Automated linear motif discovery from protein interaction network
Automated linear motif discovery from protein interaction network
... 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...
Integrating biological insights with topological characteristics for improved complex prediction from protein interaction networks
... catalogued, distinct groups of proteins forming complexes can be isolated from them: proteins within a complex form many interactions with each other than with proteins not in the complex Quite naturally, ... protein interactions from an organism are typically assembled in the form of a network with the proteins as nodes and the interactions among them as edges, commonly calle...
Báo cáo y học: "A scale of functional divergence for yeast duplicated genes revealed from analysis of the protein-protein interaction network" doc
... (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...
Efficient discovery of binding motif pairs from protein protein interactions
... of stable motif pairs derived from our starting motif pairs and those derived from 10 sets of equal size of random starting motif pairs 85 4.11 The percentage of stable and significant motif pairs ... methods for discovering binding motif pairs from different types of protein interaction data These are the discovery of binding motif pairs in the...
Báo cáo khoa học: Flexible nets The roles of intrinsic disorder in protein interaction networks potx
... 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...
Báo cáo y học: "A human functional protein interaction network and its application to cancer data analysis" potx
... 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...
Báo cáo y học: "Modular organization in the reductive evolution of protein-protein interaction networks" pps
... 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...
Báo cáo y học: "Cross-species cluster co-conservation: a new method for generating protein interaction networks" docx
... likely noise Addressing this limitation is an important area for continued effort Data availability Data are available upon request Abbreviations BFS, breadth-first search; CC, co-conservation; ... million years ago (MYA) from O157, an estimated 100 MYA from Salmonella, 200 MYA from Pseudomonas, and 1,200 MYA from Bacillus Thus, we examined a combination of pathogenic and non-pathogenic o...
Báo cáo y học: "Consistent dissection of the protein interaction network by combining global and local metrics" ppt
... 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...
Báo cáo y học: "Connecting the dots in Huntington’s disease with protein interaction networks" pptx
... 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...
Báo cáo y học: "What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae" pot
... 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...
Báo cáo y học: "Protein-protein interaction networks in the spinocerebellar ataxias" pptx
... ataxia-causing protein Y2 H prey Interaction from hORFeome Interaction from cDNA library Figure An interaction network of proteins involved in spinocerebellar ataxias The yeast two-hybrid interaction data ... modifiers confirming interactions and then assessing whether they modulate the functions of the wild-type or disease proteins Indeed, this has been demonstrated for on...
Báo cáo y học: "How complete are current yeast and human protein-interaction networks" pdf
... proteins are purified by affinity chromatography, and their copurified interaction partners are identified by mass spectrometry This assay excels at identifying in vivo protein complexes in yeast and ... degree and essentiality The primary approach to mapping human protein interactions is the same one that initiated the yeast interactome the yeast two-hybrid assay [12,13] Th...
MECHANISMS OF BINDING DIVERSITY IN PROTEIN DISORDER: MOLECULAR RECOGNITION FEATURES MEDIATING PROTEIN INTERACTION NETWORKS
... 1.2 Intrinsic Protein Disorder in Protein- Protein Interactions Many proteins execute their biological functions through protein- protein interactions By binding to interacting partners, proteins ... 1: Introduction 1.1 Intrinsic Protein Disorder and Protein Functions .1 1.2 Intrinsic Protein Disorder in Protein- Protein Interactions 1.3 Characterization of Molecular Rec...
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...
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