals insights into protein-protein interactions. J Mol Biol, 324, 177-192.
Ramani, A.K. and Marcotte, E.M. (2003) Exploiding the co-evolution of interacting proteins to discover interaction specificity. J Mol Biol, 327, 273-284.
Sato, T., Yamanishi, Y., Horimoto, K., Toh, H. and Kanehisa, M. (2003) Prediction of protein-protein interactions from phylogenetic trees using partial correlation coefficient. Genome Informatics, 14, 496-497.
Kim, W.K., Bolser, D.M. and Park, J.H. (2004) Large-scale co-evolution analysis of protein structural interlogues using the global protein structural interactomemap (PSIMAP). Bioinformatics, 20, 1138-1150. Epub 2004 Feb 1135.
Tan, S., Zhang, Z. and Ng, S. (2004) ADVICE: Automated Detection and Validation of Interaction by Co-Evolution. Nucl. Acids. Res., 32, W69-W72.
Jothi, R., Kann, M.G. and Przytycka, T.M. (2005) Predicting protein-protein interaction by searching evolutionary tree automorphism space. Bioinformatics, 21,i241-i250.
Mintseris, J. and Weng, Z. (2005) Structure, function, and evolution of transient and obligate protein-protein interactions. Proc Natl Acad Sci U S A, 102, 10930-10935.
Sato, T., Yamanishi, Y., Kanehisa, M. and Toh, H. (2005) The inference of protein-protein interactions by co-evolutionary analysis is improved by excluding the information about the phylogenetic relationships. Bioinformatics, 21, 3482-3489.
Tillier, E.R., Biro, L., Li, G. and Tillo, D. (2006) Codep: maximizing co-evolutionary interdependencies to discover interacting proteins. Proteins., 63, 822-831.
Jothi, R., Cherukuri, P.F., Tasneem, A. and Przytycka, T.M. (2006) Co-evolutionary Analysis of Domains in Interacting Proteins Reveals Insights into Domain-Domain Interactions Mediating Protein-Protein Interactions. J Mol Biol., 362, 861-875.
Tan, S., Zhang, Z. and Ng, S. (2004) ADVICE: Automated Detection and Validation of Interaction by Co-Evolution. Nucleic Acids Res., 32, W69-W72.
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MirrorTree. Variaciones
• Ramani, A.K. & Marcotte, E.M. (2003) Exploiding the co-evolution of interacting proteins to discover interaction specificity. J Mol Biol, 327, 273-284.• Tillier, E.R., Biro, L., Li, G. and Tillo, D. (2006) Codep: maximizing co-evolutionary interdependencies to discover interacting proteins. Proteins., 63, 822-831.
?
Protein family A(i.e. ligands)
Protein family B(i.e. receptors)
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HGT?.....?
HGT?.....?
Protein A 16SrRNA Protein B
Mul
tiple
seq
uenc
eal
ignm
ents
Phy
loge
netic
trees
Dis
tanc
em
atric
esC
orre
cted
dist
ance
mat
rices
Inte
ract
ion
pred
ictio
nN
on-c
anon
ical
evol
utio
nary
eve
nts
pred
ictio
n
Pazos, F., Ranea, J.A.G., Juan, D. and Sternberg, M.J.E. (2005) Assessing Protein Co-evolution in the Context of the Tree of Life Assists in the Prediction of the Interactome. J Mol Biol, 352, 1002-1015.
MirrorTree
tol-mirrortree
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tol-mirrortree
P00000List of pairs sorted by score
DIP:516 interactions (E coli)
20,087 pairs calculated(115 true)118 proteins with>=1 calculated true interactor
fraction of false positives0%: perfect50%: random
(1 int.)
sen
1-esp
ROC area1.0: perfect0.5: random
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0.9
2
0.7
35
0.5
69
0.0
66
0.9
22
0.7
96
0.5
78
0.0
97
0.9
7
0.8
29
0.6
62
0.1
06
0
0.2
0.4
0.6
0.8
1
25 50 75 100
2.8
16.5
38.7
93.1
2.9
12
35.7
89.8
1.1 6
.4
23.2
88.9
0
20
40
60
80
100
25 50 75 100
% f
alse
pos
itive
s
RO
C a
rea
% cases % cases
10 20 30 40 50 60 70 80 90 1000
10
20
30
40
50
60
70
80
90
100
0
25
50
75
100
125
150
175
200
225
250
% fa
lse
posi
tives
#pro
tein
s in
list
% cases
mirrrotree
mirrortree(tree dist.)
tol-mirrortree
tol-mirrortree
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Comparación con versiones anteriores de mirrortree
P(N) values (sign test):
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tol-mirrortreeDetección concomitante de eventos evolutivos no-estándar
00.10.20.30.40.50.60.70.80.9
1
0 0.5 1 1.5 2 2.5
a) Prolyl-tRNA synthetase
16SrRNA distances (substitutions/site)
prot
ein
dist
ance
s (s
ubst
itutio
ns/s
ite)
0
0.1
0.2
0.3
0.4
0.5
0.6
0 0.5 1 1.5 2 2.5
b) Ribosomal protein L36
16SrRNA distances (substitutions/site)
prot
ein
dist
ance
s (s
ubst
itutio
ns/s
ite)
r= 0.53 r= 0.72
r<=0.5 25% false pos (vs. 15%)Excluding them: 13.7% false pos (vs. 15%)
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A B
16SrRNA
Co-HGT events
Lawrence, J.G. (1997) Selfish operons and speciation by gene transfer. Trends Microbiol, 5, 355-359.
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0.96
0.94
0.91
0.890.87
0.850.82
0.80
0.93
0.91
0.88
0.85
0.830.80
0.77
0.740.72
0.69
SensitivityTP/(TP+FN)
1-Specificity1-TN/(TN+FP)
Tol-mirrortreeMirrortree
Sato, T., Yamanishi, Y., Kanehisa, M. and Toh, H. (2005) The inference of protein-protein interactions by co-evolutionary analysis is improved by excluding the information about the phylogenetic relationships. Bioinformatics, 21, 3482-3489.
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Mirrortree – Usando la Información del Contexto Co-evolutivo
1st level predictions
00 ,1
0 ,20 ,30 ,40 , 50 ,60 , 70 ,80 ,9
1
0 5 0 0 10 0 0 15 0 0 2 0 0 0
Number of predictions
Acc
urac
y
10th level predictions
00 , 1
0 , 20 , 3
0 , 40 ,50 , 6
0 ,70 , 8
0 , 91
0 5 0 0 10 0 0 150 0 2 0 0 0
Number of predictionsA
ccur
acy
MirrorTree
0
0 ,1
0 ,2
0 ,3
0 ,40 , 5
0 ,6
0 , 7
0 ,8
0 ,9
1
0 50 0 10 0 0 15 0 0 2 0 0 0
Number of predictions
Acc
urac
y
Juan, D., Pazos, F. & Valencia A. (2007). High-confidence prediction of global interactomes based on genome-wide co-evolutionary networks. In prep.
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Ejemplos
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Métodos Computacionales de Predicción de Compañeros de Interacción
12345678
11101011
11101101
.... .. .0.0
1.0
intra-protein inter-protein
A B C
DE
GF
√√√√
xxx
• Alfonso Valencia & Florencio Pazos (2002). Prediction of Protein Interactions with Computational Methods. Curr Op Str Biol. 12(3): 368-373. [56/67]
• Alfonso Valencia & Florencio Pazos. (2003). Prediction of protein-protein interactions from evolutionary information. Methods Biochem Anal. 44:411-426.
• Florencio Pazos & Alfonso Valencia (2006). Protein Interactions from an Evolutionary Perspective. In “Evolution of Biological Networks”. Carsten Wiuf & Michael Stumpf (Eds). Imperial College Press/World Scientific. In Press.
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Repositiorios on-line de interacciones predichas
von Mering, C., Huynen, M., Jaeggi, D., Schmidt, S., Bork, P. and Snel, B. (2003) STRING: a database of predicted functional associations between proteins. Nucleic Acids Res, 31, 258-261.
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Bibliografía
• Alm, E. and Arkin, A.P. (2003) Biological networks. Curr Opin Struct Biol, 13, 193-202.
• Xia, Y., Yu, H., Jansen, R., Seringhaus, M., Baxter, S., Greenbaum, D., Zhao, H. and Gerstein, M. (2004) Analyzing cellular biochemistry in terms of molecular networks. Annu Rev Biochem, 73, 1051-1087.
• Uetz, P. and Finley, R.L., Jr. (2005) From protein networks to biological systems. FEBS Lett, 579, 1821-1827.
• Barabasi, A.L. and Oltvai, Z.N. (2004) Network biology: understanding the cell's functional organization. Nat Rev Genet, 5, 101-113.
• Bork, P., Jensen, L.J., von Mering, C., Ramani, A.K., Lee, I. and Marcotte, E.M. (2004) Protein interaction networks from yeast to human. Curr Opin Struct Biol, 14, 292-299.
• Huynen, M.A., Snel, B., von Mering, C. and Bork, P. (2003) Function prediction and protein networks. Curr Opin Cell Biol, 15, 191-198.
• Valencia, A. & Pazos, F. (2002) Computational methods for the prediction of protein interactions. Curr Opin Struct Biol, 12, 368-373.
• Salwinski, L. & Eisenberg, D. (2003). Computational methods of analysis of protein-protein interactions. Curr Opin Struct Biol. 13, 377-382.
Florencio Pazos CabaleiroComputational Systems Biology Group (CNB-CSIC)[email protected]://pdg.cnb.uam.es