The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes.
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.
Ruepp
Andreas
A
Institute for Bioinformatics (MIPS), GSF National Research Center for Environment and Health, Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany. andreas.ruepp@gsf.de
Zollner
Alfred
A
Maier
Dieter
D
Albermann
Kaj
K
Hani
Jean
J
Mokrejs
Martin
M
Tetko
Igor
I
Güldener
Ulrich
U
Mannhaupt
Gertrud
G
Münsterkötter
Martin
M
Mewes
H Werner
HW
D000043:Abstracting and Indexing; D000818:Animals; D001331:Automation / Q000295:instrumentation / Q000379:methods; D019295:Computational Biology / Q000295:instrumentation / Q000379:methods*; D016678:Genome; D023281:Genomics / Q000295:instrumentation / Q000379:methods; D020407:Internet; D011485:Protein Binding; D011506:Proteins / Q000145:classification* / Q000235:genetics / Q000378:metabolism*; D020543:Proteome / Q000145:classification / Q000235:genetics / Q000378:metabolism; D040901:Proteomics / Q000295:instrumentation / Q000379:methods*; D015203:Reproducibility of Results; D012441:Saccharomyces cerevisiae / Q000737:chemistry / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000145:classification / Q000235:genetics / Q000378:metabolism; D012984:Software; D009626:Terminology as Topic; D014158:Transcription, Genetic / Q000235:genetics
D011506:Proteins; D020543:Proteome; D029701:Saccharomyces cerevisiae Proteins