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Characterization of Protein Hubs by Inferring Interacting Motifs from Protein Interactions

Ramon Aragues, Andrej Sali, Jaume Bonet, Marc A. Marti-Renom, Baldo Oliva
2007 PLoS Computational Biology  
Citation: Aragues R, Sali A, Bonet J, Marti-Renom MA, Oliva B (2007) Characterization of protein hubs by inferring interacting motifs from protein interactions. PLoS Comput Biol 3(9): e178.  ...  The approach is evaluated by comparing the inferred interacting motifs with domain families defined for 368 proteins in the Structural Classification of Proteins (SCOP).  ...  RA is supported by a grant from the Spanish Ministerio de Ciencia y Tecnología (MCyT, BIO2002-03609). The work has been supported by grants from the Spanish Ministerio de Educació n y Ciencia (  ... 
doi:10.1371/journal.pcbi.0030178 pmid:17941705 pmcid:PMC1976338 fatcat:ojiupuzny5dcdnyj2ebt5vudde

Characterization of Protein Hubs by Inferring Interacting Motifs from Protein Interactions

Ramon Aragues, Andrej Sali, Jaume Bonet, Marc Marti-Renom, Baldomero Oliva
2005 PLoS Computational Biology  
Citation: Aragues R, Sali A, Bonet J, Marti-Renom MA, Oliva B (2007) Characterization of protein hubs by inferring interacting motifs from protein interactions. PLoS Comput Biol 3(9): e178.  ...  The approach is evaluated by comparing the inferred interacting motifs with domain families defined for 368 proteins in the Structural Classification of Proteins (SCOP).  ...  RA is supported by a grant from the Spanish Ministerio de Ciencia y Tecnología (MCyT, BIO2002-03609). The work has been supported by grants from the Spanish Ministerio de Educació n y Ciencia (  ... 
doi:10.1371/journal.pcbi.0030178.eor fatcat:62tadnzqebalzk3qgzjzglidxy

Toward the dynamic interactome: it's about time

T. M. Przytycka, M. Singh, D. K. Slonim
2010 Briefings in Bioinformatics  
Here we review the beginnings of a new subfield within computational biology, one focused on the global inference and analysis of the dynamic interactome.  ...  Dynamic molecular interactions play a central role in regulating the functioning of cells and organisms.  ...  Acknowledgements This article was inspired by our involvement in the Pacific Symposium on Biocomputing session 'Dynamics of Biological Networks', which we are co-organizing with Tanya Berger-Wolf (University  ... 
doi:10.1093/bib/bbp057 pmid:20061351 pmcid:PMC2810115 fatcat:xbj7ugs6nbed7guys2ie5z3efa

Gene Regulatory Network Analysis of Perivascular Adipose Tissue of Abdominal Aortic Aneurysm Identifies Master Regulators of Key Pathogenetic Pathways

Luca Piacentini, Mattia Chiesa, Gualtiero Ivanoe Colombo
2020 Biomedicines  
The lack of medical therapy to treat abdominal aortic aneurysm (AAA) stems from our inadequate understanding of the mechanisms underlying AAA pathogenesis.  ...  Finally, by analyzing the topological properties of the reconstructed regulatory disease network, we prioritized putative targets for AAA interference treatment options.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/biomedicines8080288 pmid:32823940 fatcat:t3xwmycaandnhkfswopkb37oxy

Discovering functions and revealing mechanisms at molecular level from biological networks

Shihua Zhang, Guangxu Jin, Xiang-Sun Zhang, Luonan Chen
2007 Proteomics  
In particular, various types of molecular networks (e.g., protein-protein interaction (PPI) network; gene regulatory network (GRN); metabolic network (MN); gene coexpression network (GCEN)) have been extensively  ...  prediction from network analysis, inferring molecular networks from biological data as well as representative databases and software tools.  ...  (b) The appropriate domains are assigned to each of the interacting proteins. (c) Inferred DDIs from PPIs and proteins' domain information.  ... 
doi:10.1002/pmic.200700095 pmid:17703505 fatcat:spdclsqf4rdjxkxa7sts4c5u6q

Genetic Interaction Motif Finding by expectation maximization--a novel statistical model for inferring gene modules from synthetic lethality

Yan Qi, Ping Ye, Joel S Bader
2005 BMC Bioinformatics  
Interaction motifs are characterized by position weight matrices and optimized through expectation maximization.  ...  The impact of hub genes the generic probabilistic framework of GIMF may be used to group other types of biological entities such as proteins based on stochastic motifs.  ...  Acknowledgements JSB acknowledges funding from the Whitaker Foundation and the NIH.  ... 
doi:10.1186/1471-2105-6-288 pmid:16332255 pmcid:PMC1334220 fatcat:ftxtaw3tfbcxdb74a5gtbgjwra

Topological properties of protein interaction networks from a structural perspective

Attila Gursoy, Ozlem Keskin, Ruth Nussinov
2008 Biochemical Society Transactions  
We emphasize that the integration of protein interface structure into interaction graph models provides a better explanation of hub proteins, and strengthens the relationship between the role of the hubs  ...  The classification of hub proteins into date and party hubs with distinct properties has significant implications for relating topological properties to the behaviour of the network.  ...  imply endorsement by the U.S.  ... 
doi:10.1042/bst0361398 pmid:19021563 pmcid:PMC7243876 fatcat:fyye7xxguzdxhl7eg6oawqlsku

General Trends in the Evolution of Prokaryotic Transcriptional Regulatory Networks [chapter]

M. Madan Babu, S. Balaji, L. Aravind
2007 Genome Dynamics  
Several studies suggest that the transcriptional network inferred from model organisms may be approximated by a scale-free topology, which in turn implies the presence of a relatively small group of highly  ...  Gene expression in organisms is controlled by regulatory proteins termed transcription factors, which recognize and bind to specific nucleotide sequences.  ...  Acknowledgements The authors gratefully acknowledge the Intramural research program of National Institutes of Health, USA for funding their research.  ... 
doi:10.1159/000107604 pmid:18753785 fatcat:uh4wfkxmz5c7vgjrn4cbalsjqq

Extreme multifunctional proteins identified from a human protein interaction network

Charles E. Chapple, Benoit Robisson, Lionel Spinelli, Céline Guien, Emmanuelle Becker, Christine Brun
2015 Nature Communications  
Overall, extreme multifunctional proteins are enriched in linear motifs and less intrinsically disordered than network hubs.  ...  Here, we propose the first method for the identification of 'extreme multifunctional' proteins from an interactome as a first step to characterize moonlighting proteins.  ...  C.E.C. is a postdoctoral fellow of the Fondation pour la Recherche Médicale and B.R. is the recipient of a PhD fellowship from the AXA Research Fund.  ... 
doi:10.1038/ncomms8412 pmid:26054620 pmcid:PMC4468855 fatcat:xxbeoesbqjgenizijm3ypwvu34

Insights into the Organization of Biochemical Regulatory Networks Using Graph Theory Analyses

Avi Ma'ayan
2008 Journal of Biological Chemistry  
These hubs may interact with many different types of proteins at the same time and location or at different times and locations, resulting in diverse biological responses.  ...  Using graph analyses, biochemical networks are found to be scale-free and small-world, indicating that these networks contain hubs, which are proteins that interact with many other molecules.  ...  The concept of network motifs is illustrated by several examples from cell signaling (Fig. 2) .  ... 
doi:10.1074/jbc.r800056200 pmid:18940806 pmcid:PMC2645810 fatcat:dop4uanz25hg7jh7nwg6c3m3wm

The MoVIN server for the analysis of protein interaction networks

Paolo Marcatili, Giovanni Bussotti, Anna Tramontano
2008 BMC Bioinformatics  
Results: Interactions can be mediated by the presence of specific features, such as motifs, surface patches and domains.  ...  The co-occurrence of these features on proteins interacting with the same protein can indicate mutually exclusive interactions and, therefore, can be used for inferring the involvement of the proteins  ...  Acknowledgements This work was partially supported by the BioSapiens project, funded by the European Commission within its FP6 Programme, under the thematic area "Life sciences, genomics and biotechnology  ... 
doi:10.1186/1471-2105-9-s2-s11 pmid:18387199 pmcid:PMC2323660 fatcat:fsaiawgtbbemtgp3pn35bdmxxq

Protein-protein binding selectivity and network topology constrain global and local properties of interface binding networks

David O. Holland, Benjamin H. Shapiro, Pei Xue, Margaret E. Johnson
2017 Scientific Reports  
However, with limited crystal structures of proteins in complex, homology modeling 5, 14, 15 is needed to help infer domains and interfaces used for interactions.  ...  identifying linear motifs and promiscuous regions 11 , and study the structure and dynamics of multi-protein complexes 12 .  ...  Lastly, to better characterize the hub proteins in our network, some of which do not contain hub interfaces, we assessed the role of disordered regions in hub proteins for Because biological IINs are so  ... 
doi:10.1038/s41598-017-05686-2 pmid:28717235 pmcid:PMC5514078 fatcat:odxyuty3dbcchddrlmpqmfbleu

Understanding Modularity in Molecular Networks Requires Dynamics

R. P. Alexander, P. M. Kim, T. Emonet, M. B. Gerstein
2009 Science Signaling  
HighWire Press; see: cited by This article has been http://stke.sciencemag.org/cgi/content/full/sigtrans;2/81/pe44#otherarticles This article cites 32 articles, 14 of which can be accessed for free: Glossary  ...  stke.sciencemag.org/cgi/content/abstract/sigtrans;2/81/pc14 's sites: Science The editors suggest related resources on References http://stke.sciencemag.org/cgi/content/full/sigtrans;2/81/pe44#BIBL 1 article(s) hosted by  ...  First, by mapping known three-dimensional structures of interacting proteins onto the yeast protein interaction network, two classes of hubs with distinct dynamical behavior were identified (7) .  ... 
doi:10.1126/scisignal.281pe44 pmid:19638611 pmcid:PMC4243459 fatcat:hfehd27adnfwxftgsrkw5qoxem

A Network Biology Study on Circadian Rhythm by Integrating Various Omics Data

Yong Wang, Xiang-Sun Zhang, Luonan Chen
2009 Omics  
Specifically, our method integrated four phase-shift time-course gene expression datasets in rat suprachiasmatic nucleus, protein-protein interactions, phosphorylations of a set of key circadian genes,  ...  By follow-up analysis, we identified four new regulatory hubs that may play crucial roles in the regulation of circadian rhythm.  ...  Y.W. is supported by grant No. 10801131 and X.S.Z. is supported by 10631070 from the National Natural Science Foundation of China.  ... 
doi:10.1089/omi.2009.0040 pmid:19645592 fatcat:zminvropjzbo5gq4kbxl76azjy

Evolutionary Dynamics of Prokaryotic Transcriptional Regulatory Networks

M. Madan Babu, Sarah A. Teichmann, L. Aravind
2006 Journal of Molecular Biology  
types of regulatory motifs.  ...  We show that prokaryotic transcriptional regulatory networks have evolved principally through widespread tinkering of transcriptional interactions at the local level by embedding orthologous genes in different  ...  [18] [19] [20] [21] Alternatively, using an experimentally characterized transcriptional network as template, one can infer transcriptional targets of a regulator in a genome of interest by identifying  ... 
doi:10.1016/j.jmb.2006.02.019 pmid:16530225 fatcat:ygwwcvbqxrdlneo3f7lzbxvqk4
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