Tutorial videos of bioinformatics resources: online distribution trial in Japan named TogoTV

Kawano, Shin; Hiromasa, Ono; Takagi, Toshihisa; Bono, Hidemasa

doi:10.1093/bib/bbr039

Cited by 12 publications

(6 citation statements)

References 25 publications

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“…The movie originated from the contents of TogoTV 16 , which provides tutorial videos for useful databases and web tools in the life sciences, and is available on the TogoTV original website 17 and YouTube.…”

Section: Resultsmentioning

confidence: 99%

“…A RefEx help page, entitled ‘How to use RefEx’ ( http://refex.dbcls.jp/help.php?lang=en ), provides information about RefEx not only as a text manual but also as a tutorial movie ( http://doi.org/10.7875/togotv.2016.068 ). The movie originated from the contents of TogoTV 16 , which provides tutorial videos for useful databases and web tools in the life sciences, and is available on the TogoTV original website 17 and YouTube.…”

Section: Resultsmentioning

confidence: 99%

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RefEx, a reference gene expression dataset as a web tool for the functional analysis of genes

et al. 2017

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Gene expression data are exponentially accumulating; thus, the functional annotation of such sequence data from metadata is urgently required. However, life scientists have difficulty utilizing the available data due to its sheer magnitude and complicated access. We have developed a web tool for browsing reference gene expression pattern of mammalian tissues and cell lines measured using different methods, which should facilitate the reuse of the precious data archived in several public databases. The web tool is called Reference Expression dataset (RefEx), and RefEx allows users to search by the gene name, various types of IDs, chromosomal regions in genetic maps, gene family based on InterPro, gene expression patterns, or biological categories based on Gene Ontology. RefEx also provides information about genes with tissue-specific expression, and the relative gene expression values are shown as choropleth maps on 3D human body images from BodyParts3D. Combined with the newly incorporated Functional Annotation of Mammals (FANTOM) dataset, RefEx provides insight regarding the functional interpretation of unfamiliar genes. RefEx is publicly available at http://refex.dbcls.jp/.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

RefEx, a reference gene expression dataset as a web tool for the functional analysis of genes

et al. 2017

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“…Further, a tutorial movie that shows how to make use of the AOE web interface is available at https://doi.org/10.7875/togotv.2018.146. The movie originated from the contents of TogoTV, which provides tutorial videos for useful databases and web tools in the life sciences [8], and is available on the TogoTV original website (https://togotv.dbcls.jp/en/) and YouTube (https://youtube.com/togotv/). AOE web server has been maintained for five years.…”

Section: Graphical Web Interfacementioning

confidence: 99%

All of gene expression (AOE): An integrated index for public gene expression databases

Bono

2020

PLoS ONE

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Gene expression data have been archived as microarray and RNA-seq datasets in two public databases, Gene Expression Omnibus (GEO) and ArrayExpress (AE). In 2018, the DNA DataBank of Japan started a similar repository called the Genomic Expression Archive (GEA). These databases are useful resources for the functional interpretation of genes, but have been separately maintained and may lack RNA-seq data, while the original sequence data are available in the Sequence Read Archive (SRA). We constructed an index for those gene expression data repositories, called All Of gene Expression (AOE), to integrate publicly available gene expression data. The web interface of AOE can graphically query data in addition to the application programming interface. By collecting gene expression data from RNA-seq in the SRA, AOE also includes data not included in GEO and AE. AOE is accessible as a search tool from the GEA website and is freely available at https://aoe.dbcls.jp/.

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“…Further, a tutorial movie to show how to make use of AOE web interface is available at https://doi.org/10.7875/togotv.2018.146. The movie originated from the contents of TogoTV, which provides tutorial videos for useful databases and web tools in the life sciences [8], and is available on the TogoTV original website (https://togotv.dbcls.jp/en/) and YouTube (https://youtube.com/ togotv/). AOE web server has been maintained for five years.…”

Section: Graphical Web Interfacementioning

confidence: 99%

All of gene expression (AOE): an integrated index for public gene expression databases

Bono

2019

Preprint

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Gene expression data have been archived as microarray and RNA-seq datasets in two public databases, Gene Expression Omnibus (GEO) and ArrayExpress (AE). In 2018, the DNA DataBank of Japan started a similar repository called the Genomic Expression Archive (GEA). These databases are useful resources for the functional interpretation of genes, but have been separately maintained and may lack RNA-seq data, while the original sequence data are available in the Sequence Read Archive (SRA).We constructed an index for those gene expression data repositories, called All Of gene Expression (AOE), to integrate publicly available gene expression data. The web interface of AOE can graphically query data in addition to the application programming interface. By collecting gene expression data from RNA-seq in the SRA, AOE also includes data not included in GEO and AE.AOE is accessible as a search tool from the GEA website and is freely available at https://aoe.dbcls.jp/.

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Tutorial videos of bioinformatics resources: online distribution trial in Japan named TogoTV

Cited by 12 publications

References 25 publications

RefEx, a reference gene expression dataset as a web tool for the functional analysis of genes

RefEx, a reference gene expression dataset as a web tool for the functional analysis of genes

All of gene expression (AOE): An integrated index for public gene expression databases

All of gene expression (AOE): an integrated index for public gene expression databases

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