The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes.

By Andreas Ruepp, A. Zollner, D. Maier, K. Albermann, J. Hani, M. Mokrejš, Igor V. Tetko, U. Güldener, G. Mannhaupt, M. Münsterkötter and 1 more. Nucleic Acids Research, 2004

1,168 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/0ddd43c5621c850350e17a60fcc36ac9dd462bdf

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In Molecular Biology

1. Ioannis P. Vlahavas
2. Grigorios Tsoumakas
3. Saso Dzeroski
4. Ioannis Manousos Katakis
5. Andreas Ruepp
6. Hans-Werner Mewes
7. Yang Zhang
8. Christine A. Orengo

Citations in the corpus

• Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88 (2007, neutral): “The functional catalog (FunCat) classification syste”
• Mining Multi-label Data (2010, background): “An example of such a structure, called functional catalogue (FunCat) [53], is an annotation scheme for the functional description of proteins from several living organisms.”
• Using PPI network autocorrelation in hierarchical multi-label classification trees for gene function prediction (2013, background): “de/proj/funcatDB/), a scheme for classifying the functions of gene products, developed by MIPS [26].”
• CORUM: the comprehensive resource of mammalian protein complexes (2007, methodology): “We use the Functional Catalogue (FunCat) annotation scheme for protein and protein complex function characterization (14).”
• MIPS: analysis and annotation of proteins from whole genomes in 2005 (2006, methodology): “Proteins in these databases are functionally classified using the well established functional catalogue FunCat (2).”
• Gepard: a rapid and sensitive tool for creating dotplots on genome scale (2007, background): “The program includes a ‘remote mode’ in which the user can select genomic sequence contigs from the PEDANT database (Frishman et al., 2003).”
• Clustering: Science or Art? (2009, background): “Situations where one does not have a clue what one is looking for are rare, and in many cases additional information can be used.”
• QUBIC: a qualitative biclustering algorithm for analyses of gene expression data (2009, methodology): “Similar to the E. coli data analysis, we evaluated each bicluster (after removing the substantially overlapping biclusters) generated by different algorithms in terms of their functional enrichments based on GO biological processes, MIPS yeast functional catagories (33) and KEGG pathways.”
• Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics (2007, background): “The gene ontology (GO, http://www.geneontology.org) [3] is probably the most extensive scheme today for the description of gene product functions but also other systems such as enzyme codes [4], KEGG pathways [5], FunCat [6], or COG [7] are widely used within molecular databases.”
• MIPS: analysis and annotation of proteins from whole genomes in 2005 (2005, methodology): “Proteins in these databases are functionally classified using the well established functional catalogue FunCat (2).”
• BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks (2005, methodology): “Although BiNGO is primarily designed for use with GO ontologies, other classification systems [e.g. the MIPS Functional Catalogue (Ruepp et al., 2004)] can be used as well, provided that the classification information is parsed into the right format.”
• MPact: the MIPS protein interaction resource on yeast (2005, methodology): “As a consequence, our protein interaction data is well integrated with other CYGD data such as description and the localization data or functional classification of proteins, using the FunCat annotation scheme (26).”
• Machine learning for discovering missing or wrong protein function annotations (2019, background): “1), labels are structured as a tree, meaning that they can have only a single parent label [24].”
• The Arabidopsis Cold-Responsive Transcriptome and Its Regulation by ICE1w⃞ (2005, background): “…NAC family transcription factors have a conserved NAC domain at the N termini of the proteins (Olsen et al., 2005) and have been implicated in plant development (Souer et al., 1996; Aida et al., 1997; Sablowski and Meyerowitz, 1998; Xie et al., 2000; Takada et al., 2001; Vroemen et al., 2003).”
• Carotenoid oxidation products are stress signals that mediate gene responses to singlet oxygen in plants (2012, methodology): “A functional classification of differentially expressed genes by β-CC relative to water was performed by the FunCat annotation scheme (18).”
• MaGe: a microbial genome annotation system supported by synteny results (2006, background): “For this purpose, continuously updated annotations (often using experimental evidence) from specialized databases [e.g. GenprotEC (53) and Ecogene (54) for Escherichia coli, PseudoCAP for Pseudomonas aeruginosa (55) and Subtilist for Bacillus subtilis (56)] can be stored in PkGDB. Depending on the o”
• CORUM: the comprehensive resource of mammalian protein complexes—2009 (2007, methodology): “The FunCat has been used for genome annotation and was also frequently used for the analysis of protein networks and highthroughput experiments ( 13 ).”