PEATmoss (Physcomitrella Expression Atlas Tool): a unified gene expression atlas for the model plant Physcomitrella patens

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 annotat...

Descripción completa

Detalles Bibliográficos
Autores: Fernández-Pozo, Noé, Haas, Fabian B., Rabea Meyberg, Kristian K. Ullrich, Manuel Hiss, Pierre‐François Perroud, Sebastian Hanke, Viktor Kratz, Adrian F. Powell, Eleanor F. Vesty, Christopher G. Daum, Matthew Zane, Anna Lipzen, Avinash Sreedasyam, Jane Grimwood, Juliet C. Coates, Kerrie Barry, Jeremy Schmutz, Lukas A. Mueller, Stefan A. Rensing
Tipo de recurso: artículo
Fecha de publicación:2019
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/343562
Acceso en línea:http://hdl.handle.net/10261/343562
https://doi.org/10.1111/tpj.14607
Access Level:acceso abierto
Palabra clave:Physcomitrella patens
RNA-seq
annotation
bioinformatics
development
evolution
expression atlas
light
plant hormones
Descripción
Sumario: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.

Similares en LA Referencia