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

Fernandez-Pozo, N., Haas, F. B., Meyberg, R., Ullrich, K. K., Hiss, M., Perroud, P.-F., et al. (2020). PEATmoss (Physcomitrella Expression Atlas Tool): a unified gene expression atlas for the model plant Physcomitrella patens. The Plant Journal, 102(1), 165-177. doi:10.1111/tpj.14607.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0005-6895-E Version Permalink: http://hdl.handle.net/21.11116/0000-0006-B8A1-4
Genre: Journal Article

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 Creators:
Fernandez-Pozo, Noe, Author
Haas, Fabian B., Author
Meyberg, Rabea, Author
Ullrich, Kristian K.1, Author              
Hiss, Manuel, Author
Perroud, Pierre-François, Author
Hanke, Sebastian, Author
Kratz, Viktor, Author
Powell, Adrian F., Author
Vesty, Eleanor F., Author
Daum, Christopher G., Author
Zane, Matthew, Author
Lipzen, Anna, Author
Sreedasyam, Avinash, Author
Grimwood, Jane, Author
Coates, Juliet C., Author
Barry, Kerrie, Author
Schmutz, Jeremy, Author
Mueller, Lukas A., Author
Rensing, Stefan A., Author
Affiliations:
1Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Max Planck Society, ou_1445635              

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Free keywords: Physcomitrella patens, expression, atlas, RNA-seq, bioinformatics, evolution, development, plant hormones, light, annotation
 Abstract: Abstract 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

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Language(s): eng - English
 Dates: 2019-10-142019-03-262019-10-302019-11-122020-04
 Publication Status: Published in print
 Pages: -
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 Table of Contents: -
 Rev. Method: -
 Identifiers: DOI: 10.1111/tpj.14607
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Title: The Plant Journal
  Other : Plant J.
Source Genre: Journal
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Publ. Info: Oxford : Blackwell Science
Pages: - Volume / Issue: 102 (1) Sequence Number: - Start / End Page: 165 - 177 Identifier: ISSN: 0960-7412
CoNE: https://pure.mpg.de/cone/journals/resource/954925579095_1