Analysis of protein-protein interaction networks using random walks

Date

2005-08-21

Author

Can, Tolga
Singh, Ambuj K.

Metadata

Show full item record

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Item Usage Stats

226
views

0
downloads

Genome wide protein networks have become reality in recent years due to high throughput methods for detecting protein interactions. Recent studies show that a networked representation of proteins provides a more accurate model of biological systems and processes compared to conventional pair-wise analyses. Complementary to the availability of protein networks, various graph analysis techniques have been proposed to mine these networks for pathway discovery, function assignment, and prediction of complex membership. In this paper, we propose using random walks on graphs for the complex/pathway membership problem. We evaluate the proposed technique on three different probabilistic yeast networks using a benchmark dataset of 27 complexes from the MIPS complex catalog database and 10 pathways from the KEGG pathway database. Furthermore, we compare the proposed technique to two other existing techniques both in terms of accuracy and running time performance, thus addressing the scalability issue of such analysis techniques for the first time. Our experiments show that the random walk technique achieves similar or better accuracy with more than 1,000 times speed-up compared to the best competing technique.

Subject Keywords

Applied computing, Life and medical sciences

URI

https://hdl.handle.net/11511/38846

DOI

https://doi.org/10.1145/1134030.1134042

Collections

Department of Computer Engineering, Conference / Seminar

Suggestions

OpenMETU
Core

Integration of topological measures for eliminating non-specific interactions in protein interaction networks BAYIR, Murat Ali; GUNEY, Tacettin Dogacan; Can, Tolga (Elsevier BV, 2009-05-28) High-throughput protein interaction assays aim to provide a comprehensive list of interactions that govern the biological processes in a cell. These large-scale sets of interactions, represented as protein-protein interaction networks, are often analyzed by computational methods for detailed biological interpretation. However, as a result of the tradeoff between speed and accuracy, the interactions reported by high-throughput techniques occasionally include non-specific (i.e., false-positive) interactions. ...
Discovering functional interaction patterns in protein-protein interaction networks Turanalp, Mehmet E.; Can, Tolga (Springer Science and Business Media LLC, 2008-06-11) Background: In recent years, a considerable amount of research effort has been directed to the analysis of biological networks with the availability of genome-scale networks of genes and/or proteins of an increasing number of organisms. A protein-protein interaction (PPI) network is a particular biological network which represents physical interactions between pairs of proteins of an organism. Major research on PPI networks has focused on understanding the topological organization of PPI networks, evolution...
Quantitative Analysis of MAP-Mediated Regulation of Microtubule Dynamic Instability In Vitro—Focus on Tau Kiriş, Erkan; Feinstein, Stuart C. (Elsevier Science, 2010-05-01) The regulation of microtubule growing and shortening dynamics is essential for proper cell function and viability, and microtubule-associated proteins (MAPs) such as the neural protein tau are critical regulators of these dynamic processes. Further, we and our colleagues have proposed that misregulation of microtubule dynamics may contribute to tau-mediated neuronal cell death and dementia in Alzheimer's and related diseases. In the first part of this chapter, we present a general background on microtubule ...
Prediction of the effects of single amino acid variations on protein functionality with structural and annotation centric modeling Cankara, Fatma; Tunçbağ, Nurcan; Department of Bioinformatics (2020) Whole-genome and exome sequencing studies have indicated that genomic variations may cause deleterious effects on protein functionality via various mechanisms. Single nucleotide variations that alter the protein sequence, and thus, the structure and the function, namely non-synonymous SNPs (nsSNP), are associated with many genetic diseases in human. The current rate of manually annotating the reported nsSNPs cannot catch up with the rate of producing new sequencing data. To aid this process, automated compu...
Quantitative Analysis of MAP-Mediated Regulation of Microtubule Dynamic Instability In Vitro: Focus on Tau Kiriş, Erkan; Feinstein, Stuart C (Elsevier, 2010-01-01) The regulation of microtubule growing and shortening dynamics is essential for proper cell function and viability, and microtubule-associated proteins (MAPs) such as the neural protein tau are critical regulators of these dynamic processes. Further, we and our colleagues have proposed that misregulation of microtubule dynamics may contribute to tau-mediated neuronal cell death and dementia in Alzheimer’s and related diseases. In the first part of this chapter, we present a general background on microtubule ...

Citation Formats

T. Can and A. K. Singh, “Analysis of protein-protein interaction networks using random walks,” 2005, Accessed: 00, 2020. [Online]. Available: https://hdl.handle.net/11511/38846.