Lecture Notes in Bioinformatics pot

[...]... CC2002 hypothetical protein CC1365 hypothetical protein CC2003 hypothetical protein CC3206 preprotein transl CC2102 hypothetical protein CC1887 hypothetical protein Cj1518 possible molybdop Cj0156c hypothetical p Cj0881c hypothetical protein (a) C jejuni: Glycosylation CC1547 rod shape-determi (b) C crescentus: Bacterial cytoskeleton Fig 6 Case Studies (a) Network integration detects new proteins linked... transferase CC0706 hypothetical protein CC3252 hypothetical protein CC2271 hypothetical protein Cj1321 putative transferase Cj1550c e ATP/GTP- Cj0128c suhB-like pr CC2208 hypothetical p CC2428 polysaccharide de CC0827 ypothetical protein CC1543 rod shape-determi CC0082 hypothetical protein CC3483 etical protein CC0228 hypothetical protein CC1544 rod shape-determi CC3705 hypothetical protein Cj1124c putative... summary of which proteins work together within a single organism For each of the 11 organisms listed in the Appendix1 we begin by assembling a training set of known functional modules (Figure 1a) and a battery of different predictors (Figure 1b) of functional association To gain intuition for what our 1 Viewable at http://jinome.stanford.edu/pdfs/recomb06182 appendix.pdf Integrated Protein Interaction Networks... functionally linked pairs aggregate in the upper right corner of the plot, in the region of high coexpression and coinheritance 6 B.S Srinivasan et al Crucially, the linked pairs (red) are more easily distinguished from the unlinked pairs (blue) in the 2-dimensional scatter plot than they are in the accompanying 1-dimensional marginals To quantify the extent to which this is true, we begin by computing P... 306 (2004) 2246–2249 Integrated Protein Interaction Networks for 11 Microbes 13 9 Pazos, F., Valencia, A.: Similarity of phylogenetic trees as indicator of proteinprotein interaction Protein Eng 14 (2001) 609–614 Evaluation Studies 10 Gerstein, M., Lan, N., Jansen, R.: Proteomics Integrating interactomes Science 295 (2002) 284–287 Comment 11 Hoffmann, R., Valencia, A.: Protein interaction: same network,... associations in protein families and in the protein database We also use this model in optimizing site-directed recombination experiments to preserve significant interactions and thereby increase the frequency of generating useful recombinants We formulate the optimization as a sequentially-constrained hypergraph partitioning problem; the quality of recombinant libraries wrt a set of breakpoints is characterized... evolutionary interactions, and effects of site-directed protein recombination (a) Higher-order evolutionary interactions (here, order-3) determining protein stability and function are observed in the statistics of “hyperconservation” of mutually interacting positions The left edge is dominated by Ala,Val,Ile and Val,Leu,Leu interactions, while the right is dominated by Glu,Thr,Arg and Asp,Ser,Lys ones The interactions... insights into function [12, 13] This paper develops a rigorous basis for representing multi-order interactions within a protein family We generalize the traditional representations of sequence information in terms of single-position conservation and structural interactions in terms of pairwise contacts Instead, we define a hypergraph model in which edges represent pairwise and higher-order residue interactions,... method is capable of distinguishing functionally linked pairs (L = 1) from unlinked pairs (L = 0) 2.3 Network Integration For clarity, we first illustrate network integration with two evidence types (corresponding to two Euclidean dimensions) in C crescentus, and then move to the N-dimensional case Integrated Protein Interaction Networks for 11 Microbes 5 Fig 2 2D Network Integration in C crescentus (a)... contact as linked) [25] The former representation produces a nontrivial number of false positives, while the latter incurs a surfeit of false negatives We chose the “matrix” based training set because our algorithm is robust to noise in the training set so long as enough data is present Note that we have used an annotation on individual proteins to produce a training set on pairs of proteins In Figure . Copyright Law. Springer is a part of Springer Science+Business Media springer.com © Springer-Verlag Berlin Heidelberg 2006 Printed in Germany Typesetting: Camera-ready. forum. Following the decision made in 2005 by the Steering Committee, RECOMB Proceedings are published as a volume of Lecture Notes in Bioinformatics (LNBI),