Meta-analysis of the space flight and microgravity response of the Arabidopsis plant transcriptome

[1]  Brad T. Sherman,et al.  DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update) , 2022, Nucleic Acids Res..

[2]  Daniel C. Berrios,et al.  NASA GeneLab: interfaces for the exploration of space omics data , 2020, Nucleic Acids Res..

[3]  Shayoni Ray,et al.  RNAseq Analysis of Rodent Spaceflight Experiments Is Confounded by Sample Collection Techniques , 2020, bioRxiv.

[4]  Anton Nekrutenko,et al.  The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update , 2020, Nucleic Acids Res..

[5]  Marco Brandizi,et al.  KnetMiner: a comprehensive approach for supporting evidence‐based gene discovery and complex trait analysis across species , 2020, bioRxiv.

[6]  Richard Barker,et al.  Test of Arabidopsis Space Transcriptome: A Discovery Environment to Explore Multiple Plant Biology Spaceflight Experiments , 2020, Frontiers in Plant Science.

[7]  Tianwei Yu,et al.  scBatch: batch-effect correction of RNA-seq data through sample distance matrix adjustment , 2020, Bioinform..

[8]  S. Wyatt,et al.  Spaceflight induces novel regulatory responses in Arabidopsis seedling as revealed by combined proteomic and transcriptomic analyses , 2020, BMC Plant Biology.

[9]  Moritaka Nakamura,et al.  Bridging the gap between amyloplasts and directional auxin transport in plant gravitropism. , 2019, Current opinion in plant biology.

[10]  James E. Allen,et al.  Ensembl Genomes 2020—enabling non-vertebrate genomic research , 2019, Nucleic Acids Res..

[11]  Tianwei Yu,et al.  Batch Effect Correction of RNA-seq Data through Sample Distance Matrix Adjustment , 2019, bioRxiv.

[12]  Olga Tanaseichuk,et al.  Metascape provides a biologist-oriented resource for the analysis of systems-level datasets , 2019, Nature Communications.

[13]  Simon Gilroy,et al.  Variation in the transcriptome of different ecotypes of Arabidopsis thaliana reveals signatures of oxidative stress in plant responses to spaceflight. , 2019, American journal of botany.

[14]  Runan Yao,et al.  iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data , 2018, BMC Bioinformatics.

[15]  Damian Szklarczyk,et al.  STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets , 2018, Nucleic Acids Res..

[16]  Anushya Muruganujan,et al.  PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools , 2018, Nucleic Acids Res..

[17]  Robert J Ferl,et al.  Comparing RNA‐Seq and microarray gene expression data in two zones of the Arabidopsis root apex relevant to spaceflight , 2018, Applications in plant sciences.

[18]  Daniel C. Berrios,et al.  GeneLab: Omics database for spaceflight experiments , 2018, Bioinform..

[19]  Nuno A. Fonseca,et al.  Expression Atlas: gene and protein expression across multiple studies and organisms , 2017, Nucleic Acids Res..

[20]  Thawfeek M. Varusai,et al.  The Reactome Pathway Knowledgebase , 2017, Nucleic Acids Res..

[21]  Robert J Ferl,et al.  ARG1 Functions in the Physiological Adaptation of Undifferentiated Plant Cells to Spaceflight. , 2017, Astrobiology.

[22]  Robert D. Finn,et al.  Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species , 2017, Nucleic Acids Res..

[23]  P. Masson,et al.  Molecular Mechanisms of Root Gravitropism , 2017, Current Biology.

[24]  Melanie J Correll,et al.  Comparative transcriptomics indicate changes in cell wall organization and stress response in seedlings during spaceflight. , 2017, American journal of botany.

[25]  Agata K. Zupanska,et al.  Patterns of Arabidopsis gene expression in the face of hypobaric stress , 2017 .

[26]  Robert J Ferl,et al.  Genetic dissection of the Arabidopsis spaceflight transcriptome: Are some responses dispensable for the physiological adaptation of plants to spaceflight? , 2017, PloS one.

[27]  Raymond M. Wheeler,et al.  Agriculture for Space: People and Places Paving the Way , 2017 .

[28]  Minoru Kanehisa,et al.  KEGG: new perspectives on genomes, pathways, diseases and drugs , 2016, Nucleic Acids Res..

[29]  Julio Saez-Rodriguez,et al.  OmniPath: guidelines and gateway for literature-curated signaling pathway resources , 2016, Nature Methods.

[30]  D. Hincha,et al.  Natural Variation of Cold Deacclimation Correlates with Variation of Cold-Acclimation of the Plastid Antioxidant System in Arabidopsis thaliana Accessions , 2016, Front. Plant Sci..

[31]  Emily M. Strait,et al.  The arabidopsis information resource: Making and mining the “gold standard” annotated reference plant genome , 2015, Genesis.

[32]  Matthew E. Ritchie,et al.  limma powers differential expression analyses for RNA-sequencing and microarray studies , 2015, Nucleic acids research.

[33]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[34]  G. Bingham,et al.  Genome-wide expression analysis of reactive oxygen species gene network in Mizuna plants grown in long-term spaceflight , 2014, BMC Plant Biology.

[35]  Laura L. Elo,et al.  Comparison of software packages for detecting differential expression in RNA-seq studies , 2013, Briefings Bioinform..

[36]  S. Munné-Bosch,et al.  JUNGBRUNNEN1, a Reactive Oxygen Species–Responsive NAC Transcription Factor, Regulates Longevity in Arabidopsis[W][OA] , 2012, Plant Cell.

[37]  Robert J Ferl,et al.  Spaceflight transcriptomes: unique responses to a novel environment. , 2012, Astrobiology.

[38]  Colin N. Dewey,et al.  RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome , 2011, BMC Bioinformatics.

[39]  J. Msanne,et al.  Characterization of abiotic stress-responsive Arabidopsis thaliana RD29A and RD29B genes and evaluation of transgenes , 2011, Planta.

[40]  Rafael A. Irizarry,et al.  A framework for oligonucleotide microarray preprocessing , 2010, Bioinform..

[41]  Miyo Terao Morita,et al.  Directional gravity sensing in gravitropism. , 2010, Annual Review of Plant Biology.

[42]  F. Mafessoni,et al.  The Heat-Inducible Transcription Factor HsfA2 Enhances Anoxia Tolerance in Arabidopsis[W] , 2010, Plant Physiology.

[43]  Y. Kitaya,et al.  Effects of Gravity on Transpiration of Plant Leaves , 2009, Annals of the New York Academy of Sciences.

[44]  A. Weber,et al.  Transcriptional profiling of Arabidopsis heat shock proteins and transcription factors reveals extensive overlap between heat and non-heat stress response pathways , 2007, BMC Genomics.

[45]  Mike Tyers,et al.  BioGRID: a general repository for interaction datasets , 2005, Nucleic Acids Res..

[46]  P. Perata,et al.  A Genome-Wide Analysis of the Effects of Sucrose on Gene Expression in Arabidopsis Seedlings under Anoxia[w] , 2005, Plant Physiology.

[47]  A. Altman,et al.  Role of plant heat-shock proteins and molecular chaperones in the abiotic stress response. , 2004, Trends in plant science.

[48]  S. Rhee,et al.  AraCyc: A Biochemical Pathway Database for Arabidopsis1 , 2003, Plant Physiology.

[49]  Rafael A Irizarry,et al.  Exploration, normalization, and summaries of high density oligonucleotide array probe level data. , 2003, Biostatistics.

[50]  Gary D Bader,et al.  BMC Bioinformatics Methodology article Statistical significance for hierarchical clustering in genetic association and microarray expression studies , 2003 .

[51]  D. Marshall Porterfield,et al.  The Biophysical Limitations in Physiological Transport and Exchange in Plants Grown in Microgravity , 2002, Journal of Plant Growth Regulation.

[52]  D M Porterfield,et al.  Evidence of Root Zone Hypoxia in Brassica rapa L. Grown in Microgravity , 2001, International Journal of Plant Sciences.

[53]  OUP accepted manuscript , 2022, Nucleic Acids Research.

[54]  S. Brunak,et al.  A scored human protein–protein interaction network to catalyze genomic interpretation , 2017, Nature Methods.

[55]  Yuhong Tang,et al.  Transcriptional response of Arabidopsis seedlings during spaceflight reveals peroxidase and cell wall remodeling genes associated with root hair development. , 2015, American journal of botany.

[56]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[57]  Fiona C. Denison,et al.  Spaceflight engages heat shock protein and other molecular chaperone genes in tissue culture cells of Arabidopsis thaliana. , 2013, American journal of botany.

[58]  K. Shinozaki,et al.  Characterization of the expression of a desiccation-responsive rd29 gene of Arabidopsis thaliana and analysis of its promoter in transgenic plants , 2004, Molecular and General Genetics MGG.

[59]  T. Hoson,et al.  New aspects of gravity responses in plant cells. , 2003, International review of cytology.

[60]  E Goto,et al.  The effect of gravity on surface temperature and net photosynthetic rate of plant leaves. , 2001, Advances in space research : the official journal of the Committee on Space Research.

[61]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .