The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
Inferring subnetworks from perturbed expression profiles
Abstract
Genome-wide expression profiles of genetic mutants provide a wide variety of measurements of cellular responses to perturbations. Typical analysis of such data identifies genes affected by perturbation and uses clustering to group genes of similar function. In this paper we discover a finer structure of interactions between genes, such as causality, mediation, activation, and inhibition by using a Bayesian network framework. We extend this framework to correctly handle perturbations, and to identify significant subnetworks of interacting genes. We apply this method to expression data of S. cerevisiae mutants and uncover a variety of structured metabolic, signaling and regulatory pathways. Contact: danab@cs.huji.ac.il
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Citations
Cites
Genomic Expression Programs in the Response of Yeast Cells to Environmental Changes
Gasch, A. P., Spellman, P. T., Kao, C. M., Carmel-Harel, O., Eisen, M. B., Storz, G., Botstein, D., & Brown, P. O. (2000) · Molecular Biology of the Cell · doi:10.1091/mbc.11.12.4241 · Cited by 4,815
Cited by
Computational and analytical challenges in single-cell transcriptomics
Stegle, O., Teichmann, S. A., & Marioni, J. C. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3833 · Cited by 1,170
Machine learning in bioinformatics
Larrañaga, P., Calvo, B., Santana, R., Bielza, C., Galdiano, J., Inza, I., Lozano, J. A., Armañanzas, R., Santafé, G., Pérez, A., et al. (2006) · Briefings in Bioinformatics · doi:10.1093/bib/bbk007 · Cited by 867
Inferring gene networks from time series microarray data using dynamic Bayesian networks
Kim, S. Y. (2003) · Briefings in Bioinformatics · doi:10.1093/bib/4.3.228 · Cited by 308
Kim, S., Imoto, S., & Miyano, S. (2004) · Biosystems · doi:10.1016/j.biosystems.2004.03.004 · Cited by 224
An integrative genomics approach to the reconstruction of gene networks in segregating populations
Zhu, J., Lum, P. Y., Lamb, J., GuhaThakurta, D., Edwards, S. W., Thieringer, R., Berger, J. P., Wu, M. S., Thompson, J., Sachs, A. B., et al. (2004) · Cytogenetic and Genome Research · doi:10.1159/000078209 · Cited by 221
Metadata
- Authors
- Pe’er, D., Regev, A., Elidan, G., & Friedman, N.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2001-06-01
- Volume
- 17
- Issue
- suppl_1
- Pages
- S215-S224
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2100603120
- Cited by
- 548
- References
- 1
- FWCI
- 11.62
- Type
- journal article
- Language
- en
- Open access
- closed
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- Pe’er, D., Regev, A., Elidan, G., & Friedman, N. (2001). Inferring subnetworks from perturbed expression profiles. Bioinformatics. https://doi.org/10.1093/bioinformatics/17.suppl_1.s215
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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
