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Plant Reactome: a knowledgebase and resource for comparative pathway analysis
2019
Nucleic Acids Research
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Plant Reactome (https://plantreactome.gramene.org) is an open-source, comparative plant pathway knowledgebase of the Gramene project. ...
It uses Oryza sativa (rice) as a reference species for manual curation of pathways and extends pathway knowledge to another 82 plant species via gene-orthology projection using the Reactome data model ...
We acknowledge Robin Haw, Joel Weiser, Guanming Wu, and Lisa Matthews from the human Reactome project and the Ontario Institute for Cancer Research for providing access to the Reactome central curation ...
doi:10.1093/nar/gkz996
pmid:31680153
pmcid:PMC7145600
fatcat:ykzfjhf4hvgs7keopndswr5req
Arabidopsis Reactome: A Foundation Knowledgebase for Plant Systems Biology
2008
The Plant Cell
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ACKNOWLEDGMENTS We thank the Reactome development team for their support and useful criticism and Yunhai Li for the glucose microarray data and analysis. ...
However, it lacks a standard format for exchanging pathway information with other pathway resources, and it lacks the level of detail of reactions compared with Reactome due to its ontology-based structure ...
We show, using examples based on the mitotic cell cycle, that the knowledgebase has wide applicability for exchanging structured data with other databases, for comparative network analysis, data integration ...
doi:10.1105/tpc.108.057976
pmid:18591350
pmcid:PMC2483364
fatcat:nbeoeptqarcfxbppii23jd7f6y
Gramene 2018: unifying comparative genomics and pathway resources for plant research
2017
Nucleic Acids Research
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Gramene (http://www.gramene.org) is a knowledgebase for comparative functional analysis in major crops and model plant species. ...
Gramene's Plant Reactome provides a knowledgebase of cellular-level plant pathway networks. ...
We also thank Peter van Buren from Cold Spring Harbor Laboratory for system administration support, and David Croft (EBI) and Robin Haw (OICR) for technical support of Plant Reactome development. ...
doi:10.1093/nar/gkx1111
pmid:29165610
pmcid:PMC5753211
fatcat:bxgarlrs6rab5lwpixua6gotgq
Gramene 2021: harnessing the power of comparative genomics and pathways for plant research
2020
Nucleic Acids Research
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Gramene (http://www.gramene.org), a knowledgebase founded on comparative functional analyses of genomic and pathway data for model plants and major crops, supports agricultural researchers worldwide. ...
Plant Reactome portrays pathway networks using a combination of manual biocuration in rice (320 reference pathways) and orthology-based projections to 106 species. ...
In addition, we thank CyVerse for providing a mirror Plant Reactome server under the Powered-by-CyVerse program. ...
doi:10.1093/nar/gkaa979
pmid:33170273
fatcat:atundz637bfalivwtye3vb3twe
Evolution and applications of plant pathway resources and databases
2011
Briefings in Bioinformatics
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In this article we review plant pathway databases and the resources that are currently available. ...
Plants are increasingly gaining importance as drug and fuel resources, bioremediation tools and as tools for recombinant technology. ...
Eve Syrkin Wurtele and Dr Julie Dickerson at Iowa State University, who supported us in a number of ways with encouragement, sound advice, guidance and lots of good ideas. ...
doi:10.1093/bib/bbq083
pmid:21949268
fatcat:v4w7i5b47zhj7idwb7k5wrpdgi
Metabolic pathway databases and model repositories
2017
Quantitative Biology
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The review aims to help researchers choose a suitable database or model repository according to the information and data required, by providing an insight look of each pathway resource. ...
Here we present a review of the most popular metabolic pathway databases and model repositories, focusing on their scope, content including reactions, enzymes, compounds, and genes, and applicability. ...
This article is a review article and does not contain any studies with human or animal subjects performed by any of the authors. ...
doi:10.1007/s40484-017-0108-3
fatcat:j6osebecqjehzj6lkchtldkwke
Bioinformatic Tools for Inferring Functional Information from Plant Microarray Data II: Analysis Beyond Single Gene
2008
International Journal of Plant Genomics
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Here, we highlight selected tools and resources for gene class level ontology analysis (Section 2), gene coexpression analysis (Section 3), gene network analysis (Section 4), biological pathway analysis ...
While it is possible to interpret microarray experiments a single gene at a time, most studies generate long lists of differentially expressed genes whose interpretation requires the integration of prior ...
serves as a comprehensive public repository for gene expression for plants and plant pathogens [30] . ...
doi:10.1155/2008/893941
pmid:18615189
pmcid:PMC2443398
fatcat:nvqj4qu6tfhatghnzofvebf7sm
VitisCyc: a metabolic pathway knowledgebase for grapevine (Vitis vinifera)
2014
Frontiers in Plant Science
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VitisCyc, as a community resource, can aid in the discovery of candidate genes and pathways that are regulated during plant growth and development, and in response to biotic and abiotic stress signals ...
Furthermore, VitisCyc was enriched for plant-specific pathways and grape-specific metabolites, reactions and pathways. ...
Waddell and Laurent G. Deluc contributed in writing and editing the of the manuscript. We are grateful to Peter Karp, from SRI for excellent Pathway Tools support. This work ...
doi:10.3389/fpls.2014.00644
pmid:25538713
pmcid:PMC4260676
fatcat:ccymcgqlvnba7cn75k5c3ffoz4
Are we ready for genome-scale modeling in plants?
2012
Plant Science
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This review presents a critical discussion of the advantages of existing plant GEMs, while identifies key targets for future improvements. ...
AraGEM is the first GEM describing a photosynthetic and photorespiring plant cell (Arabidopsis thaliana). ...
Acknowledgements Research funding was obtained from NSF-MCB-1052145 and the Biodesign and Bioprocessing Research Center at Virginia Tech. EC is primarily responsible for writing the review. ...
doi:10.1016/j.plantsci.2012.04.010
pmid:22682565
fatcat:f2av6w5hvvdcvbtmwdftm7om3e
Plant systems biology: insights, advances and challenges
2014
Planta
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In this review, we discuss the basics of systems biology including the various 'omics' approaches and their integration, the modeling aspects and the tools needed for the plant systems research. ...
A particular emphasis is given to the recent analytical advances, updated published examples of plant systems biology studies and the future trends. ...
Acknowledgements The authors would like to thank Centre for Advanced Studies in Plant Biotechnology and Genetic engineering (CPBGe), Govt. of Gujarat and Department of Biosciences, Saurashtra University ...
doi:10.1007/s00425-014-2059-5
pmid:24671625
fatcat:5krvjspz65dera6elsq3oznhh4
In silico approach in reveal traditional medicine plants pharmacological material basis
2018
Chinese Medicine
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In this review, we first provide a detailed research routine for examining traditional medicinal plants by in silico techniques and elaborate on their theoretical principles. ...
We also survey common databases, software programs and website tools that can be used for virtual screening and pharmacological network construction. ...
Jun Xu (Research Centerfor Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou) for his valuable suggestions. ...
doi:10.1186/s13020-018-0190-0
pmid:29946351
pmcid:PMC6006786
fatcat:btf7nau2wbeyrkrgxvuvvkn26i
Vision, challenges and opportunities for a Plant Cell Atlas
2021
eLife
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This framework, called the Plant Cell Atlas (PCA), will be critical for understanding and engineering plant development, physiology and environmental responses. ...
Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, environmental stewardship, energy, technology and healthcare. ...
Acknowledgements The PCA community-building activities are funded in part by the National Science Foundation grant numbers MCB-1916797 and MCB-2052590 ...
doi:10.7554/elife.66877
pmid:34491200
pmcid:PMC8423441
fatcat:xq6vypwp4rbbjfkhtl5l2ty35q
Taking the Next Step: Building an Arabidopsis Information Portal
2012
The Plant Cell
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ACKNOWLEDGMENTS The IAIC and its activities, including the AIP Design Workshop, are supported by the National Science Foundation ( ...
The AIP will provide a mechanism by which disparate databases, and the data that they house, can be compared and connected, linking global scientific resources, scientists, and analysis tools into a cohesive ...
Can the AIP for the reference plant Arabidopsis serve as a model informatics interface for all plant species? A PATH TOWARD A POSSIBLE SOLUTION Step 1. ...
doi:10.1105/tpc.112.100669
pmid:22751211
pmcid:PMC3406920
fatcat:cirk36yx5fagplo72o3ndlb5qu
Natural Product Target Network Reveals Potential for Cancer Combination Therapies
2019
Frontiers in Pharmacology
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in the Cancer Targetome, a resource for evidence-based drug-target interactions. ...
A body of research demonstrates examples of in vitro and in vivo synergy between natural products and anti-neoplastic drugs for some cancers. ...
SC, AB, GW, LS, GC, MK-M, and SM contributed to the study design, development of analysis plan, as well as development and refinement of the manuscript. ...
doi:10.3389/fphar.2019.00557
pmid:31214023
pmcid:PMC6555193
fatcat:57bcirnbtfbxtltqwhosin73ae
Increasing rigor in NMR-based metabolomics through validated and open source tools
2017
Current Opinion in Biotechnology
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The metabolome, the collection of small molecules associated with an organism, is a growing subject of inquiry, with the data utilized for data-intensive systems biology, disease diagnostics, biomarker ...
The field of metabolomics identifies and quantifies endogenous and exogenous metabolites in biological samples. ...
Acknowledgments Research of the authors received support from NIH R01 GM109046 and P41GM103399 (to JLM), P41GM111135 (to HRE). ...
doi:10.1016/j.copbio.2016.08.005
pmid:27643760
pmcid:PMC5305618
fatcat:hp5icuycjbgavjnzbw3hvt4iue
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