The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
A Multiparameter Network Reveals Extensive Divergence between C. elegans bHLH Transcription Factors
Open accessAbstract
SUMMARY Differences in expression, protein interactions and DNA binding of paralogous transcription factors (“TF parameters”) are thought to be important determinants of regulatory and biological specificity. However, both the extent of TF divergence and the relative contribution of individual TF parameters remain undetermined. We comprehensively identify dimerization partners, spatiotemporal expression patterns and DNA binding specificities for the C. elegans bHLH family of TFs, and model these data into an integrated network. This network displays both specificity and promiscuity, as some bHLH proteins, DNA sequences, and tissues are highly connected, whereas others are not. By comparing all bHLH TFs, we find extensive divergence, and that all three parameters contribute equally to bHLH divergence. Our approach provides a framework for examining divergence for other protein families in C. elegans and in other complex multicellular organisms, including humans. Cross-species comparisons of integrated networks may provide further insights into molecular features underlying protein family evolution.
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Smyth, G. K. (2004) · Statistical Applications in Genetics and Molecular Biology · doi:10.2202/1544-6115.1027 · Cited by 11,829
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Saeed, A. I., Sharov, V., White, J., Li, J., Liang, W., Bhagabati, N., Braisted, J., Klapa, M., Currier, T., Thiagarajan, M., et al. (2003) · BioTechniques · doi:10.2144/03342mt01 · Cited by 4,837
High-Quality Binary Protein Interaction Map of the Yeast Interactome Network
Yu, H., Braun, P., Yıldırım, M. A., Lemmens, I., Venkatesan, K., Sahalie, J., Hirozane-Kishikawa, T., Gebreab, F., Li, N., Simonis, N., et al. (2008) · Science · doi:10.1126/science.1158684 · Cited by 1,392
Variation in Homeodomain DNA Binding Revealed by High-Resolution Analysis of Sequence Preferences
Berger, M. F., Badis, G., Gehrke, A. R., Talukder, S., Philippakis, A. A., Peña-Castillo, L., Alleyne, T. M., Mnaimneh, S., Botvinnik, O. B., Chan, E. T., et al. (2008) · Cell · doi:10.1016/j.cell.2008.05.024 · Cited by 606
Self-citationHollenhorst, P. C., Shah, A. A., Hopkins, C., & Graves, B. J. (2007) · Genes & Development · doi:10.1101/gad.1561707 · Cited by 290
Lee, I., Lehner, B., Crombie, C., Wong, W., Fraser, A. G., & Marcotte, E. M. (2008) · Nature Genetics · doi:10.1038/ng.2007.70 · Cited by 281 · cited 1×
“The second is a probabilistic network that used various data types and that can be used to predict genetic interactions (Lee et al., 2008).”
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Metadata
- Authors
- Grove, C. A., De Masi, F., Barrasa, M. I., Newburger, D. E., Alkema, M. J., Bulyk, M. L., & Walhout, A. J. M.
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2009-07
- Volume
- 138
- Issue
- 2
- Pages
- 314-327
- ISSN
- 0092-8674 (ISSN-L)
- OpenAlex
- W2112019511
- Cited by
- 265
- References
- 6
- FWCI
- 8.64
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Grove, C. A., De Masi, F., Barrasa, M. I., Newburger, D. E., Alkema, M. J., Bulyk, M. L., & Walhout, A. J. M. (2009). A Multiparameter Network Reveals Extensive Divergence between C. elegans bHLH Transcription Factors. Cell. https://doi.org/10.1016/j.cell.2009.04.058
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