The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes
Open accessAbstract
In this paper, we present the Functional Catalogue (FunCat), a hierarchically structured, organism-independent, flexible and scalable controlled classification system enabling the functional description of proteins from any organism. FunCat has been applied for the manual annotation of prokaryotes, fungi, plants and animals. We describe how FunCat is implemented as a highly efficient and robust tool for the manual and automatic annotation of genomic sequences. Owing to its hierarchical architecture, FunCat has also proved to be useful for many subsequent downstream bioinformatic applications. This is illustrated by the analysis of large-scale experiments from various investigations in transcriptomics and proteomics, where FunCat was used to project experimental data into functional units, as 'gold standard' for functional classification methods, and also served to compare the significance of different experimental methods. Over the last decade, the FunCat has been established as a robust and stable annotation scheme that offers both, meaningful and manageable functional classification as well as ease of perception.
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Cites
Gene Ontology: tool for the unification of biology
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000) · Nature Genetics · doi:10.1038/75556 · Cited by 43,206
A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae
Uetz, P., Giot, L., Cagney, G., Mansfield, T. A., Judson, R. S., Knight, J. R., Lockshon, D., Narayan, V., Srinivasan, M., Pochart, P., et al. (2000) · Nature · doi:10.1038/35001009 · Cited by 4,706
Functional profiling of the Saccharomyces cerevisiae genome
Giaever, G., Chu, A. M., Ni, L., Connelly, C., Riles, L., Véronneau, S., Dow, S., Lucau-Danila, A., Anderson, K., André, B., et al. (2002) · Nature · doi:10.1038/nature00935 · Cited by 4,316
Functional Characterization of the S. cerevisiae Genome by Gene Deletion and Parallel Analysis
Winzeler, E. A., Shoemaker, D. D., Astromoff, A., Liang, H., Anderson, K., Andre, B., Bangham, R., Benito, R., Boeke, J. D., Bussey, H., et al. (1999) · Science · doi:10.1126/science.285.5429.901 · Cited by 3,953
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Genome sequencing and analysis of the filamentous fungus Penicillium chrysogenum
van den Berg, M. A., Albang, R., Albermann, K., Badger, J. H., Daran, J.-M., M Driessen, A. J., Garcia-Estrada, C., Fedorova, N. D., Harris, D. M., Heijne, W. H. M., et al. (2008) · Nature Biotechnology · doi:10.1038/nbt.1498 · Cited by 473
Wang, Y., Zhang, W.-Z., Song, L.-F., Zou, J.-J., Su, Z., & Wu, W.-H. (2008) · Plant Physiology · doi:10.1104/pp.108.126375 · Cited by 466
Adaptation of Hansenula polymorpha to methanol: a transcriptome analysis
van Zutphen, T., Baerends, R. J., Susanna, K. A., de Jong, A., Kuipers, O. P., Veenhuis, M., & van der Klei, I. J. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-1 · Cited by 350
Genome-Wide Analysis of mRNA Decay Rates and Their Determinants in Arabidopsis thaliana
Narsai, R., Howell, K. A., Millar, A. H., O'Toole, N., Small, I., & Whelan, J. (2007) · The Plant Cell · doi:10.1105/tpc.107.055046 · Cited by 328
Compact integration of multi-network topology for functional analysis of genes
Cho, H., Berger, B., & Peng, J. (2016) · Cell Systems · doi:10.1016/j.cels.2016.10.017 · Cited by 241
Metadata
- Authors
- Ruepp, A.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2004-10-11
- Volume
- 32
- Issue
- 18
- Pages
- 5539-5545
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2137917513
- Cited by
- 1,133
- References
- 4
- FWCI
- 15.53
- Type
- journal article
- Language
- en
- Open access
- bronze
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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.
