Filters








45,937 Hits in 4.1 sec

Physical protein–protein interactions predicted from microarrays

Ta-tsen Soong, Kazimierz O. Wrzeszczynski, Burkhard Rost
2008 Computer applications in the biosciences : CABIOS  
Predicting physical interactions directly from microarrays is both a challenging and important task that we addressed by developing a novel machine learning method optimized for this task.  ...  Motivation: Microarray expression data reveal functionally associated proteins. However, most proteins that are associated are not actually in direct physical contact.  ...  Our method predicted physical protein-protein interactions better than the conventional correlation method, and it discovered meaningful new physical interactions.  ... 
doi:10.1093/bioinformatics/btn498 pmid:18829707 pmcid:PMC2579715 fatcat:7un37scd2rh7npboddsef2iwbe

Genome-Scale Gene Function Prediction Using Multiple Sources of High-Throughput Data in Yeast Saccharomyces cerevisiae

Trupti Joshi, Yu Chen, Jeffrey M. Becker, Nickolai Alexandrov, Dong Xu
2004 Omics  
interactions, protein complexes, microarray gene expression profiles, and annotations of known proteins through an integrative statistical model.  ...  To address this challenge, we have developed GeneFAS (Gene Function Annotation System), a new integrated probabilistic method for cellular function prediction by combining information from protein-protein  ...  ACKNOWLEDGMENTS This work has been supported by Nation Science Foundation (EIA-0325386) and a research contract from Ceres Inc., Malibu, CA. We would like to thank Drs.  ... 
doi:10.1089/omi.2004.8.322 pmid:15703479 fatcat:366hs7jntfb6toozotsgm2sx2e

Introduction: advanced intelligent computing theories and their applications in bioinformatics

M Michael Gromiha, De-Shuang Huang
2012 BMC Bioinformatics  
[10] analyzed the whole brain microarray data and physical connectivity of hippocampus with other brain regions to identify the genes related to Alzheimer's disease and their interactions with proteins  ...  relationship, protein interactions, genome annotation, gene expression, microarray data analysis and so on.  ... 
doi:10.1186/1471-2105-13-s7-i1 pmid:22594994 pmcid:PMC3348015 fatcat:xz3nujn7o5ck3i4o4sehr7nxda

FUNCTION PREDICTION OF UNCHARACTERIZED PROTEINS

TROY HAWKINS, DAISUKE KIHARA
2007 Journal of Bioinformatics and Computational Biology  
Function prediction of uncharacterized protein sequences generated by genome projects has emerged as an important focus for computational biology.  ...  Here, first we review the definition of protein function. Then the recent developments of these methods are introduced with special focus on the type of predictions that can be made.  ...  They combined the orthologous interactions with localization data from GO and microarray expression clusters from both human and yeast cell cycle microarray databases.  ... 
doi:10.1142/s0219720007002503 pmid:17477489 fatcat:n7a5cf3hkbaivbyv6yyjm45wdq

Putting microarrays in a context: Integrated analysis of diverse biological data

O. G. Troyanskaya
2005 Briefings in Bioinformatics  
The focus of this review is on the use of such methods for gene function prediction, understanding of protein regulation and modelling of biological networks.  ...  This review presents an overview of recently developed methods that integrate the analysis of microarray data with sequence, interaction, localisation and literature data, and further outlines current  ...  The databases provide search and download interfaces for physical and genomic interaction data sets, as well as other data collected from multiple publications.  ... 
doi:10.1093/bib/6.1.34 pmid:15826355 fatcat:pjhdv2r3enehhhu23wj6moxojm

Computational Prediction of Protein–Protein Interactions

Lucy Skrabanek, Harpreet K. Saini, Gary D. Bader, Anton J. Enright
2007 Molecular Biotechnology  
Recently a number of computational approaches have been developed for the prediction of protein-protein interactions.  ...  These methods utilize the structural, genomic and biological context of proteins and genes in complete genomes to predict protein interaction networks and functional linkages between proteins.  ...  Acknowledgements The authors would like to thank Ronald Jansen for providing information about Bayesian network based prediction of protein-protein interactions and the graph used for Figure 4 .  ... 
doi:10.1007/s12033-007-0069-2 pmid:18095187 fatcat:6ydmlbymobeghgnqc5r3evlhuq

Mining DNA microarray data using a novel approach based on graph theory

Gabriel del Rio, Theodore F Bartley, Heberto del-Rio, Rammohan Rao, KunLin Jin, David A Greenberg, Mark Eshoo, Dale E Bredesen
2001 FEBS Letters  
The recent demonstration that biochemical pathways from diverse organisms are arranged in scale-free, rather than random, systems [Jeong et al., Nature 407 (2000) 651^654], emphasizes the importance of  ...  Peter Bacchetti from the department of epidemiology and biostatistics at UCSF.  ...  combining data from genomics (microarray technology) and proteomics (protein^protein interactions).  ... 
doi:10.1016/s0014-5793(01)03165-9 pmid:11741594 fatcat:wyz3q73divbjzdstkbvmmejsha

A map of human protein interactions derived from co-expression of human mRNAs and their orthologs

Arun K Ramani, Zhihua Li, G Traver Hart, Mark W Carlson, Daniel R Boutz, Edward M Marcotte
2008 Molecular Systems Biology  
This meta-analysis therefore exploits non-protein-based data, but successfully predicts associations, including 5589 novel human physical protein associations, with measured accuracies of 54±10%, comparable  ...  To evaluate the accuracy of the predicted physical associations, we apply quantitative mass spectrometry shotgun proteomics to measure elution profiles of 3013 human proteins during native biochemical  ...  This study was supported by grants from the NSF (IIS-0325116, EIA-0219061), NIH (GM06779-01, GM076536-01), Welch (F1515), and a Packard Fellowship (EMM).  ... 
doi:10.1038/msb.2008.19 pmid:18414481 pmcid:PMC2387231 fatcat:pzzvxmqwujgfnc2dp2yconvpxq

Interactome Data and Databases: Different Types of Protein Interaction

Javier De Las Rivas, Alberto de Luis
2004 Comparative and Functional Genomics  
is in development and will be applied to browsing protein interaction databases.  ...  Finally, we comment on some assignments of interactome data to defined types of protein interaction and we present a new bioinformatic tool called APIN (Agile Protein Interaction Network browser), which  ...  This system provides a large-scale experimental approach to determine whether or not each pair of proteins from the yeast proteome physically interact.  ... 
doi:10.1002/cfg.377 pmid:18629062 pmcid:PMC2447346 fatcat:c3qxyfxt4necbonzkjkmttkt7a

Computational Prediction of Protein-Protein Interactions [chapter]

Anton J. Enright, Lucy Skrabanek, Gary D. Bader
2005 The Proteomics Protocols Handbook  
Recently a number of computational approaches have been developed for the prediction of protein-protein interactions.  ...  These methods utilize the structural, genomic, and biological context of proteins and genes in complete genomes to predict protein interaction networks and functional linkages between proteins.  ...  Acknowledgment The authors would like to thank Ronald Jansen for providing information about Bayesian network based prediction of protein-protein interactions and the graph used for Fig. 4 .  ... 
doi:10.1385/1-59259-890-0:629 fatcat:felws6qjivaj5mrop42e3dobpq

A Bayesian framework for combining heterogeneous data sources for gene function prediction (inSaccharomyces cerevisiae)

Olga G. Troyanskaya, Kara Dolinski, Art B. Owen, Russ B. Altman, David Botstein
2003 Proceedings of the National Academy of Sciences of the United States of America  
We applied MAGIC to Saccharomyces cerevisiae genetic and physical interactions, microarray, and transcription factor binding sites data and assessed the biological relevance of gene groupings using Gene  ...  A variety of functional genomics experimental techniques are available, from classic methods such as affinity precipitation to advanced high-throughput techniques such as gene expression microarrays.  ...  We appreciate valuable input from Gavin Sherlock, Dianna Fisk, Mike Liang, and Peter Kasson.  ... 
doi:10.1073/pnas.0832373100 pmid:12826619 pmcid:PMC166232 fatcat:txdhacvjp5gnbf6mt6fqntwkzi

DISCOVERING PROTEIN-PROTEIN INTERACTIONS [chapter]

Soon-Heng Tan, See-Kiong Ng
2004 The Practical Bioinformatician  
Next we present various computational approaches to predict protein interactions. The approaches presented include structure-based predictions such as structural homology.  ...  Lastly, we conclude with a caution on the need to counter check detected and/or predicted protein interactions using multiple approaches.  ...  to be physically interacting.  ... 
doi:10.1142/9789812562340_0013 fatcat:iysu4yt4jbb6ze54bqsv2t5dn4

DISCOVERING PROTEIN–PROTEIN INTERACTIONS

SEE-KIONG NG, SOON-HENG TAN
2004 Journal of Bioinformatics and Computational Biology  
Next we present various computational approaches to predict protein interactions. The approaches presented include structure-based predictions such as structural homology.  ...  Lastly, we conclude with a caution on the need to counter check detected and/or predicted protein interactions using multiple approaches.  ...  to be physically interacting.  ... 
doi:10.1142/s0219720004000600 pmid:15290761 fatcat:spjgainxt5crldjikmoyawvb7u

Clustering, Pathway Enrichment, and Protein-Protein Interaction Analysis of Gene Expression in Neurodevelopmental Disorders

Ruchi Yadav, Prachi Srivastava
2018 Advances in Pharmacological Sciences  
A protein-protein interaction study was done to identify proteins that belong to the same pathway.  ...  In this study, we have used four samples of microarray neuronal developmental data: control, RV (resveratrol), NGF (nerve growth factor), and RV + NGF.  ...  have physical interaction with coexpressed proteins [58] .  ... 
doi:10.1155/2018/3632159 pmid:30598663 pmcid:PMC6288580 fatcat:6gznptdvdngftc5bvw5zwp4vsm

Cellular function prediction and biological pathway discovery in Arabidopsis thaliana using microarray data

Trupti Joshi, Yu Chen, Nickolai N. Alexandrov, Dong Xu
2005 International Journal of Bioinformatics Research and Applications  
interactions and annotations of known proteins.  ...  To address this challenge, we have developed a new integrated probabilistic method for cellular function prediction using microarray gene expression profiles, in conjunction with predicted protein-protein  ...  and predicted protein-protein interactions from genomic sequences.  ... 
doi:10.1504/ijbra.2005.007910 pmid:18048140 fatcat:mxvhoqwlyjhf5id35pkqkmezvy
« Previous Showing results 1 — 15 out of 45,937 results