PEATmoss ( Physcomitrella Expression Atlas Tool): a unified gene expression atlas for the model plant Physcomitrella patens
- Authors:
-
[1];
[1];
[1];
[2];
[1];
[3];
[6];
[4];
[5];
[7];
[3];
[8]
- Plant Cell Biology, Faculty of Biology University of Marburg Marburg Germany
- Plant Cell Biology, Faculty of Biology University of Marburg Marburg Germany, Department of Evolutionary Genetics Max Planck Institute for Evolutionary Biology Ploen Germany
- Boyce Thompson Institute Ithaca NY USA
- School of Biosciences University of Birmingham Birmingham UK
- US Department of Energy (DOE) Joint Genome Institute Walnut Creek CA 94598 USA
- HudsonAlpha Institute for Biotechnology Huntsville AL 35806 USA
- US Department of Energy (DOE) Joint Genome Institute Walnut Creek CA 94598 USA, HudsonAlpha Institute for Biotechnology Huntsville AL 35806 USA
- 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 Volume: 102 Journal Issue: 1; 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 = 1,
volume = 102,
place = {United Kingdom},
year = {2020},
month = {1}
}
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DOI: 10.1111/tpj.14607
DOI: 10.1111/tpj.14607
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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
Network Theory Inspired Analysis of Time-Resolved Expression Data Reveals Key Players Guiding P. patens Stem Cell Development
journal, April 2013
- Busch, Hauke; Boerries, Melanie; Bao, Jie
- PLoS ONE, Vol. 8, Issue 4
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
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
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
Nutrient Sensing and Signaling: NPKS
journal, June 2007
- Schachtman, Daniel P.; Shin, Ryoung
- Annual Review of Plant Biology, Vol. 58, Issue 1
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
Insights from the cold transcriptome of Physcomitrella patens : global specialization pattern of conserved transcriptional regulators and identification of orphan genes involved in cold acclimation
journal, September 2014
- Beike, Anna K.; Lang, Daniel; Zimmer, Andreas D.
- New Phytologist, Vol. 205, Issue 2
Involvement of calmodulin and calmodulin-like proteins in plant responses to abiotic stresses
journal, August 2015
- Zeng, Houqing; Xu, Luqin; Singh, Amarjeet
- Frontiers in Plant Science, Vol. 6
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
Phosphate sensing in higher plants
journal, May 2002
- Abel, Steffen; Ticconi, Carla A.; Delatorre, Carla A.
- Physiologia Plantarum, Vol. 115, Issue 1
Fast and SNP-tolerant detection of complex variants and splicing in short reads
journal, February 2010
- Wu, T. D.; Nacu, S.
- Bioinformatics, Vol. 26, Issue 7, p. 873-881
Large-scale gene expression profiling data for the model moss Physcomitrella patens aid understanding of developmental progression, culture and stress conditions
journal, July 2014
- Hiss, Manuel; Laule, Oliver; Meskauskiene, Rasa M.
- The Plant Journal, Vol. 79, Issue 3
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
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
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
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
Great moments in evolution: the conquest of land by plants
journal, April 2018
- Rensing, Stefan A.
- Current Opinion in Plant Biology, Vol. 42
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
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
The Sequence Read Archive
journal, November 2010
- Leinonen, R.; Sugawara, H.; Shumway, M.
- Nucleic Acids Research, Vol. 39, Issue Database
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
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
An “Electronic Fluorescent Pictograph” Browser for Exploring and Analyzing Large-Scale Biological Data Sets
journal, August 2007
- Winter, Debbie; Vinegar, Ben; Nahal, Hardeep
- PLoS ONE, Vol. 2, Issue 8
Ethylene and plant responses to phosphate deficiency
journal, September 2015
- Song, Li; Liu, Dong
- Frontiers in Plant Science, Vol. 6
How to usefully compare homologous plant genes and chromosomes as DNA sequences: How to usefully compare plant genomes
journal, February 2008
- Lyons, Eric; Freeling, Michael
- The Plant Journal, Vol. 53, Issue 4
The arabidopsis information resource: Making and mining the “gold standard” annotated reference plant genome: Tair: Making and Mining the “Gold Standard” Plant Genome
journal, August 2015
- Berardini, Tanya Z.; Reiser, Leonore; Li, Donghui
- genesis, Vol. 53, Issue 8
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
UniProt: the universal protein knowledgebase
journal, February 2018
- UniProt Consortium, The
- Nucleic Acids Research, Vol. 46, Issue 5
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
The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants
journal, December 2007
- Rensing, S. A.; Lang, D.; Zimmer, A. D.
- Science, Vol. 319, Issue 5859
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
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
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
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
Identification of vacuolar phosphate efflux transporters in land plants
journal, January 2019
- Xu, Lei; Zhao, Hongyu; Wan, Renjing
- Nature Plants, Vol. 5, Issue 1
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
journal, November 2009
- Robinson, M. D.; McCarthy, D. J.; Smyth, G. K.
- Bioinformatics, Vol. 26, Issue 1
Characterization of Phytochrome Interacting Factors from the Moss Physcomitrella patens Illustrates Conservation of Phytochrome Signaling Modules in Land Plants
journal, January 2017
- Possart, Anja; Xu, Tengfei; Paik, Inyup
- The Plant Cell, Vol. 29, Issue 2
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
Arabidopsis Ferritin 1 ( AtFer1 ) Gene Regulation by the Phosphate Starvation Response 1 (AtPHR1) Transcription Factor Reveals a Direct Molecular Link between Iron and Phosphate Homeostasis
journal, June 2013
- Bournier, Marc; Tissot, Nicolas; Mari, Stéphane
- Journal of Biological Chemistry, Vol. 288, Issue 31
Characterization of the PHO1 Gene Family and the Responses to Phosphate Deficiency of Physcomitrella patens
journal, November 2007
- Wang, Yong; Secco, David; Poirier, Yves
- Plant Physiology, Vol. 146, Issue 2
BEDTools: a flexible suite of utilities for comparing genomic features
journal, January 2010
- Quinlan, Aaron R.; Hall, Ira M.
- Bioinformatics, Vol. 26, Issue 6
Phosphate deficiency promotes modification of iron distribution in Arabidopsis plants
journal, November 2006
- Hirsch, J.; Marin, E.; Floriani, M.
- Biochimie, Vol. 88, Issue 11
Phosphate starvation and membrane lipid remodeling in seed plants
journal, January 2013
- Nakamura, Yuki
- Progress in Lipid Research, Vol. 52, Issue 1
BLAST+: architecture and applications
journal, January 2009
- Camacho, Christiam; Coulouris, George; Avagyan, Vahram
- BMC Bioinformatics, Vol. 10, Issue 1
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
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
ABA-Induced Vegetative Diaspore Formation in Physcomitrella patens
journal, March 2019
- Arif, M. Asif; Hiss, Manuel; Tomek, Marta
- Frontiers in Plant Science, Vol. 10
ArrayExpress update—simplifying data submissions
journal, October 2014
- Kolesnikov, Nikolay; Hastings, Emma; Keays, Maria
- Nucleic Acids Research, Vol. 43, Issue D1
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
Reannotation and extended community resources for the genome of the non-seed plant Physcomitrella patens provide insights into the evolution of plant gene structures and functions
journal, January 2013
- Zimmer, Andreas D.; Lang, Daniel; Buchta, Karol
- BMC Genomics, Vol. 14, Issue 1
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
BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks
journal, June 2005
- Maere, S.; Heymans, K.; Kuiper, M.
- Bioinformatics, Vol. 21, Issue 16
Plant hormones and nutrient signaling
journal, August 2008
- Rubio, Vicente; Bustos, Regla; Irigoyen, María Luisa
- Plant Molecular Biology, Vol. 69, Issue 4
Why we need more non-seed plant models
journal, February 2017
- Rensing, Stefan A.
- New Phytologist, Vol. 216, Issue 2
Physiological and comparative proteome analyses reveal low-phosphate tolerance and enhanced photosynthesis in a maize mutant owing to reinforced inorganic phosphate recycling
journal, June 2016
- Zhang, Kewei; Liu, Hanhan; Song, Jiuling
- BMC Plant Biology, Vol. 16, Issue 1
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
Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
journal, January 1995
- Benjamini, Yoav; Hochberg, Yosef
- Journal of the Royal Statistical Society: Series B (Methodological), Vol. 57, Issue 1
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
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
The Tomato Expression Atlas
journal, March 2017
- Fernandez-Pozo, Noe; Zheng, Yi; Snyder, Stephen I.
- Bioinformatics, Vol. 33, Issue 15
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
journal, December 2014
- Love, Michael I.; Huber, Wolfgang; Anders, Simon
- Genome Biology, Vol. 15, Issue 12
The phosphate transporter PHT4;1 is a salicylic acid regulator likely controlled by the circadian clock protein CCA1
journal, December 2014
- Wang, Guoying; Zhang, Chong; Battle, Stephanie
- Frontiers in Plant Science, Vol. 5