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A-WINGS: an integrated genome database for Pleurocybella porrigens (Angel's wing oyster mushroom, Sugihiratake).

Yamamoto N, Suzuki T, Kobayashi M, Dohra H, Sasaki Y, Hirai H, Yokoyama K, Kawagishi H, Yano K - BMC Res Notes (2014)

Bottom Line: Digital gene expression profiles were derived from RNA sequencing (RNA-seq) analysis in the fruiting bodies and mycelia.The omics information stored in the database is freely accessible through interactive and graphical interfaces by search functions that include 'GO TREE VIEW' browsing, keyword searches, and BLAST searches.The A-WINGS database will accelerate omics studies on specific aspects of the angel's wing oyster mushroom and the family Tricholomataceae.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Kawasaki 214-8571, Japan. achkawa@ipc.shizuoka.ac.jp.

ABSTRACT

Background: The angel's wing oyster mushroom (Pleurocybella porrigens, Sugihiratake) is a well-known delicacy. However, its potential risk in acute encephalopathy was recently revealed by a food poisoning incident. To disclose the genes underlying the accident and provide mechanistic insight, we seek to develop an information infrastructure containing omics data. In our previous work, we sequenced the genome and transcriptome using next-generation sequencing techniques. The next step in achieving our goal is to develop a web database to facilitate the efficient mining of large-scale omics data and identification of genes specifically expressed in the mushroom.

Findings: This paper introduces a web database A-WINGS (http://bioinf.mind.meiji.ac.jp/a-wings/) that provides integrated genomic and transcriptomic information for the angel's wing oyster mushroom. The database contains structure and functional annotations of transcripts and gene expressions. Functional annotations contain information on homologous sequences from NCBI nr and UniProt, Gene Ontology, and KEGG Orthology. Digital gene expression profiles were derived from RNA sequencing (RNA-seq) analysis in the fruiting bodies and mycelia. The omics information stored in the database is freely accessible through interactive and graphical interfaces by search functions that include 'GO TREE VIEW' browsing, keyword searches, and BLAST searches.

Conclusions: The A-WINGS database will accelerate omics studies on specific aspects of the angel's wing oyster mushroom and the family Tricholomataceae.

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Related in: MedlinePlus

The database structure of A-WINGS. The omics data are accessible through the search functions in tab-based interfaces. The graphical, interactive web interfaces allow users seamless access to information available in A-WINGS.
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Fig1: The database structure of A-WINGS. The omics data are accessible through the search functions in tab-based interfaces. The graphical, interactive web interfaces allow users seamless access to information available in A-WINGS.

Mentions: A-WINGS was developed by the LAMP (Linux, Apache, MySQL and Perl) stack. We stored omics data of the angel's wing [12] into MySQL database (version 5.0.95) on an Apache HTTP server (version 2.2.27) running on a Linux operating system (CentOS release 5.11, 64-bit). We then developed an interactive and graphical web-interface written in PHP and HTML for the data access. The database was equipped with three search functions—Keyword Search, GO Tree View and BLAST Search—provided by tab-based interfaces on the web page (Figures 1 and 2A).Figure 1


A-WINGS: an integrated genome database for Pleurocybella porrigens (Angel's wing oyster mushroom, Sugihiratake).

Yamamoto N, Suzuki T, Kobayashi M, Dohra H, Sasaki Y, Hirai H, Yokoyama K, Kawagishi H, Yano K - BMC Res Notes (2014)

The database structure of A-WINGS. The omics data are accessible through the search functions in tab-based interfaces. The graphical, interactive web interfaces allow users seamless access to information available in A-WINGS.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4289373&req=5

Fig1: The database structure of A-WINGS. The omics data are accessible through the search functions in tab-based interfaces. The graphical, interactive web interfaces allow users seamless access to information available in A-WINGS.
Mentions: A-WINGS was developed by the LAMP (Linux, Apache, MySQL and Perl) stack. We stored omics data of the angel's wing [12] into MySQL database (version 5.0.95) on an Apache HTTP server (version 2.2.27) running on a Linux operating system (CentOS release 5.11, 64-bit). We then developed an interactive and graphical web-interface written in PHP and HTML for the data access. The database was equipped with three search functions—Keyword Search, GO Tree View and BLAST Search—provided by tab-based interfaces on the web page (Figures 1 and 2A).Figure 1

Bottom Line: Digital gene expression profiles were derived from RNA sequencing (RNA-seq) analysis in the fruiting bodies and mycelia.The omics information stored in the database is freely accessible through interactive and graphical interfaces by search functions that include 'GO TREE VIEW' browsing, keyword searches, and BLAST searches.The A-WINGS database will accelerate omics studies on specific aspects of the angel's wing oyster mushroom and the family Tricholomataceae.

View Article: PubMed Central - PubMed

Affiliation: Bioinformatics Laboratory, School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Kawasaki 214-8571, Japan. achkawa@ipc.shizuoka.ac.jp.

ABSTRACT

Background: The angel's wing oyster mushroom (Pleurocybella porrigens, Sugihiratake) is a well-known delicacy. However, its potential risk in acute encephalopathy was recently revealed by a food poisoning incident. To disclose the genes underlying the accident and provide mechanistic insight, we seek to develop an information infrastructure containing omics data. In our previous work, we sequenced the genome and transcriptome using next-generation sequencing techniques. The next step in achieving our goal is to develop a web database to facilitate the efficient mining of large-scale omics data and identification of genes specifically expressed in the mushroom.

Findings: This paper introduces a web database A-WINGS (http://bioinf.mind.meiji.ac.jp/a-wings/) that provides integrated genomic and transcriptomic information for the angel's wing oyster mushroom. The database contains structure and functional annotations of transcripts and gene expressions. Functional annotations contain information on homologous sequences from NCBI nr and UniProt, Gene Ontology, and KEGG Orthology. Digital gene expression profiles were derived from RNA sequencing (RNA-seq) analysis in the fruiting bodies and mycelia. The omics information stored in the database is freely accessible through interactive and graphical interfaces by search functions that include 'GO TREE VIEW' browsing, keyword searches, and BLAST searches.

Conclusions: The A-WINGS database will accelerate omics studies on specific aspects of the angel's wing oyster mushroom and the family Tricholomataceae.

Show MeSH
Related in: MedlinePlus