메뉴 건너뛰기




Volumn 4532 LNBI, Issue , 2007, Pages 14-28

Probabilistic paths for protein complex inference

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; BAYESIAN NETWORKS; PROBABILITY;

EID: 38049144771     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-73060-6_2     Document Type: Conference Paper
Times cited : (9)

References (34)
  • 3
    • 0037050026 scopus 로고    scopus 로고
    • Gavin, A.C., Bosche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J.M., Michon, A.M., Cruciat, C.M., Remor, M., Hofert, C., Schelder, M., Brajenovic, M., Ruffner, H., Merino, A., Klein, K., Hudak, M., Dickson, D., Rudi, T., Gnau, V., Bauch, A., Bastuck, S., Huhse, B., Leutwein, C., Heurtier, M.A., Copley, R.R., Edelmann, A., Querfurth, E., Rybin, V., Drewes, G., Raida, M., Bouwmeester, T., Bork, P., Seraphin, B., Kuster, B., Neubauer, G., Superti-Furga, G.: Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141-147 (2002)
    • Gavin, A.C., Bosche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J.M., Michon, A.M., Cruciat, C.M., Remor, M., Hofert, C., Schelder, M., Brajenovic, M., Ruffner, H., Merino, A., Klein, K., Hudak, M., Dickson, D., Rudi, T., Gnau, V., Bauch, A., Bastuck, S., Huhse, B., Leutwein, C., Heurtier, M.A., Copley, R.R., Edelmann, A., Querfurth, E., Rybin, V., Drewes, G., Raida, M., Bouwmeester, T., Bork, P., Seraphin, B., Kuster, B., Neubauer, G., Superti-Furga, G.: Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141-147 (2002)
  • 4
    • 0037050004 scopus 로고    scopus 로고
    • Ho, Y., Gruhler, A., Heilbut, A., Bader, G.D., Moore, L., Adams, S.L., Millar, A., Taylor, P., Bennett, K., Boutilier, K., Yang, L., Woking, C., Donaldson, I., Schandorff, S., Shewnarane, J., Vo, M., Taggart, J., Goudreault, M., Muskat, B., Alfarano, C., Dewar, D., Lin, Z., Michalickova, K., Willems, A.R., Sassi, H., Nielsen, P.A., Rasmussen, K.J., Andersen, J.R., Johansen, L.E., Hansen, L.H., Jespersen, H., Podtelejnikov, A., Nielsen, E., Crawford, J., Poulsen, V., Sorensen, B.D., Matthiesen, J., Hendrickson, R.C., Gleeson, F., Pawson, T., Moran, M.F., Durocher, D., Mann, M., Hogue, C.W., Figeys, D., Tyers, M.: Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415, 180-183 (2002)
    • Ho, Y., Gruhler, A., Heilbut, A., Bader, G.D., Moore, L., Adams, S.L., Millar, A., Taylor, P., Bennett, K., Boutilier, K., Yang, L., Woking, C., Donaldson, I., Schandorff, S., Shewnarane, J., Vo, M., Taggart, J., Goudreault, M., Muskat, B., Alfarano, C., Dewar, D., Lin, Z., Michalickova, K., Willems, A.R., Sassi, H., Nielsen, P.A., Rasmussen, K.J., Andersen, J.R., Johansen, L.E., Hansen, L.H., Jespersen, H., Podtelejnikov, A., Nielsen, E., Crawford, J., Poulsen, V., Sorensen, B.D., Matthiesen, J., Hendrickson, R.C., Gleeson, F., Pawson, T., Moran, M.F., Durocher, D., Mann, M., Hogue, C.W., Figeys, D., Tyers, M.: Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415, 180-183 (2002)
  • 5
    • 0036580169 scopus 로고    scopus 로고
    • Protein interactions: Two methods for assessment of the reliability of high throughput observations
    • Deane, C.M., Salwinski, L., Xenarios, I., Eisenberg, D.: Protein interactions: two methods for assessment of the reliability of high throughput observations. Mol. Cell Proteomics 1, 349-356 (2002)
    • (2002) Mol. Cell Proteomics , vol.1 , pp. 349-356
    • Deane, C.M.1    Salwinski, L.2    Xenarios, I.3    Eisenberg, D.4
  • 6
    • 0037161731 scopus 로고    scopus 로고
    • Comparative assessment of large-scale data sets of protein-protein interactions
    • von Mering, C., Krause, R., Snel, B., Cornell, M., Oliver, S.G., Fields, S., Bork, P.: Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417, 399-403 (2002)
    • (2002) Nature , vol.417 , pp. 399-403
    • von Mering, C.1    Krause, R.2    Snel, B.3    Cornell, M.4    Oliver, S.G.5    Fields, S.6    Bork, P.7
  • 7
    • 9144264169 scopus 로고    scopus 로고
    • Li, S., Armstrong, C.M., Bertin, N., Ge, H., Milstein, S., Boxem, M., Vidalain, P.O., Han, J.D., Chesneau, A., Hao, T., Goldberg, D.S., Li, N., Martinez, M., Rual, J.F., Lamesch, P., Xu, L., Tewari, M., Wong, S.L., Zhang, L.V., Berriz, G.F., Jacotot, L., Vaglio, P., Reboul, J., Hirozane-Kishikawa, T., Li, Q., Gabel, H.W., Elewa, A., Baumgartner, B., Rose, D.J., Yu, H., Bosak, S., Sequerra, R., Fraser, A., Mango, S.E., Saxton, W.M., Strome, S., Van Den Heuvel, S., Piano, F., Vandenhaute, J., Sardet, C., Gerstein, M., Doucette-Stamm, L., Gunsalus, K.C., Harper, J.W., Cusick, M.E., Roth, F.P., Hill, D.E., Vidal, M.: A map of the interactome network of the metazoan C. elegans. Science 303, 540-543 (2004)
    • Li, S., Armstrong, C.M., Bertin, N., Ge, H., Milstein, S., Boxem, M., Vidalain, P.O., Han, J.D., Chesneau, A., Hao, T., Goldberg, D.S., Li, N., Martinez, M., Rual, J.F., Lamesch, P., Xu, L., Tewari, M., Wong, S.L., Zhang, L.V., Berriz, G.F., Jacotot, L., Vaglio, P., Reboul, J., Hirozane-Kishikawa, T., Li, Q., Gabel, H.W., Elewa, A., Baumgartner, B., Rose, D.J., Yu, H., Bosak, S., Sequerra, R., Fraser, A., Mango, S.E., Saxton, W.M., Strome, S., Van Den Heuvel, S., Piano, F., Vandenhaute, J., Sardet, C., Gerstein, M., Doucette-Stamm, L., Gunsalus, K.C., Harper, J.W., Cusick, M.E., Roth, F.P., Hill, D.E., Vidal, M.: A map of the interactome network of the metazoan C. elegans. Science 303, 540-543 (2004)
  • 8
    • 0345600247 scopus 로고    scopus 로고
    • Giot, L., Bader, J.S., Brouwer, C., Chaudhuri, A., Kuang, B., Li, Y., Hao, Y.L., Ooi, C.E., Godwin, B., Vitols, E., Vijayadamodar, G., Pochart, P., Machineni, H., Welsh, M., Kong, Y., Zerhusen, B., Malcolm, R., Varrone, Z., Collis, A., Minto, M., Burgess, S., McDaniel, L., Stimpson, E., Spriggs, F., Williams, J., Neurath, K., Ioime, N., Agee, M., Voss, E., Furtak, K., Renzulli, R., Aanensen, N., Carrolla, S., Bickelhaupt, E., Lazovatsky, Y., DaSilva, A., Zhong, J., Stanyon, C.A., Finley, R.L., White Jr., K.P., Braverman, M., Jarvie, T., Gold, S., Leach, M., Knight, J., Shimkets, R.A., McKenna, M.P., Chant, J., Rothberg, J.M.: A Protein Interaction Map of Drosophila melanogaster. Science 302, 1727-1736 (2003)
    • Giot, L., Bader, J.S., Brouwer, C., Chaudhuri, A., Kuang, B., Li, Y., Hao, Y.L., Ooi, C.E., Godwin, B., Vitols, E., Vijayadamodar, G., Pochart, P., Machineni, H., Welsh, M., Kong, Y., Zerhusen, B., Malcolm, R., Varrone, Z., Collis, A., Minto, M., Burgess, S., McDaniel, L., Stimpson, E., Spriggs, F., Williams, J., Neurath, K., Ioime, N., Agee, M., Voss, E., Furtak, K., Renzulli, R., Aanensen, N., Carrolla, S., Bickelhaupt, E., Lazovatsky, Y., DaSilva, A., Zhong, J., Stanyon, C.A., Finley, R.L., White Jr., K.P., Braverman, M., Jarvie, T., Gold, S., Leach, M., Knight, J., Shimkets, R.A., McKenna, M.P., Chant, J., Rothberg, J.M.: A Protein Interaction Map of Drosophila melanogaster. Science 302, 1727-1736 (2003)
  • 9
    • 3042523388 scopus 로고    scopus 로고
    • Predicting Protein Complex Membership Using Probabilistic Network Reliability
    • Asthana, S., King, O.D., Gibbons, F.D., Roth, F.P.: Predicting Protein Complex Membership Using Probabilistic Network Reliability. Genome Res. 14, 1170-1175 (2004)
    • (2004) Genome Res , vol.14 , pp. 1170-1175
    • Asthana, S.1    King, O.D.2    Gibbons, F.D.3    Roth, F.P.4
  • 10
    • 0347473809 scopus 로고    scopus 로고
    • Gaining confidence in high-throughput protein interaction networks
    • Bader, J.S., Chaudhuri, A., Rothberg, J.M., Chant, J.: Gaining confidence in high-throughput protein interaction networks. Nat. Biotechnol. 22, 78-85 (2004)
    • (2004) Nat. Biotechnol , vol.22 , pp. 78-85
    • Bader, J.S.1    Chaudhuri, A.2    Rothberg, J.M.3    Chant, J.4
  • 12
    • 2942541277 scopus 로고    scopus 로고
    • Predicting co-complexed protein pairs using genomic and proteomic data integration
    • Zhang, L.V., Wong, S.L., King, O.D., Roth, F.P.: Predicting co-complexed protein pairs using genomic and proteomic data integration. BMC Bioinformatics 5, 38 (2004)
    • (2004) BMC Bioinformatics , vol.5 , pp. 38
    • Zhang, L.V.1    Wong, S.L.2    King, O.D.3    Roth, F.P.4
  • 14
    • 0037447257 scopus 로고    scopus 로고
    • Assessing experimentally derived interactions in a small world
    • Goldberg, D.S., Roth, F.P.: Assessing experimentally derived interactions in a small world. Proc Natl Acad Sci. USA 100, 4372-4376 (2003)
    • (2003) Proc Natl Acad Sci. USA , vol.100 , pp. 4372-4376
    • Goldberg, D.S.1    Roth, F.P.2
  • 16
    • 0038492417 scopus 로고    scopus 로고
    • A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae)
    • Troyanskaya, O.G., Dolinski, K., Owen, A.B., Altman, R.B., Botstein, D.: A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae). Proc Natl Acad Sci. USA 100, 8348-8353 (2003)
    • (2003) Proc Natl Acad Sci. USA , vol.100 , pp. 8348-8353
    • Troyanskaya, O.G.1    Dolinski, K.2    Owen, A.B.3    Altman, R.B.4    Botstein, D.5
  • 20
    • 9444239213 scopus 로고    scopus 로고
    • A probabilistic functional network of yeast genes
    • Lee, I., Date, S.V., Adai, A.T., Marcotte, E.M.: A probabilistic functional network of yeast genes. Science 306, 1555-1558 (2004)
    • (2004) Science , vol.306 , pp. 1555-1558
    • Lee, I.1    Date, S.V.2    Adai, A.T.3    Marcotte, E.M.4
  • 21
    • 1542271409 scopus 로고    scopus 로고
    • Predicting protein function from protein/protein interaction data: A probabilistic approach
    • Letovsky, S., Kasif, S.: Predicting protein function from protein/protein interaction data: a probabilistic approach. Bioinformatics 19, 197-204 (2003)
    • (2003) Bioinformatics , vol.19 , pp. 197-204
    • Letovsky, S.1    Kasif, S.2
  • 22
    • 0142241336 scopus 로고    scopus 로고
    • Greedily building protein networks with confidence
    • Bader, J.S.: Greedily building protein networks with confidence. Bioinformatics 19, 1869-1874 (2003)
    • (2003) Bioinformatics , vol.19 , pp. 1869-1874
    • Bader, J.S.1
  • 24
    • 2942552459 scopus 로고    scopus 로고
    • An automated method for finding molecular complexes in large protein interaction networks
    • Bader, G.D., Hogue, C.W.: An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 4, 2 (2003)
    • (2003) BMC Bioinformatics , vol.4 , pp. 2
    • Bader, G.D.1    Hogue, C.W.2
  • 25
    • 0142059836 scopus 로고    scopus 로고
    • Protein complexes and functional modules in molecular networks
    • Spirin, V., Mirny, L.A.: Protein complexes and functional modules in molecular networks. Proc Natl Acad Sci. USA 100, 12123-12128 (2003)
    • (2003) Proc Natl Acad Sci. USA , vol.100 , pp. 12123-12128
    • Spirin, V.1    Mirny, L.A.2
  • 29
    • 0038699587 scopus 로고    scopus 로고
    • Global protein function prediction from protein-protein interaction networks
    • Vazquez, A., Flammini, A., Maritan, A., Vespignani, A.: Global protein function prediction from protein-protein interaction networks. Nat. Biotechnol. 21, 697-700 (2003)
    • (2003) Nat. Biotechnol , vol.21 , pp. 697-700
    • Vazquez, A.1    Flammini, A.2    Maritan, A.3    Vespignani, A.4
  • 30
    • 13444311045 scopus 로고    scopus 로고
    • Predicting protein functions with message passing algorithms
    • Leone, M., Pagnani, A.: Predicting protein functions with message passing algorithms. Bioinformatics 21, 239-247 (2005)
    • (2005) Bioinformatics , vol.21 , pp. 239-247
    • Leone, M.1    Pagnani, A.2
  • 32
    • 38049123293 scopus 로고    scopus 로고
    • Making sense of high-throughput protein-protein interaction data. Stat Appl Genet Mol Biol
    • Scholtens, D., Gentleman, R.: Making sense of high-throughput protein-protein interaction data. Stat Appl Genet Mol Biol. 3 Article39 (2004)
    • (2004) Article39 , vol.3
    • Scholtens, D.1    Gentleman, R.2
  • 33
    • 24144486554 scopus 로고    scopus 로고
    • Local modeling of global interactome networks
    • Scholtens, D., Vidal, M., Gentleman, R.: Local modeling of global interactome networks. Bioinformatics 21, 3548-3557 (2005)
    • (2005) Bioinformatics , vol.21 , pp. 3548-3557
    • Scholtens, D.1    Vidal, M.2    Gentleman, R.3
  • 34
    • 38049178390 scopus 로고    scopus 로고
    • Califano, A., Stolovitzky, G.: DREAM Project. http://magnet.c2b2. columbia.edu/news/DREAMInitiative.pdf
    • Califano, A., Stolovitzky, G.: DREAM Project. http://magnet.c2b2. columbia.edu/news/DREAMInitiative.pdf


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.