Published online 14 October 2004
Nucleic Acids Research, Vol. 32 No. 18 © Oxford University Press 2004; all rights reserved
The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes
1 Institute for Bioinformatics (MIPS), GSF National Research Center for Environment and Health, Ingolstaedter Landstraße 1, D-85764 Neuherberg, Germany, 2 Biomax Informatics AG, Lochhamerstr. 11, D-82152 Martinsried, Germany, 3 Faculty of Science, Charles University, Vinicna 5, 128 42 Prague, Czech Republic and 4 Technische Universität München, Chair of Genome Oriented Bioinformatics, Center of Life and Food Science, D-85350 Freising-Weihenstephan, Germany
* To whom correspondence should be addressed. Tel: +49 89 3187 3189; Fax: +49 89 3187 3585; Email: andreas.ruepp{at}gsf.de
Received July 30, 2004; Revised September 9, 2004; Accepted September 28, 2004
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.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  E. Vollmeister, C. Haag, K. Zarnack, S. Baumann, J. Konig, G. Mannhaupt, and M. Feldbrugge Tandem KH domains of Khd4 recognize AUACCC and are essential for regulation of morphology as well as pathogenicity in Ustilago maydis RNA, December 1, 2009; 15(12): 2206 - 2218. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. G. Gibbons, E. M. Janson, C. T. Hittinger, M. Johnston, P. Abbot, and A. Rokas Benchmarking Next-Generation Transcriptome Sequencing for Functional and Evolutionary Genomics Mol. Biol. Evol., December 1, 2009; 26(12): 2731 - 2744. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Ruepp, B. Waegele, M. Lechner, B. Brauner, I. Dunger-Kaltenbach, G. Fobo, G. Frishman, C. Montrone, and H.-W. Mewes CORUM: the comprehensive resource of mammalian protein complexes--2009 Nucleic Acids Res., November 1, 2009; (2009) gkp914v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 V. Meyer, M. Arentshorst, S. J. Flitter, B. M. Nitsche, M. J. Kwon, C. G. Reynaga-Pena, S. Bartnicki-Garcia, C. A. M. J. J. van den Hondel, and A. F. J. Ram Reconstruction of Signaling Networks Regulating Fungal Morphogenesis by Transcriptomics Eukaryot. Cell, November 1, 2009; 8(11): 1677 - 1691. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. A. Grobei, E. Qeli, E. Brunner, H. Rehrauer, R. Zhang, B. Roschitzki, K. Basler, C. H. Ahrens, and U. Grossniklaus Deterministic protein inference for shotgun proteomics data provides new insights into Arabidopsis pollen development and function Genome Res., October 1, 2009; 19(10): 1786 - 1800. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Huttenhower, M. A. Hibbs, C. L. Myers, A. A. Caudy, D. C. Hess, and O. G. Troyanskaya The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction Bioinformatics, September 15, 2009; 25(18): 2404 - 2410. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Videira, T. Kasuga, C. Tian, C. Lemos, A. Castro, and N. L. Glass Transcriptional analysis of the response of Neurospora crassa to phytosphingosine reveals links to mitochondrial function Microbiology, September 1, 2009; 155(9): 3134 - 3141. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Li, Q. Ma, H. Tang, A. H. Paterson, and Y. Xu QUBIC: a qualitative biclustering algorithm for analyses of gene expression data Nucleic Acids Res., August 1, 2009; 37(15): e101 - e101. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Khozoie, R. J. Pleass, and S. V. Avery The Antimalarial Drug Quinine Disrupts Tat2p-mediated Tryptophan Transport and Causes Tryptophan Starvation J. Biol. Chem., July 3, 2009; 284(27): 17968 - 17974. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. Gasic, D. O. Gonzalez, J. Thimmapuram, L. Liu, M. Malnoy, G. Gong, Y. Han, L. O. Vodkin, H. S. Aldwinckle, N. J. Carroll, et al. Comparative Analysis and Functional Annotation of a Large Expressed Sequence Tag Collection of Apple The Plant Genome, March 1, 2009; 2(1): 23 - 38. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 N. Yagi, S. Takeda, N. Matsumoto, and K. Okada VAJ/GFA1/CLO is Involved in the Directional Control of Floral Organ Growth Plant Cell Physiol., March 1, 2009; 50(3): 515 - 527. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. G. Gibbons and A. Rokas Comparative and Functional Characterization of Intragenic Tandem Repeats in 10 Aspergillus Genomes Mol. Biol. Evol., March 1, 2009; 26(3): 591 - 602. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. C. Walter, T. Rattei, R. Arnold, U. Guldener, M. Munsterkotter, K. Nenova, G. Kastenmuller, P. Tischler, A. Wolling, A. Volz, et al. PEDANT covers all complete RefSeq genomes Nucleic Acids Res., January 1, 2009; 37(suppl_1): D408 - D411. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Nevarez, V. Vasseur, G. Le Drean, A. Tanguy, I. Guisle-Marsollier, R. Houlgatte, and G. Barbier Isolation and analysis of differentially expressed genes in Penicillium glabrum subjected to thermal stress Microbiology, December 1, 2008; 154(12): 3752 - 3765. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. Loizeau, V. De Brouwer, B. Gambonnet, A. Yu, J.-P. Renou, D. Van Der Straeten, W. E. Lambert, F. Rebeille, and S. Ravanel A Genome-Wide and Metabolic Analysis Determined the Adaptive Response of Arabidopsis Cells to Folate Depletion Induced by Methotrexate Plant Physiology, December 1, 2008; 148(4): 2083 - 2095. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Wang, W.-Z. Zhang, L.-F. Song, J.-J. Zou, Z. Su, and W.-H. Wu Transcriptome Analyses Show Changes in Gene Expression to Accompany Pollen Germination and Tube Growth in Arabidopsis Plant Physiology, November 1, 2008; 148(3): 1201 - 1211. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Schonig, D. W. Brown, B. Oeser, and B. Tudzynski Cross-Species Hybridization with Fusarium verticillioides Microarrays Reveals New Insights into Fusarium fujikuroi Nitrogen Regulation and the Role of AreA and NMR Eukaryot. Cell, October 1, 2008; 7(10): 1831 - 1846. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Choudhury and A. Lahiri Arabidopsis thaliana regulatory element analyzer Bioinformatics, October 1, 2008; 24(19): 2263 - 2264. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Kasuga and N. L. Glass Dissecting Colony Development of Neurospora crassa Using mRNA Profiling and Comparative Genomics Approaches Eukaryot. Cell, September 1, 2008; 7(9): 1549 - 1564. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Waegele, T. Schmidt, H. W. Mewes, and A. Ruepp OREST: the online resource for EST analysis Nucleic Acids Res., July 1, 2008; 36(suppl_2): W140 - W144. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. C. Cushman, R. L. Tillett, J. A. Wood, J. M. Branco, and K. A. Schlauch Large-scale mRNA expression profiling in the common ice plant, Mesembryanthemum crystallinum, performing C3 photosynthesis and Crassulacean acid metabolism (CAM) J. Exp. Bot., May 1, 2008; 59(7): 1875 - 1894. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. V. Tetko, I. V. Rodchenkov, M. C. Walter, T. Rattei, and H.-W. Mewes Beyond the 'best' match: machine learning annotation of protein sequences by integration of different sources of information Bioinformatics, March 1, 2008; 24(5): 621 - 628. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Valentini and N. Cesa-Bianchi HCGene: a software tool to support the hierarchical classification of genes Bioinformatics, March 1, 2008; 24(5): 729 - 731. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. G. Slattery, D. Liko, and W. Heideman Protein Kinase A, TOR, and Glucose Transport Control the Response to Nutrient Repletion in Saccharomyces cerevisiae Eukaryot. Cell, February 1, 2008; 7(2): 358 - 367. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Ruepp, B. Brauner, I. Dunger-Kaltenbach, G. Frishman, C. Montrone, M. Stransky, B. Waegele, T. Schmidt, O. N. Doudieu, V. Stumpflen, et al. CORUM: the comprehensive resource of mammalian protein complexes Nucleic Acids Res., January 11, 2008; 36(suppl_1): D646 - D650. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Yeats, J. Lees, A. Reid, P. Kellam, N. Martin, X. Liu, and C. Orengo Gene3D: comprehensive structural and functional annotation of genomes Nucleic Acids Res., January 11, 2008; 36(suppl_1): D414 - D418. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. W. Mewes, S. Dietmann, D. Frishman, R. Gregory, G. Mannhaupt, K. F. X. Mayer, M. Munsterkotter, A. Ruepp, M. Spannagl, V. Stumpflen, et al. MIPS: analysis and annotation of genome information in 2007 Nucleic Acids Res., January 11, 2008; 36(suppl_1): D196 - D201. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. Meyer, R. A. Damveld, M. Arentshorst, U. Stahl, C. A. M. J. J. van den Hondel, and A. F. J. Ram Survival in the Presence of Antifungals: GENOME-WIDE EXPRESSION PROFILING OF ASPERGILLUS NIGER IN RESPONSE TO SUBLETHAL CONCENTRATIONS OF CASPOFUNGIN AND FENPROPIMORPH J. Biol. Chem., November 9, 2007; 282(45): 32935 - 32948. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. Narsai, K. A. Howell, A. H. Millar, N. O'Toole, I. Small, and J. Whelan Genome-Wide Analysis of mRNA Decay Rates and Their Determinants in Arabidopsis thaliana PLANT CELL, November 1, 2007; 19(11): 3418 - 3436. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Breakspear and M. Momany Aspergillus nidulans Conidiation Genes dewA, fluG, and stuA Are Differentially Regulated in Early Vegetative Growth Eukaryot. Cell, September 1, 2007; 6(9): 1697 - 1700. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Yu, R. Jansen, G. Stolovitzky, and M. Gerstein Total ancestry measure: quantifying the similarity in tree-like classification, with genomic applications Bioinformatics, August 15, 2007; 23(16): 2163 - 2173. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. H. Ohn, J. Kim, and J. H. Kim Genomic characterization of perturbation sensitivity Bioinformatics, July 1, 2007; 23(13): i354 - i358. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
O. Krinke, E. Ruelland, O. Valentova, C. Vergnolle, J.-P. Renou, L. Taconnat, M. Flemr, L. Burketova, and A. Zachowski Phosphatidylinositol 4-Kinase Activation Is an Early Response to Salicylic Acid in Arabidopsis Suspension Cells Plant Physiology, July 1, 2007; 144(3): 1347 - 1359. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Tian, T. Kasuga, M. S. Sachs, and N. L. Glass Transcriptional Profiling of Cross Pathway Control in Neurospora crassa and Comparative Analysis of the Gcn4 and CPC1 Regulons Eukaryot. Cell, June 1, 2007; 6(6): 1018 - 1029. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Ferrari, R. Galletti, C. Denoux, G. De Lorenzo, F. M. Ausubel, and J. Dewdney Resistance to Botrytis cinerea Induced in Arabidopsis by Elicitors Is Independent of Salicylic Acid, Ethylene, or Jasmonate Signaling But Requires PHYTOALEXIN DEFICIENT3 Plant Physiology, May 1, 2007; 144(1): 367 - 379. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Joosen, J. Cordewener, E. D. J. Supena, O. Vorst, M. Lammers, C. Maliepaard, T. Zeilmaker, B. Miki, T. America, J. Custers, et al. Combined Transcriptome and Proteome Analysis Identifies Pathways and Markers Associated with the Establishment of Rapeseed Microspore-Derived Embryo Development Plant Physiology, May 1, 2007; 144(1): 155 - 172. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. G Bragg and A. Wagner Protein carbon content evolves in response to carbon availability and may influence the fate of duplicated genes Proc R Soc B, April 22, 2007; 274(1613): 1063 - 1070. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. Godard, A. Urrestarazu, S. Vissers, K. Kontos, G. Bontempi, J. van Helden, and B. Andre Effect of 21 Different Nitrogen Sources on Global Gene Expression in the Yeast Saccharomyces cerevisiae Mol. Cell. Biol., April 15, 2007; 27(8): 3065 - 3086. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Krumsiek, R. Arnold, and T. Rattei Gepard: a rapid and sensitive tool for creating dotplots on genome scale Bioinformatics, April 15, 2007; 23(8): 1026 - 1028. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. Fernandez-Arenas, V. Cabezon, C. Bermejo, J. Arroyo, C. Nombela, R. Diez-Orejas, and C. Gil Integrated Proteomics and Genomics Strategies Bring New Insight into Candida albicans Response upon Macrophage Interaction Mol. Cell. Proteomics, March 1, 2007; 6(3): 460 - 478. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Lee, K. He, V. Stolc, H. Lee, P. Figueroa, Y. Gao, W. Tongprasit, H. Zhao, I. Lee, and X. W. Deng Analysis of Transcription Factor HY5 Genomic Binding Sites Revealed Its Hierarchical Role in Light Regulation of Development PLANT CELL, March 1, 2007; 19(3): 731 - 749. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. H. Ahn, J. Kim, S. J. Yoo, S. Y. Yoo, H. Roh, J.-H. Choi, M. S. Choi, K. S. Chung, E. J. Han, S. M. Hong, et al. Isolation of 151 Mutants that Have Developmental Defects from T-DNA Tagging Plant Cell Physiol., January 1, 2007; 48(1): 169 - 178. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Serrano, H. Martin, A. Casamayor, and J. Arino Signaling Alkaline pH Stress in the Yeast Saccharomyces cerevisiae through the Wsc1 Cell Surface Sensor and the Slt2 MAPK Pathway J. Biol. Chem., December 29, 2006; 281(52): 39785 - 39795. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Huttenhower, M. Hibbs, C. Myers, and O. G. Troyanskaya A scalable method for integration and functional analysis of multiple microarray datasets Bioinformatics, December 1, 2006; 22(23): 2890 - 2897. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Li, Y. Huang, X. Xia, and Z. Sun Preferential Duplication in the Sparse Part of Yeast Protein Interaction Network Mol. Biol. Evol., December 1, 2006; 23(12): 2467 - 2473. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Gonzalez, A. Ruiz, R. Serrano, J. Arino, and A. Casamayor Transcriptional Profiling of the Protein Phosphatase 2C Family in Yeast Provides Insights into the Unique Functional Roles of Ptc1 J. Biol. Chem., November 17, 2006; 281(46): 35057 - 35069. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Journot-Catalino, I. E. Somssich, D. Roby, and T. Kroj The Transcription Factors WRKY11 and WRKY17 Act as Negative Regulators of Basal Resistance in Arabidopsis thaliana PLANT CELL, November 1, 2006; 18(11): 3289 - 3302. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. P. Gerke, C. T. L. Chen, and B. A. Cohen Natural Isolates of Saccharomyces cerevisiae Display Complex Genetic Variation in Sporulation Efficiency Genetics, October 1, 2006; 174(2): 985 - 997. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Bryson, V. Loux, R. Bossy, P. Nicolas, S. Chaillou, M. van de Guchte, S. Penaud, E. Maguin, M. Hoebeke, P. Bessieres, et al. AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system Nucleic Acids Res., July 19, 2006; 34(12): 3533 - 3545. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. N. Chua, W.-K. Sung, and L. Wong Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions Bioinformatics, July 1, 2006; 22(13): 1623 - 1630. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. van der Graaff, R. Schwacke, A. Schneider, M. Desimone, U.-I. Flugge, and R. Kunze Transcription Analysis of Arabidopsis Membrane Transporters and Hormone Pathways during Developmental and Induced Leaf Senescence Plant Physiology, June 1, 2006; 141(2): 776 - 792. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. D. Newcomb, R. N. Crowhurst, A. P. Gleave, E. H.A. Rikkerink, A. C. Allan, L. L. Beuning, J. H. Bowen, E. Gera, K. R. Jamieson, B. J. Janssen, et al. Analyses of Expressed Sequence Tags from Apple Plant Physiology, May 1, 2006; 141(1): 147 - 166. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Piippo, Y. Allahverdiyeva, V. Paakkarinen, U.-M. Suoranta, N. Battchikova, and E.-M. Aro Chloroplast-mediated regulation of nuclear genes in Arabidopsis thaliana in the absence of light stress Physiol Genomics, March 13, 2006; 25(1): 142 - 152. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Vallenet, L. Labarre, Z. Rouy, V. Barbe, S. Bocs, S. Cruveiller, A. Lajus, G. Pascal, C. Scarpelli, and C. Medigue MaGe: a microbial genome annotation system supported by synteny results Nucleic Acids Res., January 10, 2006; 34(1): 53 - 65. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. V. Antonov, I. V. Tetko, and H. W. Mewes A systematic approach to infer biological relevance and biases of gene network structures Nucleic Acids Res., January 10, 2006; 34(1): e6 - e6. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. W. Mewes, D. Frishman, K. F. X. Mayer, M. Munsterkotter, O. Noubibou, P. Pagel, T. Rattei, M. Oesterheld, A. Ruepp, and V. Stumpflen MIPS: analysis and annotation of proteins from whole genomes in 2005 Nucleic Acids Res., January 1, 2006; 34(suppl_1): D169 - D172. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
U. Guldener, M. Munsterkotter, M. Oesterheld, P. Pagel, A. Ruepp, H.-W. Mewes, and V. Stumpflen MPact: the MIPS protein interaction resource on yeast Nucleic Acids Res., January 1, 2006; 34(suppl_1): D436 - D441. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
U. Guldener, G. Mannhaupt, M. Munsterkotter, D. Haase, M. Oesterheld, V. Stumpflen, H.-W. Mewes, and G. Adam FGDB: a comprehensive fungal genome resource on the plant pathogen Fusarium graminearum Nucleic Acids Res., January 1, 2006; 34(suppl_1): D456 - D458. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Ruepp, O. N. Doudieu, J. van den Oever, B. Brauner, I. Dunger-Kaltenbach, G. Fobo, G. Frishman, C. Montrone, C. Skornia, S. Wanka, et al. The Mouse Functional Genome Database (MfunGD): functional annotation of proteins in the light of their cellular context Nucleic Acids Res., January 1, 2006; 34(suppl_1): D568 - D571. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Prokisch, C. Andreoli, U. Ahting, K. Heiss, A. Ruepp, C. Scharfe, and T. Meitinger MitoP2: the mitochondrial proteome database--now including mouse data Nucleic Acids Res., January 1, 2006; 34(suppl_1): D705 - D711. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 N. Dephoure, R. W. Howson, J. D. Blethrow, K. M. Shokat, and E. K. O'Shea Combining chemical genetics and proteomics to identify protein kinase substrates PNAS, December 13, 2005; 102(50): 17940 - 17945. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Kasuga, J. P. Townsend, C. Tian, L. B. Gilbert, G. Mannhaupt, J. W. Taylor, and N. L. Glass Long-oligomer microarray profiling in Neurospora crassa reveals the transcriptional program underlying biochemical and physiological events of conidial germination Nucleic Acids Res., November 14, 2005; 33(20): 6469 - 6485. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B.-h. Lee, D. A. Henderson, and J.-K. Zhu The Arabidopsis Cold-Responsive Transcriptome and Its Regulation by ICE1 PLANT CELL, November 1, 2005; 17(11): 3155 - 3175. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Conesa, R. Ruotolo, P. Soularue, T. A. Simms, D. Donze, A. Sentenac, and G. Dieci Modulation of Yeast Genome Expression in Response to Defective RNA Polymerase III-Dependent Transcription Mol. Cell. Biol., October 1, 2005; 25(19): 8631 - 8642. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. Holme and M. Huss Role-similarity based functional prediction in networked systems: application to the yeast proteome J R Soc Interface, September 22, 2005; 2(4): 327 - 333. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Maere, K. Heymans, and M. Kuiper BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks Bioinformatics, August 15, 2005; 21(16): 3448 - 3449. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. V. Tetko, B. Brauner, I. Dunger-Kaltenbach, G. Frishman, C. Montrone, G. Fobo, A. Ruepp, A. V. Antonov, D. Surmeli, and H.-W. Mewes MIPS bacterial genomes functional annotation benchmark dataset Bioinformatics, May 15, 2005; 21(10): 2520 - 2521. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 U. de Lichtenberg, L. J. Jensen, S. Brunak, and P. Bork Dynamic Complex Formation During the Yeast Cell Cycle Science, February 4, 2005; 307(5710): 724 - 727. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. L. Riley, T. Schmidt, C. Wagner, H.-W. Mewes, and D. Frishman The PEDANT genome database in 2005 Nucleic Acids Res., January 1, 2005; 33(suppl_1): D308 - D310. [Abstract] [Full Text] [PDF]
|
|