FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki

Imad Abugessaisa, Hisashi Shimoji, Serkan Sahin, Atsushi Kondo, Jayson Harshbarger, Marina Lizio, Yoshihide Hayashizaki, Piero Carninci, Alistair Forrest, Takeya Kasukawa, Hideya Kawaji
2016 Database: The Journal of Biological Databases and Curation  
Citation details: Abugessaisa,I., Shimoji,H., Sahin,S. et al. FANTOM5 transcriptome catalog of cellular states based on semantic MediaWiki. Abstract The Functional Annotation of the Mammalian Genome project (FANTOM5) mapped transcription start sites (TSSs) and measured their activities in a diverse range of biological samples. The FANTOM5 project generated a large data set; including detailed information about the profiled samples, the uncovered TSSs at high base-pair resolution on the genome,
more » ... heir transcriptional initiation activities, and further information of transcriptional regulation. Data sets to explore transcriptome in individual cellular states encoded in the mammalian genomes have been enriched by a series of additional analysis, based on the raw experimental data, along with the progress of the research activities. 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 V C The Author(s)
doi:10.1093/database/baw105 pmid:27402679 pmcid:PMC4940433 fatcat:7yz5abo4vvdbva3mgewtnc7j5m