CADRE: the Central Aspergillus Data REpository

Mabey, J. E.

doi:10.1093/nar/gkh009

Cited by 65 publications

(61 citation statements)

References 16 publications

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“…In an attempt to move towards a consistent nomenclature for A. fumigatus proteins, the annotation described by Mabey et al and employed on the CADRE website at http://www.cadre.man.ac.uk has been adopted [9]. The initial availability of the unannotated genome of the A. fumigatus [http://www.tigr.org] and subsequently that of thein silico annotated version at http://www.cadre.man.…”

Section: Discussionmentioning

confidence: 99%

“…Protein identification was carried out either by m/z data interrogation of (i) the NCBI nr database available as part of the mass spectrometer Evaluation Software Version 2.01 or (ii) a local FASTA version of the annotated A. fumigatus genome available at http://www.cadre.man.ac.uk. The annotation system employed on this website (i.e., AfuNg where N and g define the chromosome and gene number, respectively) and described by Mabey et al [9] has been adopted in this manuscript. Tandem mass spectrometry was performed by commercial arrangement (Taplin Biological Mass Spectrometry Facility, Harvard Medical School, MA, USA) using an LCQ DECAXP Plus ion-trap mass spectrometer (ThermoFinnigan, San Jose, CA).…”

Section: Methodsmentioning

confidence: 99%

“…The recent completion of the sequencing of the A. fumigatus genome and the availability of the in silico annotated genome at http://www.cadre.man.ac.uk [9] should enable detailed molecular dissection of the biology of this organism. Moreover, both unannotated and annotated genome data can be interrogated to further our knowledge of the A. fumigatus proteome and the organismal response to altered environmental conditions.…”

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confidence: 99%

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Analysis of major intracellular proteins of Aspergillus fumigatus by MALDI mass spectrometry: Identification and characterisation of an elongation factor 1B protein with glutathione transferase activity

Carberry

Neville

Kavanagh

et al. 2006

Biochemical and Biophysical Research Communications

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Aspergillus fumigatus is a recognised human pathogen, especially in immunocompromised individuals. The availability of the annotated A. fumigatus genome sequence will significantly accelerate our understanding of this organism. However, limited information is available with respect to the A. fumigatus proteome. Here, both a direct proteomic approach (2D-PAGE and MALDI-MS) and a sub-proteomic strategy involving initial glutathione affinity chromatography have been deployed to identify 54 proteins from A. fumigatus primarily involved in energy metabolism and protein biosynthesis. Furthermore, two novel eukaryotic elongation factor proteins (eEF1Bc), termed ElfA and B have been identified and phylogenetically confirmed to belong to the eEF1Bc class of GST-like proteins. One of these proteins (ElfA) has been purified to homogeneity, identified as a monomeric enzyme (molecular mass = 20 kDa; pI = 5.9 and 6.5), and found to exhibit glutathione transferase activity specific activities (mean ± standard deviation, n = 3) of 3.13 ± 0.27 and 3.43 ± 1.0 lmol/min/mg, using CDNB and ethacrynic acid, respectively. Overall, these data highlight the importance of new approaches to dissect the proteome of, and elucidate novel functions within, A. fumigatus.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

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Analysis of major intracellular proteins of Aspergillus fumigatus by MALDI mass spectrometry: Identification and characterisation of an elongation factor 1B protein with glutathione transferase activity

Carberry

Neville

Kavanagh

et al. 2006

Biochemical and Biophysical Research Communications

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“…Originally based on parasexual genetics (Käfer 1958; Pontecorvo & Käfer 1958) and later incorporating meiotic mapping data (Dorn 1967), the genetic map made the assembly of the sequenced genome robust and authoritative (Galagan et al 2005). Other data resources for A. nidulans include a curated gene compendium (http://www.fgsc.net/Aspergillus/gene_list/index.html) and annual bibliography (http://www.fgsc.net/scripts/biblioNEW.asp) as well as collaborative genome tools, including a central data repository (Mabey et al 2004) and also the Aspergillus Genome Database (Arnaud et al 2012). With a general move away from organism-specific database resources, the A. nidulans community has migrated to the fungiDB integrated genomics database for fungi (Stajich et al 2012).…”

Section: Aspergillus Speciesmentioning

confidence: 99%

Diverse data supports the transition of filamentous fungal model organisms into the post-genomics era

McCluskey

Baker

2017

Mycology

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Filamentous fungi have been important as model organisms since the beginning of modern biological inquiry and have benefitted from open data since the earliest genetic maps were shared. From early origins in simple Mendelian genetics of mating types, parasexual genetics of colony colour, and the foundational demonstration of the segregation of a nutritional requirement, the contribution of research systems utilising filamentous fungi has spanned the biochemical genetics era, through the molecular genetics era, and now are at the very foundation of diverse omics approaches to research and development. Fungal model organisms have come from most major taxonomic groups although Ascomycete filamentous fungi have seen the most major sustained effort. In addition to the published material about filamentous fungi, shared molecular tools have found application in every area of fungal biology. Similarly, shared data has contributed to the success of model systems. The scale of data supporting research with filamentous fungi has grown by 10 to 12 orders of magnitude. From genetic to molecular maps, expression databases, and finally genome resources, the open and collaborative nature of the research communities has assured that the rising tide of data has lifted all of the research systems together.

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“…The Aspergillus fumigatus genome offers a unique insight into the comparison between the automated method and the manual. The A. fumigatus genome has been sequenced and annotation is currently underway by a team of human experts [32].…”

Section: The Data Setsmentioning

confidence: 99%

Applying OWL Reasoning to Genomic Data

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Abstract:The core part of the Web Ontology Language (OWL) is based on Description Logic (DL) theory, which has been investigated for more than 25 years. OWL reasoning systems offer various DL-based inference services such as (i) checking class descriptions for consistency and automatically organizing them into classification hierarchies, (ii) checking descriptions about individuals for consistency and recognizing individuals as instances of class descriptions. These services can therefore be utilized in a variety of application domains concerned with representation of and reasoning about knowledge, for example, in biological sciences. Classification is an integral part of all biological sciences, including the new discipline of genomics. Biologists not only wish to build complex descriptions of the categories of biological molecules, but also to classify instances of new molecules against these class level descriptions. In this chapter we introduce to the non-expert reader the basics of OWL DL and its related reasoning patterns such as classification. We use a case study of building an ontology of a protein family and then classifying all members of that family from a genome using DL technology. We show how a technically straight-forward use of these technologies can have far-reaching effects in genomic science.

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CADRE: the Central Aspergillus Data REpository

Cited by 65 publications

References 16 publications

Analysis of major intracellular proteins of Aspergillus fumigatus by MALDI mass spectrometry: Identification and characterisation of an elongation factor 1B protein with glutathione transferase activity

Analysis of major intracellular proteins of Aspergillus fumigatus by MALDI mass spectrometry: Identification and characterisation of an elongation factor 1B protein with glutathione transferase activity

Diverse data supports the transition of filamentous fungal model organisms into the post-genomics era

Applying OWL Reasoning to Genomic Data

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