skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

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

Authors:
ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [2];  [1]; ORCiD logo [1];  [1];  [1]; ORCiD logo [3];  [4];  [5];  [5];  [5]; ORCiD logo [6];  [6]; ORCiD logo [4]; ORCiD logo [5]; ORCiD logo [7]; ORCiD logo [3]; ORCiD logo [8]
  1. Plant Cell Biology, Faculty of Biology University of Marburg Marburg Germany
  2. Plant Cell Biology, Faculty of Biology University of Marburg Marburg Germany, Department of Evolutionary Genetics Max Planck Institute for Evolutionary Biology Ploen Germany
  3. Boyce Thompson Institute Ithaca NY USA
  4. School of Biosciences University of Birmingham Birmingham UK
  5. US Department of Energy (DOE) Joint Genome Institute Walnut Creek CA 94598 USA
  6. HudsonAlpha Institute for Biotechnology Huntsville AL 35806 USA
  7. US Department of Energy (DOE) Joint Genome Institute Walnut Creek CA 94598 USA, HudsonAlpha Institute for Biotechnology Huntsville AL 35806 USA
  8. Plant Cell Biology, Faculty of Biology University of Marburg Marburg Germany, BIOSS Centre for Biological Signalling Studies University of Freiburg Freiburg Germany, LOEWE Center for Synthetic Microbiology (SYNMIKRO) University of Marburg Germany
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1582466
Alternate Identifier(s):
OSTI ID: 1582467
Grant/Contract Number:  
DE‐AC02‐05CH11231
Resource Type:
Published Article
Journal Name:
The Plant Journal
Additional Journal Information:
Journal Name: The Plant Journal; Journal ID: ISSN 0960-7412
Publisher:
Wiley-Blackwell
Country of Publication:
United Kingdom
Language:
English

Citation Formats

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., and Rensing, Stefan A. PEATmoss ( Physcomitrella Expression Atlas Tool): a unified gene expression atlas for the model plant Physcomitrella patens. United Kingdom: N. p., 2020. Web. doi:10.1111/tpj.14607.
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. PEATmoss ( Physcomitrella Expression Atlas Tool): a unified gene expression atlas for the model plant Physcomitrella patens. United Kingdom. doi:10.1111/tpj.14607.
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., and Rensing, Stefan A. Sat . "PEATmoss ( Physcomitrella Expression Atlas Tool): a unified gene expression atlas for the model plant Physcomitrella patens". United Kingdom. doi:10.1111/tpj.14607.
@article{osti_1582466,
title = {PEATmoss ( Physcomitrella Expression Atlas Tool): a unified gene expression atlas for the model plant Physcomitrella patens},
author = {Fernandez‐Pozo, Noe and Haas, Fabian B. and Meyberg, Rabea and Ullrich, Kristian K. and Hiss, Manuel and Perroud, Pierre‐François and Hanke, Sebastian and Kratz, Viktor and Powell, Adrian F. and Vesty, Eleanor F. and Daum, Christopher G. and Zane, Matthew and Lipzen, Anna and Sreedasyam, Avinash and Grimwood, Jane and Coates, Juliet C. and Barry, Kerrie and Schmutz, Jeremy and Mueller, Lukas A. and Rensing, Stefan A.},
abstractNote = {},
doi = {10.1111/tpj.14607},
journal = {The Plant Journal},
number = ,
volume = ,
place = {United Kingdom},
year = {2020},
month = {1}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1111/tpj.14607

Save / Share:

Works referenced in this record:

Ensembl Genomes 2016: more genomes, more complexity
journal, November 2015

  • Kersey, Paul Julian; Allen, James E.; Armean, Irina
  • Nucleic Acids Research, Vol. 44, Issue D1
  • DOI: 10.1093/nar/gkv1209

Vacuolar Ca 2+ /H + Transport Activity Is Required for Systemic Phosphate Homeostasis Involving Shoot-to-Root Signaling in Arabidopsis
journal, May 2011

  • Liu, Tzu-Yin; Aung, Kyaw; Tseng, Ching-Ying
  • Plant Physiology, Vol. 156, Issue 3
  • DOI: 10.1104/pp.111.175257

AP2/ERF family transcription factors in plant abiotic stress responses
journal, February 2012

  • Mizoi, Junya; Shinozaki, Kazuo; Yamaguchi-Shinozaki, Kazuko
  • Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Vol. 1819, Issue 2
  • DOI: 10.1016/j.bbagrm.2011.08.004

The Physcomitrella patens gene atlas project: large-scale RNA-seq based expression data
journal, June 2018

  • Perroud, Pierre-François; Haas, Fabian B.; Hiss, Manuel
  • The Plant Journal, Vol. 95, Issue 1
  • DOI: 10.1111/tpj.13940

Nutrient Sensing and Signaling: NPKS
journal, June 2007


Sexual reproduction, sporophyte development and molecular variation in the model moss Physcomitrella patens : introducing the ecotype Reute
journal, March 2017

  • Hiss, Manuel; Meyberg, Rabea; Westermann, Jens
  • The Plant Journal, Vol. 90, Issue 3
  • DOI: 10.1111/tpj.13501

Involvement of calmodulin and calmodulin-like proteins in plant responses to abiotic stresses
journal, August 2015


Physcomitrella patens Reute mC herry as a tool for efficient crossing within and between ecotypes
journal, May 2018

  • Perroud, P. ‐F.; Meyberg, R.; Rensing, S. A.
  • Plant Biology, Vol. 21, Issue S1
  • DOI: 10.1111/plb.12840

Phosphate sensing in higher plants
journal, May 2002


Fast and SNP-tolerant detection of complex variants and splicing in short reads
journal, February 2010


A Transcriptome Atlas of Physcomitrella patens Provides Insights into the Evolution and Development of Land Plants
journal, February 2016

  • Ortiz-Ramírez, Carlos; Hernandez-Coronado, Marcela; Thamm, Anna
  • Molecular Plant, Vol. 9, Issue 2
  • DOI: 10.1016/j.molp.2015.12.002

Hemerythrin E3 Ubiquitin Ligases as Negative Regulators of Iron Homeostasis in Plants
journal, February 2019

  • Rodríguez-Celma, Jorge; Chou, Hsuan; Kobayashi, Takanori
  • Frontiers in Plant Science, Vol. 10
  • DOI: 10.3389/fpls.2019.00098

Phylogenomic analysis of gene co-expression networks reveals the evolution of functional modules
journal, March 2017

  • Ruprecht, Colin; Proost, Sebastian; Hernandez-Coronado, Marcela
  • The Plant Journal, Vol. 90, Issue 3
  • DOI: 10.1111/tpj.13502

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
journal, September 1997

  • Altschul, Stephen F.; Madden, Thomas L.; Schäffer, Alejandro A.
  • Nucleic Acids Research, Vol. 25, Issue 17, p. 3389-3402
  • DOI: 10.1093/nar/25.17.3389

Great moments in evolution: the conquest of land by plants
journal, April 2018


The transcription factor PHR1 regulates lipid remodeling and triacylglycerol accumulation in Arabidopsis thaliana during phosphorus starvation
journal, February 2015

  • Pant, Bikram Datt; Burgos, Asdrubal; Pant, Pooja
  • Journal of Experimental Botany, Vol. 66, Issue 7
  • DOI: 10.1093/jxb/eru535

The Sol Genomics Network (SGN)—from genotype to phenotype to breeding
journal, November 2014

  • Fernandez-Pozo, Noe; Menda, Naama; Edwards, Jeremy D.
  • Nucleic Acids Research, Vol. 43, Issue D1
  • DOI: 10.1093/nar/gku1195

The Sequence Read Archive
journal, November 2010

  • Leinonen, R.; Sugawara, H.; Shumway, M.
  • Nucleic Acids Research, Vol. 39, Issue Database
  • DOI: 10.1093/nar/gkq1019

Phytozome: a comparative platform for green plant genomics
journal, November 2011

  • Goodstein, David M.; Shu, Shengqiang; Howson, Russell
  • Nucleic Acids Research, Vol. 40, Issue D1
  • DOI: 10.1093/nar/gkr944

A genome-wide transcriptional analysis using Arabidopsis thaliana Affymetrix gene chips determined plant responses to phosphate deprivation
journal, August 2005

  • Misson, J.; Raghothama, K. G.; Jain, A.
  • Proceedings of the National Academy of Sciences, Vol. 102, Issue 33
  • DOI: 10.1073/pnas.0505266102

An “Electronic Fluorescent Pictograph” Browser for Exploring and Analyzing Large-Scale Biological Data Sets
journal, August 2007


Ethylene and plant responses to phosphate deficiency
journal, September 2015


Coexpression-Based Clustering of Arabidopsis Root Genes Predicts Functional Modules in Early Phosphate Deficiency Signaling
journal, January 2011

  • Lin, Wen-Dar; Liao, Ya-Yun; Yang, Thomas J. W.
  • Plant Physiology, Vol. 155, Issue 3
  • DOI: 10.1104/pp.110.166520

UniProt: the universal protein knowledgebase
journal, February 2018

  • UniProt Consortium, The
  • Nucleic Acids Research, Vol. 46, Issue 5
  • DOI: 10.1093/nar/gky092

Sensing and Signaling of Phosphate Starvation: From Local to Long Distance
journal, July 2018

  • Chien, Pei-Shan; Chiang, Chih-Pin; Leong, Shang Jye
  • Plant and Cell Physiology, Vol. 59, Issue 9
  • DOI: 10.1093/pcp/pcy148

The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants
journal, December 2007


Phosphorus Uptake by Plants: From Soil to Cell
journal, February 1998

  • Schachtman, Daniel P.; Reid, Robert J.; Ayling, S. M.
  • Plant Physiology, Vol. 116, Issue 2
  • DOI: 10.1104/pp.116.2.447

Phosphate deficiency-induced cell wall remodeling: Linking gene networks with polysaccharide meshworks
journal, May 2011

  • Liao, Ya-Yun; Buckhout, Thomas J.; Schmidt, Wolfgang
  • Plant Signaling & Behavior, Vol. 6, Issue 5
  • DOI: 10.4161/psb.6.5.15051

The Impacts of Phosphorus Deficiency on the Photosynthetic Electron Transport Chain
journal, March 2018

  • Carstensen, Andreas; Herdean, Andrei; Schmidt, Sidsel Birkelund
  • Plant Physiology, Vol. 177, Issue 1
  • DOI: 10.1104/pp.17.01624

Comprehensive Genome-Wide Classification Reveals That Many Plant-Specific Transcription Factors Evolved in Streptophyte Algae
journal, December 2017

  • Wilhelmsson, Per K. I.; Mühlich, Cornelia; Ullrich, Kristian K.
  • Genome Biology and Evolution, Vol. 9, Issue 12
  • DOI: 10.1093/gbe/evx258

Identification of vacuolar phosphate efflux transporters in land plants
journal, January 2019


edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
journal, November 2009


Physiological and Transcriptome Analysis of Iron and Phosphorus Interaction in Rice Seedlings
journal, July 2009

  • Zheng, Luqing; Huang, Fangliang; Narsai, Reena
  • Plant Physiology, Vol. 151, Issue 1
  • DOI: 10.1104/pp.109.141051

Characterization of the PHO1 Gene Family and the Responses to Phosphate Deficiency of Physcomitrella patens
journal, November 2007


BEDTools: a flexible suite of utilities for comparing genomic features
journal, January 2010


Phosphate deficiency promotes modification of iron distribution in Arabidopsis plants
journal, November 2006


Phosphate starvation and membrane lipid remodeling in seed plants
journal, January 2013


BLAST+: architecture and applications
journal, January 2009

  • Camacho, Christiam; Coulouris, George; Avagyan, Vahram
  • BMC Bioinformatics, Vol. 10, Issue 1
  • DOI: 10.1186/1471-2105-10-421

The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution
journal, January 2018

  • Lang, Daniel; Ullrich, Kristian K.; Murat, Florent
  • The Plant Journal, Vol. 93, Issue 3
  • DOI: 10.1111/tpj.13801

Global transcriptome profile of rice root in response to essential macronutrient deficiency
journal, June 2013

  • Takehisa, Hinako; Sato, Yutaka; Antonio, Baltazar A.
  • Plant Signaling & Behavior, Vol. 8, Issue 6
  • DOI: 10.4161/psb.24409

ABA-Induced Vegetative Diaspore Formation in Physcomitrella patens
journal, March 2019


ArrayExpress update—simplifying data submissions
journal, October 2014

  • Kolesnikov, Nikolay; Hastings, Emma; Keays, Maria
  • Nucleic Acids Research, Vol. 43, Issue D1
  • DOI: 10.1093/nar/gku1057

PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics
journal, October 2017

  • Van Bel, Michiel; Diels, Tim; Vancaester, Emmelien
  • Nucleic Acids Research, Vol. 46, Issue D1
  • DOI: 10.1093/nar/gkx1002

Genevestigator V3: A Reference Expression Database for the Meta-Analysis of Transcriptomes
journal, January 2008

  • Hruz, Tomas; Laule, Oliver; Szabo, Gabor
  • Advances in Bioinformatics, Vol. 2008
  • DOI: 10.1155/2008/420747

BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks
journal, June 2005


Plant hormones and nutrient signaling
journal, August 2008

  • Rubio, Vicente; Bustos, Regla; Irigoyen, María Luisa
  • Plant Molecular Biology, Vol. 69, Issue 4
  • DOI: 10.1007/s11103-008-9380-y

Why we need more non-seed plant models
journal, February 2017


Algal ancestor of land plants was preadapted for symbiosis
journal, October 2015

  • Delaux, Pierre-Marc; Radhakrishnan, Guru V.; Jayaraman, Dhileepkumar
  • Proceedings of the National Academy of Sciences, Vol. 112, Issue 43
  • DOI: 10.1073/pnas.1515426112

Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
journal, January 1995


Linking phosphorus availability with photo-oxidative stress in plants
journal, March 2015

  • Hernández, Iker; Munné-Bosch, Sergi
  • Journal of Experimental Botany, Vol. 66, Issue 10
  • DOI: 10.1093/jxb/erv056

Phosphate Deficiency Induces the Jasmonate Pathway and Enhances Resistance to Insect Herbivory
journal, March 2016

  • Khan, Ghazanfar Abbas; Vogiatzaki, Evangelia; Glauser, Gaétan
  • Plant Physiology, Vol. 171, Issue 1
  • DOI: 10.1104/pp.16.00278

The Tomato Expression Atlas
journal, March 2017


Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
journal, December 2014


The phosphate transporter PHT4;1 is a salicylic acid regulator likely controlled by the circadian clock protein CCA1
journal, December 2014