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Plant Reactome: a knowledgebase and resource for comparative pathway analysis

2019 Nucleic Acids Research  
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

N. Tsesmetzis, M. Couchman, J. Higgins, A. Smith, J. H. Doonan, G. J. Seifert, E. E. Schmidt, I. Vastrik, E. Birney, G. Wu, P. D'Eustachio, L. D. Stein (+3 others)
2008 The Plant Cell  
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

Marcela K Tello-Ruiz, Sushma Naithani, Joshua C Stein, Parul Gupta, Michael Campbell, Andrew Olson, Sharon Wei, Justin Preece, Matthew J Geniza, Yinping Jiao, Young Koung Lee, Bo Wang (+27 others)
2017 Nucleic Acids Research  
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

Marcela K Tello-Ruiz, Sushma Naithani, Parul Gupta, Andrew Olson, Sharon Wei, Justin Preece, Yinping Jiao, Bo Wang, Kapeel Chougule, Priyanka Garg, Justin Elser, Sunita Kumari (+17 others)
2020 Nucleic Acids Research  
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

Y. Sucaet, T. Deva
2011 Briefings in Bioinformatics  
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

Abraham A. Labena, Yi-Zhou Gao, Chuan Dong, Hong-li Hua, Feng-Biao Guo
2017 Quantitative Biology  
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

Issa Coulibaly, Grier P. Page
2008 International Journal of Plant Genomics  
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)

Sushma Naithani, Rajani Raja, Elijah N. Waddell, Justin Elser, Satyanarayana Gouthu, Laurent G. Deluc, Pankaj Jaiswal
2014 Frontiers in Plant Science  
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?

Eva Collakova, Jiun Y. Yen, Ryan S. Senger
2012 Plant Science  
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

Bhavisha P. Sheth, Vrinda S. Thaker
2014 Planta  
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

Fan Yi, Li Li, Li-jia Xu, Hong Meng, Yin-mao Dong, Hai-bo Liu, Pei-gen Xiao
2018 Chinese Medicine  
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

Plant Cell Atlas Consortium, Jahed Ahmed, Oluwafemi Alaba, Gazala Ameen, Vaishali Arora, Mario A Arteaga-Vazquez, Alok Arun, Julia Bailey-Serres, Laura E Bartley, George W Bassel, Dominique C Bergmann, Edoardo Bertolini (+137 others)
2021 eLife  
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  
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

Steven R. Chamberlin, Aurora Blucher, Guanming Wu, Lynne Shinto, Gabrielle Choonoo, Molly Kulesz-Martin, Shannon McWeeney
2019 Frontiers in Pharmacology  
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

Hamid R Eghbalnia, Pedro R Romero, William M Westler, Kumaran Baskaran, Eldon L Ulrich, John L Markley
2017 Current Opinion in Biotechnology  
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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