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FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki.

Abugessaisa I, Shimoji H, Sahin S, Kondo A, Harshbarger J, Lizio M, Hayashizaki Y, Carninci P, FANTOM consortiumForrest A, Kasukawa T, Kawaji H - Database (Oxford) (2016)

Bottom Line: To make the heterogeneous data set accessible and useful for investigators, we developed a web-based database called Semantic catalog of Samples, Transcription initiation And Regulators (SSTAR).SSTAR utilizes the open source wiki software MediaWiki along with the Semantic MediaWiki (SMW) extension, which provides flexibility to model, store, and display a series of data sets produced during the course of the FANTOM5 project.Our use of SMW demonstrates the utility of the framework for dissemination of large-scale analysis results.

View Article: PubMed Central - PubMed

Affiliation: Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies (CLST), Kanagawa 230-0045, Japan.

No MeSH data available.


Related in: MedlinePlus

Graphical representation of a gene (MYB). (A) Result of the search for MYB gene in SSTAR, with its associated Motifs and list of TSS regions. The user is able to get UCSC genome browser view of the MYB gene. (B) The table shows the expression of five TSS regions associated with MYB. (C) The graphical representation of the B) in which X-axis represents individual samples and y-axis represents expression intensities.
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baw105-F3: Graphical representation of a gene (MYB). (A) Result of the search for MYB gene in SSTAR, with its associated Motifs and list of TSS regions. The user is able to get UCSC genome browser view of the MYB gene. (B) The table shows the expression of five TSS regions associated with MYB. (C) The graphical representation of the B) in which X-axis represents individual samples and y-axis represents expression intensities.

Mentions: In addition to the standard layouts in MediaWiki we enhanced the function of data tables in the SSTAR system to enable search, export, and data plotting using various JavaScript libraries. We further added components to support specific visualizations for the FANTOM5 data set such as a genomic view with UCSC genome browser (Figure 3A) and a tree view of the ontology structure with NCBO’s ontology visualization widget (http://www.bioontology.org/wiki/index.php/NCBO_Widgets#Ontology_visualization_widget; Supplementary Figure S2C). These functions are implemented as custom extensions to MediaWiki, which calls external services or API (Application Program Interface) provided outside of SSTAR.Figure 3.


FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki.

Abugessaisa I, Shimoji H, Sahin S, Kondo A, Harshbarger J, Lizio M, Hayashizaki Y, Carninci P, FANTOM consortiumForrest A, Kasukawa T, Kawaji H - Database (Oxford) (2016)

Graphical representation of a gene (MYB). (A) Result of the search for MYB gene in SSTAR, with its associated Motifs and list of TSS regions. The user is able to get UCSC genome browser view of the MYB gene. (B) The table shows the expression of five TSS regions associated with MYB. (C) The graphical representation of the B) in which X-axis represents individual samples and y-axis represents expression intensities.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4940433&req=5

baw105-F3: Graphical representation of a gene (MYB). (A) Result of the search for MYB gene in SSTAR, with its associated Motifs and list of TSS regions. The user is able to get UCSC genome browser view of the MYB gene. (B) The table shows the expression of five TSS regions associated with MYB. (C) The graphical representation of the B) in which X-axis represents individual samples and y-axis represents expression intensities.
Mentions: In addition to the standard layouts in MediaWiki we enhanced the function of data tables in the SSTAR system to enable search, export, and data plotting using various JavaScript libraries. We further added components to support specific visualizations for the FANTOM5 data set such as a genomic view with UCSC genome browser (Figure 3A) and a tree view of the ontology structure with NCBO’s ontology visualization widget (http://www.bioontology.org/wiki/index.php/NCBO_Widgets#Ontology_visualization_widget; Supplementary Figure S2C). These functions are implemented as custom extensions to MediaWiki, which calls external services or API (Application Program Interface) provided outside of SSTAR.Figure 3.

Bottom Line: To make the heterogeneous data set accessible and useful for investigators, we developed a web-based database called Semantic catalog of Samples, Transcription initiation And Regulators (SSTAR).SSTAR utilizes the open source wiki software MediaWiki along with the Semantic MediaWiki (SMW) extension, which provides flexibility to model, store, and display a series of data sets produced during the course of the FANTOM5 project.Our use of SMW demonstrates the utility of the framework for dissemination of large-scale analysis results.

View Article: PubMed Central - PubMed

Affiliation: Division of Genomic Technologies (DGT), RIKEN Center for Life Science Technologies (CLST), Kanagawa 230-0045, Japan.

No MeSH data available.


Related in: MedlinePlus