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Enumeration of condition-dependent dense modules in protein interaction networks

Elisabeth Georgii, Sabine Dietmann, Takeaki Uno, Philipp Pagel, Koji Tsuda
2009 Computer applications in the biosciences : CABIOS  
While previous approaches use approximations to extract dense modules, our approach exactly solves the problem of dense module enumeration.  ...  Moreover, by enhancing the yeast network with phenotypic and phylogenetic profiles and the human network with tissue-specific expression data, we identified condition-dependent complex variants.  ...  Dense module enumeration Formally, let us consider the interaction network as undirected weighted graph with node set V .  ... 
doi:10.1093/bioinformatics/btp080 pmid:19213739 pmcid:PMC2660875 fatcat:ebyfhicb4rbyjndosyh7zivzd4

Mining expression-dependent modules in the human interaction network

Elisabeth Georgii, Sabine Dietmann, Takeaki Uno, Philipp Pagel, Koji Tsuda
2007 BMC Bioinformatics  
Acknowledgements We are grateful to Andreas Rüpp for providing a curated set of known human complexes and to Gunnar Rätsch for his encouragement and support.  ...  Many proteins are not steadily present in the cell, but are specifically expressed in dependence of cell type, environmental conditions, and developmental state.  ...  While most previous approaches for module discovery are based on graph partitioning [1] , our algorithm can efficiently enumerate all densely connected modules in the network.  ... 
doi:10.1186/1471-2105-8-s8-s4 fatcat:xjktx57huzft7fqysmp53kleyy

DENSE: efficient and prior knowledge-driven discovery of phenotype-associated protein functional modules

Willam Hendrix, Andrea M Rocha, Kanchana Padmanabhan, Alok Choudhary, Kathleen Scott, James R Mihelcic, Nagiza F Samatova
2011 BMC Systems Biology  
query proteins and identify all the dense functional modules in a biological network that contain some part of the query vertices.  ...  The density (in terms of the number of network egdes) and the enrichment (the number of query proteins in the resulting functional module) can be manipulated via two parameters γ and μ, respectively.  ...  This work was supported in part by the U.  ... 
doi:10.1186/1752-0509-5-172 pmid:22024446 pmcid:PMC3231954 fatcat:4mm2c2qg3fed5nfienikm7rxrm

Protein complexes and functional modules in molecular networks

V. Spirin, L. A. Mirny
2003 Proceedings of the National Academy of Sciences of the United States of America  
Proteins, nucleic acids, and small molecules form a dense network of molecular interactions in a cell. Molecules are nodes of this network, and the interactions between them are edges.  ...  Here, by analyzing the multibody structure of the network of protein-protein interactions, we discovered molecular modules that are densely connected within themselves but sparsely connected with the rest  ...  First, we found experimental complexes that are consistent with the studied network of protein-protein interactions, i.e., that correspond to dense regions of the network.  ... 
doi:10.1073/pnas.2032324100 pmid:14517352 pmcid:PMC218723 fatcat:zalrgffgrzderjwimqtdopihg4

IDENTIFYING DYNAMIC NETWORK MODULES WITH TEMPORAL AND SPATIAL CONSTRAINTS

RUOMING JIN, SCOTT MCCALLEN, CHUN-CHI LIU, YANG XIANG, EIVIND ALMAAS, XIANGHONG JASMINE ZHOU
2008 Biocomputing 2009  
We define a dynamic network module to be a set of proteins satisfying two conditions: (1) they form a connected component in the protein-protein interaction (PPI) network; and (2) their expression profiles  ...  We develop an efficient mining algorithm to discover dynamic modules in a temporal network.  ...  Acknowledgments This work of CCL and XJZ was supported by the grants NIH R01GM074163, NIH U54CA112952, NSF 0515936, and NSF 0747475.  ... 
doi:10.1142/9789812836939_0020 fatcat:ltx7yg7wfrcvzfacw7mxygtz3u

Identifying protein complexes and functional modules--from static PPI networks to dynamic PPI networks

B. Chen, W. Fan, J. Liu, F.-X. Wu
2013 Briefings in Bioinformatics  
In this article, we review computational algorithms for identifying protein complexes and/or functional modules from protein ^protein interaction (PPI) networks.  ...  Then based on types of data used and main ideas involved, we briefly describe protein complex and/or functional module identification algorithms in four categories: (i) those based on topological structures  ...  [91] develop the DME (Dense Module Enumeration) to detect all clusters that satisfy a user-defined minimum density threshold in a given weighted network.  ... 
doi:10.1093/bib/bbt039 pmid:23780996 fatcat:rqgsiknpgvabrcxjvcz5qqvldy

SPICE: discovery of phenotype-determining component interplays

Zhengzhang Chen, Kanchana Padmanabhan, Andrea M Rocha, Yekaterina Shpanskaya, James Mihelcic, Kathleen Scott, Nagiza F Samatova
2012 BMC Systems Biology  
SPICE can be applied to both instance-based data and network-based data.  ...  function; and (3) to improve the predictive skill of the system's phenotype(s) when used collectively in the ensemble of predictive models.  ...  This work was supported in part by the U.S. Department of Energy, Office of Science, the Office of Advanced Scientific Computing Research (ASCR) and the Office of  ... 
doi:10.1186/1752-0509-6-40 pmid:22583800 pmcid:PMC3515406 fatcat:qu42hpuhdjbv5ezdttnjutojfa

Complex Detection in Protein-Protein Interaction Networks: A Compact Overview for Researchers and Practitioners [chapter]

Clara Pizzuti, Simona E. Rombo, Elena Marchiori
2012 Lecture Notes in Computer Science  
The availability of large volumes of protein-protein interaction data has allowed the study of biological networks to unveil the complex structure and organization in the cell.  ...  It has been recognized by biologists that proteins interacting with each other often participate in the same biological processes, and that protein modules may be often associated with specific biological  ...  Protein-protein interaction (PPI) networks can be used for discovering (putative) functional modules, or complexes, consisting of proteins sharing a common function.  ... 
doi:10.1007/978-3-642-29066-4_19 fatcat:y56zkiktwjatber44aocp75auu

Current progress in network research: toward reference networks for key model organisms

B. S. Srinivasan, N. H. Shah, J. A. Flannick, E. Abeliuk, A. F. Novak, S. Batzoglou
2007 Briefings in Bioinformatics  
Rather than clustering a single dataset to produce a static map of functional modules, the focus today is on data integration, network alignment, interactive visualization and ontological markup.  ...  In this review, we briefly survey available datasets in functional genomics, review methods for data integration and network alignment, and describe recent work on using network models to guide experimental  ...  APPLICATIONS OF NETWORK MODELS In the recent past, network analyses often concluded with a list of modules and an enumeration of topological statistics.  ... 
doi:10.1093/bib/bbm038 pmid:17728341 fatcat:bf4b3vro4zf5lngqey4ini4ofq

Module Discovery by Exhaustive Search for Densely Connected, Co-Expressed Regions in Biomolecular Interaction Networks

Recep Colak, Flavia Moser, Jeffrey Shih-Chieh Chu, Alexander Schönhuth, Nansheng Chen, Martin Ester, Raya Khanin
2010 PLoS ONE  
Conclusion/Significance: We demonstrate that the computation of all densely connected and co-expressed regions in interaction networks is an approach to module discovery of considerable value.  ...  To benchmark the predictive power inherent to the approach, we computed all co-expressed, dense regions in physical protein and genetic interaction networks from human and yeast.  ...  This applies in particular for protein-protein interaction networks (e.g. [8, 9] ) since the physical interaction of two gene products is vital for the two genes to commonly exert function.  ... 
doi:10.1371/journal.pone.0013348 pmid:21049092 pmcid:PMC2963598 fatcat:j4tqhvtflbg5dmbwgtpoukobsu

Complex Disease Interventions from a Network Model for Type 2 Diabetes

Deniz Rende, Nihat Baysal, Betul Kirdar, Thierry Alquier
2013 PLoS ONE  
The functional modules in this network were scored and evaluated in terms of shared pathways, co-localization, co-expression and associations with similar diseases.  ...  There is accumulating evidence that the proteins encoded by the genes associated with a common disorder interact with each other, participate in similar pathways and share GO terms.  ...  Enumeration of Functional Modules in T2DFN Genes participate in similar biological processes, share GO terms and operate in similar functions have a tendency to localize as dense groups in interaction  ... 
doi:10.1371/journal.pone.0065854 pmid:23776558 pmcid:PMC3679160 fatcat:ur6lacibdvdx7b4pffxd3emjne

A Survey of Graph Mining Techniques for Biological Datasets [chapter]

S. Parthasarathy, S. Tatikonda, D. Ucar
2010 Managing and Mining Graph Data  
The field of bioinformatics has emerged as important application area in this context. Examples abound ranging from the analysis of protein interaction networks to the analysis of phylogenetic data.  ...  Mining structured information has been the source of much research in the data mining community over the last decade.  ...  Acknowledgments The authors wish to acknowledge the support of NSF CAREER Grant IIS-0347662.  ... 
doi:10.1007/978-1-4419-6045-0_18 dblp:series/ads/ParthasarathyTU10 fatcat:aeu53r3dbzd67d5whkjypv64uq

Modularity and Dynamics of Cellular Networks

Yuan Qi, Hui Ge
2006 PLoS Computational Biology  
Traditionally, focus has been given to the characterization of individual genes/proteins or individual interactions during cellular events.  ...  Rather, they arise from characteristics of cellular networks, which represent connections between molecules in cells.  ...  Zhang for critical reading of the manuscript. We also thank two anonymous reviewers for their invaluable inputs. We thank T. S. Jaakkola and D. K. Gifford for their support. Author contributions. Y.  ... 
doi:10.1371/journal.pcbi.0020174 pmid:17196032 pmcid:PMC1761653 fatcat:lbh3p667kbhubegexlnfmglw24

Efficient α, β-motif finder for identification of phenotype-related functional modules

Matthew C Schmidt, Andrea M Rocha, Kanchana Padmanabhan, Zhengzhang Chen, Kathleen Scott, James R Mihelcic, Nagiza F Samatova
2011 BMC Bioinformatics  
By comparing dozens of genome-scale networks of functionally associated proteins, our method efficiently identifies those statistically significant functional modules that are in at least a networks of  ...  The functional module is modeled as an (a, b)-clique, where a and b are two criteria introduced in this work. We also propose a novel network model, called the two-typed, divided network.  ...  The maximal clique enumeration problem depends on the number of cliques in the input graph, and in worst case that number can be 3 n 3 , where n is the number of vertices in the graph [32] .  ... 
doi:10.1186/1471-2105-12-440 pmid:22078292 pmcid:PMC3287386 fatcat:yaxcqiogqjd2dmz7vrkwt7wk4a

ModuleDiscoverer: Identification of regulatory modules in protein-protein interaction networks [article]

Sebastian Vlaic, Christian Tokarski-Schnelle, Mika Gustafsson, Uta Dahmen, Reinhard Guthke, Stefan Schuster
2017 bioRxiv   pre-print
The identification of disease associated modules based on protein-protein interaction networks (PPINs) and gene expression data has provided new insights into the mechanistic nature of diverse diseases  ...  Current strategies solve the maximal clique enumeration (MCE) problem, i.e., the enumeration of all non-extendable groups of proteins, where each pair of proteins is connected by an edge.  ...  Jens Schumacher (Institute of Stochastics) and Stefan Lang (Institute for Bioinformatics) from the Friedrich-Schiller-University Jena for helpful discussions.  ... 
doi:10.1101/119099 fatcat:qadzz7kldrczdd74nfoyic4utq
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