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

Ruepp, Andreas; Zollner, Alfred; Maier, Dieter; Albermann, Kaj; Hani, Jean; Mokrejš, Martin; Tetko, Igor V.; Güldener, Ulrich; Mannhaupt, Gertrud; Münsterkötter, Martin; Mewes, Hans‐Werner

doi:10.1093/nar/gkh894

Cited by 1,015 publications

(1,012 citation statements)

References 44 publications

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“…BLAST searching against the FUNCAT database and PHI (pathogen–host interaction) provided a global view of the gene functions (Ruepp et al 2004; Winnenburg et al 2006). Statistics for the gene abundance were performed by t -test and was corrected by false discovery rate (FDR) test with the p < 0.01.…”

Section: Methodsmentioning

confidence: 99%

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Introgression and gene family contraction drive the evolution of lifestyle and host shifts of hypocrealean fungi

Zhang

Wang

et al. 2018

Mycology

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Hypocrealean fungi (Ascomycota) are known for their diversity of lifestyles. Their vital influences on agricultural and natural ecosystems have resulted in a number of sequenced genomes, which provide essential data for genomic analysis. Totally, 45 hypocrealean fungal genomes constructed a phylogeny. The phylogeny showed that plant pathogens in Nectriaceae diverged earliest, followed by animal pathogens in Cordycipitaceae, Ophiocordycipitaceae and Clavicipitaceae with mycoparasites in Hypocreaceae. Insect/nematode pathogens and grass endophytes in Clavicipitaceae diverged at last. Gene families associated with host-derived nutrients are significantly contracted in diverged lineages compared with the ancestral species. Introgression was detected in certain lineages of hypocrealean fungi, and the main functions of the genes located in the introgressed regions are involved in host recognition, transcriptional regulation, stress response and cell growth regulation. These results indicate that contraction of gene families and introgression might be main mechanisms to drive lifestyle differentiation and evolution and host shift of hypocrealean fungi.

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Section: Methodsmentioning

confidence: 99%

“…Genes that cover at least one introgressed locus were extracted. Functions of these genes were annotated by blasting against PFAM, FUNCAT and GO database (Harris et al 2004; Ruepp et al 2004; Marco et al 2012). …”

Section: Methodsmentioning

confidence: 99%

Introgression and gene family contraction drive the evolution of lifestyle and host shifts of hypocrealean fungi

Zhang

Wang

et al. 2018

Mycology

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“…We performed predictions of gene functions at genome-wide level in the S.cerevisiae organism (yeast), using the whole FunCat ontology (Ruepp et al, 2004) 2 . FunCat (Functional Categories) is one of the most used biological taxonomy to classify gene functions.…”

Section: Methodsmentioning

confidence: 99%

“…Finally, in Sect. 6 we apply COSNet to the genome-wide prediction of gene functions in a model organism, including 232 functional classes of the FunCat taxonomy (Ruepp et al, 2004), and using six different types of biomolecular data. The paper ends with the conclusions.…”

Section: Introductionmentioning

confidence: 99%

A neural network algorithm for semi-supervised node label learning from unbalanced data

et al. 2013

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Given a weighted graph and a partial node labeling, the graph classification problem consists in predicting the labels of all the nodes. In several application domains, from gene to social network analysis, the labeling is unbalanced: for instance positive labels may be much less than negatives. In this paper we present COSNet (COst Sensitive neural Network), a neural algorithm for predicting node labels in graphs with unbalanced labels. COSNet is based on a 2-parameters family of Hopfield networks, and consists of two main steps: 1) the network parameters are learned through a costsensitive optimization procedure; 2) a suitable Hopfield network restricted to the unlabeled nodes is considered and simulated. The reached equilibrium point induces the classification of the unlabeled nodes. The restriction of the dynamics leads to a significant reduction in time complexity and allows the algorithm to nicely scale with large networks. An experimental analysis on real-world unbalanced data, in the context of the genome-wide prediction of gene functions, shows the effectiveness of the proposed approach.

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“…Protein association with detergent-resistant membranes (DRM) was inferred from the DRM proteomes of M. truncatula roots either non-mycorrhizal (Lefebvre et al 2007;Guillier et al 2014) or mycorrhizal (Lemaître-Guillier, personal communication). Functional classification was performed according to the FunCat scheme (Ruepp et al 2004). …”

Section: Digital Immunoblotting and Protein Characterizationmentioning

confidence: 99%

The plasma membrane proteome of Medicago truncatula roots as modified by arbuscular mycorrhizal symbiosis

Aloui¹,

Recorbet²,

Lemaître‐Guillier³

et al. 2017

Mycorrhiza

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In arbuscular mycorrhizal (AM) roots, the plasma membrane (PM) of the host plant is involved in all developmental stages of the symbiotic interaction, from initial recognition to intracellular accommodation of intra-radical hyphae and arbuscules. Although the role of the PM as the agent for cellular morphogenesis and nutrient exchange is especially accentuated in endosymbiosis, very little is known regarding the PM protein composition of mycorrhizal roots. To obtain a global overview at the proteome level of the host PM proteins as modified by symbiosis, we performed a comparative protein profiling of PM fractions from Medicago truncatula roots either inoculated or not with the AM fungus Rhizophagus irregularis. PM proteins were isolated from root microsomes using an optimized discontinuous sucrose gradient; their subsequent analysis by liquid chromatography followed by mass spectrometry (MS) identified 674 proteins. Cross-species sequence homology searches combined with MS-based quantification clearly confirmed enrichment in PM-associated proteins and depletion of major microsomal contaminants. Changes in protein amounts between the PM proteomes of mycorrhizal and non-mycorrhizal roots were monitored further by spectral counting. This workflow identified a set of 82 mycorrhiza-responsive proteins that provided insights into the plant PM response to mycorrhizal symbiosis. Among them, the association of one third of the mycorrhiza-responsive proteins with detergent-resistant membranes pointed at partitioning to PM microdomains. The PM-associated proteins responsive to mycorrhization also supported host plant control of sugar uptake to limit fungal colonization, and lipid turnover events in the PM fraction of symbiotic roots. Because of the depletion upon symbiosis of proteins mediating the replacement of phospholipids by phosphorus-free lipids in the plasmalemma, we propose a role of phosphate nutrition in the PM composition of mycorrhizal roots.

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

Cited by 1,015 publications

References 44 publications

Introgression and gene family contraction drive the evolution of lifestyle and host shifts of hypocrealean fungi

Introgression and gene family contraction drive the evolution of lifestyle and host shifts of hypocrealean fungi

A neural network algorithm for semi-supervised node label learning from unbalanced data

The plasma membrane proteome of Medicago truncatula roots as modified by arbuscular mycorrhizal symbiosis

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