期刊
PLANT JOURNAL
卷 102, 期 1, 页码 165-177出版社
WILEY
DOI: 10.1111/tpj.14607
关键词
Physcomitrella patens; expression atlas; RNA-seq; bioinformatics; evolution; development; plant hormones; light; annotation
资金
- German Research Foundation (DFG) [INST 37/935-1 FUGG]
- DFG [DFG RE 1697/6-1]
- Office of Science of the US Department of Energy [DE-AC02-05CH11231]
- High Performance and Cloud Computing Group at the Zentrum fur Datenverarbeitung of the University of Tubingen, the state of Baden-Wurttemberg, Germany, through bwHPC
Physcomitrella patens is a bryophyte model plant that is often used to study plant evolution and development. Its resources are of great importance for comparative genomics and evo-devo approaches. However, expression data from Physcomitrella patens were so far generated using different gene annotation versions and three different platforms: CombiMatrix and NimbleGen expression microarrays and RNA sequencing. The currently available P. patens expression data are distributed across three tools with different visualization methods to access the data. Here, we introduce an interactive expression atlas, Physcomitrella Expression Atlas Tool (PEATmoss), that unifies publicly available expression data for P. patens and provides multiple visualization methods to query the data in a single web-based tool. Moreover, PEATmoss includes 35 expression experiments not previously available in any other expression atlas. To facilitate gene expression queries across different gene annotation versions, and to access P. patens annotations and related resources, a lookup database and web tool linked to PEATmoss was implemented. PEATmoss can be accessed at
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