Some problems in protein protein interaction network growth processes

... without investigation into the links between biological molecules, in particular, protein- protein interactions (PPI) Protein- protein interactions are physical contacts between two or more proteins ... nodes are proteins and edges are protein- protein interactions Usually, a PPI network represents a collection of protein- protein interaction data in an organism For example, by in...

Ngày tải lên: 10/09/2015, 09:24

... number of protein protein interactions ⁄ number of complexes (inter ⁄ comp.), while the STRING search results are presented as number of protein protein interactions (inter.) only Proteins are ... contained regions of intrinsic disorder One example of an ordered hub, calmodulin, makes use of a flexible hinge to facilitate binding diversity Each of these classes and thei...

Ngày tải lên: 07/03/2014, 21:20

... procedures to construct this FI network (Figure 1), and apply this network to the study of glioblastoma multiforme (GBM) and other cancer types by expanding a human curated GBM pathway using our ... of the proteins in the hand-curated GBM pathway In this way we were able to extend the hand-curated pathway from 73 proteins and 187 interactions to 181 proteins and 768 in...

Ngày tải lên: 09/08/2014, 20:22

... robust in terms of discovering protein interaction modules in protein interaction networks than either the global or local algorithm by application to the large yeast protein interaction network Genome ... Ultimately, the global metric in the GN algorithm behaves differently from the local metric in the ECC algorithm In this paper, we propose to resolve t...

Ngày tải lên: 14/08/2014, 08:20

... (Table 2) The evolution of cellular function: from the scale of functional divergence to the evolutionary fates of the duplicated genes Our study was driven by the idea that investigating the cellular ... proposal of a functional scale of divergence for yeast duplicated genes As our work makes use of functional gene annotations and interact...

Ngày tải lên: 14/08/2014, 14:21

... cutoffs, most of the FYI party hubs also qualify as party hubs in the DIP network and the FYI date hubs as DIP date hubs (Figure 2) The resulting number of proteins in each category in the respective ... static hubs (party hubs) and dynamic hubs (date hubs) [14] The party hubs are found in static complexes where they interact with most of their partners at the same tim...

Ngày tải lên: 14/08/2014, 16:21

... neither motifs can 22 Protein A Motif Discovery Algorithms Figure The One-to-Many (OTM) approach to finding motif from interaction data Dotted arrow denotes interaction between two sequences Motifs ... directly for motifs Specifically, not many motif discovery algorithms (in fact, only one algorithm to the best of our knowledge) have been designed to mine motifs directly fr...

Ngày tải lên: 30/09/2015, 14:24

... excludes the possibility of it being nominative, then the relative pronoun may be taken to be the subject of the clause This applies to about half of all the instances where the function of the relative ... fact only in subordinate clauses and in the part of a main clause after the finite verb Since in a main clause, unless it is interrogative or imperative,...

Ngày tải lên: 07/03/2014, 18:20

Ngày tải lên: 23/06/2014, 00:20

Ngày tải lên: 14/11/2014, 12:24

... Predicting protein–protein interaction sites (Eur J Biochem 269) 1357 More recently, methods were devised for predicting residues involved in protein interaction sites in the absence of any structural ... (1997) Analysis of protein–protein interaction sites using surface patches J Mol Biol 272, 121–132 14 Jones, S & Thornton, J.M (1997) Prediction of protein–prote...

Ngày tải lên: 21/02/2014, 15:20

... completeness of information obtained from abstracts in comparison to the full-length articles as a measure of reliability of abstracts as sources of protein interaction data METHODS Selection of articles ... (proprietary protein interactions maps database from Jubilant Biosys Ltd.) was used IMaps is a manually curated database with more than 200 000 protein- protein,...

Ngày tải lên: 22/06/2014, 19:20

... Therefore, rather than fragmenting the network, the removal of nodes and links in the Buchnera network maintains the global topology of the network, preserving the main interaction backbone The prefer- ... within the interaction network are important in the reductive process Accordingly, the importance of the roles of the proteins must be taken into c...

Ngày tải lên: 14/08/2014, 07:21

... shown that by combining protein- protein data and phylogenetic information it is possible to systematically describe biologically relevant modules in protein networks which partially correlate ... reviews Proteins Proteins Proteins Module Proteins comment Species Module Proteins Poyatos and Hurst R93.3 (b) Interaction matrix Proteins Proteins (a) Genome Biology 2004, R93.4 Genome B...

Ngày tải lên: 14/08/2014, 14:21

... hypothetical protein- protein interaction network Each sphere represents a protein and the connecting lines represent protein- protein interactions Within an interaction network, smaller local interaction ... and independently fusing these domains with candidate interacting proteins [21,22] Constructs encoding these fusion proteins are transformed into yeast cells; if the two...

Ngày tải lên: 14/08/2014, 14:21