PEATmoss (Physcomitrella Expression Atlas Tool): a unified gene expression atlas for the model plant Physcomitrella patens. (11th January 2020)

• Record Type: Journal Article
• Authors: Fernandez‐Pozo, Noe; Haas, Fabian B.; Meyberg, Rabea; Ullrich, Kristian K.; Hiss, Manuel; Perroud, Pierre‐François; Hanke, Sebastian; Kratz, Viktor; Powell, Adrian F.; Vesty, Eleanor F.; Daum, Christopher G.; Zane, Matthew; Lipzen, Anna; Sreedasyam, Avinash; Grimwood, Jane; Coates, Juliet C.; Barry, Kerrie; Schmutz, Jeremy; Mueller, Lukas A.; Rensing, Stefan A.
• Is Part Of: Plant journal. Volume 102:Number 1(2020)
• Page Start: 165
• Page End: 177
• Publication Date: 2020-01-11
• Subjects: Physcomitrella patens -- expression atlas -- RNA‐seq -- bioinformatics -- evolution -- development -- plant hormones -- light -- annotation; Plant molecular biology -- Periodicals; Plant cells and tissues -- Periodicals; Botany -- Periodicals; 580
• DOI: 10.1111/tpj.14607
• Languages: English
• ISSNs: 0960-7412

Abstract

Summary: 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 https://peatmoss.online.uni-marburg.de Significance Statement: PEATmoss is a web tool that unifies multiple sources of expression data from Physcomitrella patens and provides numerous visualization tools . The aim of this tool is to become the main resource for P. patens expression data, to be easily expandable in terms of expression data as well as annotation and cross‐linked resources.