MapMan4: A Refined Protein Classification and Annotation Framework Applicable to Multi-Omics Data Analysis.
Rainer Schwacke,Gabriel Y. Ponce-Soto,Kirsten Krause,Anthony Bolger,Borjana Arsova,Asis Hallab,Kristina Gruden,Mark Stitt,Marie E. Bolger,Björn Usadel +9 more
TLDR
A redesigned and significantly enhanced MapMan4 framework is presented, together with a revised version of the associated online Mercator annotation tool, providing protein annotations for all embryophytes with a comparably high quality.About:
This article is published in Molecular Plant.The article was published on 2019-06-03 and is currently open access. It has received 276 citations till now. The article focuses on the topics: Protein Annotation & Annotation.read more
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Nitrate in 2020: Thirty Years from Transport to Signaling Networks.
Elena A. Vidal,Elena A. Vidal,José M. Alvarez,José M. Alvarez,José M. Alvarez,Viviana Araus,Eleodoro Riveras,Eleodoro Riveras,Matthew D. Brooks,Gabriel Krouk,Sandrine Ruffel,Laurence Lejay,Nigel M. Crawford,Gloria M. Coruzzi,Rodrigo A. Gutiérrez,Rodrigo A. Gutiérrez +15 more
TL;DR: This review provides an overview of key findings in nitrate research, spanning biochemistry, molecular genetics, genomics, and systems biology, and discusses how the current view of nitrate transport, local and systemic nitrate sensing/signaling, and the regulatory networks underlying nitrate-controlled outputs in plants are reached.
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Systematic Multi-Omics Integration (MOI) Approach in Plant Systems Biology.
Ili Nadhirah Jamil,Juwairiah Remali,Kamalrul Azlan Azizan,Nor Azlan Nor Muhammad,Masanori Arita,Hoe-Han Goh,Wan Mohd Aizat +6 more
TL;DR: This review thoroughly classify multi-omics studies on plants and proposes three levels of MOI, namely element-based, pathway-based (level 2), and mathematical-based integration (level 3), which are described in relation to recent publications and tools to highlight their practicality and function.
Journal ArticleDOI
PLAZA 5.0: extending the scope and power of comparative and functional genomics in plants.
Michiel Van Bel,Francesca Silvestri,Eric Weitz,Lukasz Kreft,Alexander Botzki,Frederik Coppens,Klaas Vandepoele +6 more
TL;DR: PLAZA as discussed by the authors is a platform for comparative, evolutionary, and functional plant genomics, which makes a broad set of genomes, data types and analysis tools available to researchers through a user-friendly website, an API, and bulk downloads.
Journal ArticleDOI
Plant Reactome: a knowledgebase and resource for comparative pathway analysis.
Sushma Naithani,Parul Gupta,Justin Preece,Peter D'Eustachio,Justin Elser,Priyanka Garg,Daemon A Dikeman,Jason Kiff,Justin Cook,Andrew Olson,Sharon Wei,Marcela K. Tello-Ruiz,Antonio Fabregat Mundo,Alfonso Munoz-Pomer,Suhaib Mohammed,Tiejun Cheng,Evan E Bolton,Irene Papatheodorou,Lincoln Stein,Doreen Ware,Doreen Ware,Pankaj Jaiswal +21 more
TL;DR: The Plant Reactome supports, implements and collaborates with the wider community to make data and tools related to genes, genomes, and pathways Findable, Accessible, Interoperable and Re-usable (FAIR).
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Systematic analysis of 1298 RNA‐Seq samples and construction of a comprehensive soybean (Glycine max) expression atlas
Fabricio B. Machado,Kanhu C. Moharana,Fabricio Almeida-Silva,Rajesh Kumar Gazara,Francisnei Pedrosa-Silva,Fernanda S. Coelho,Clícia Grativol,Thiago M. Venancio +7 more
TL;DR: This comprehensive transcriptome atlas will likely accelerate research on soybean genetics and genomics and constitute a new resource for the community.
References
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UniProt: the Universal Protein knowledgebase
Rolf Apweiler,Amos Marc Bairoch,Cathy H. Wu,Winona C. Barker,Brigitte Boeckmann,Serenella Ferro,Elisabeth Gasteiger,Hongzhan Huang,Rodrigo Lopez,Michele Magrane,Maria Jesus Martin,Darren A. Natale,Claire O'Donovan,Nicole Redaschi,Lai-Su L. Yeh +14 more
TL;DR: The Swiss-Prot, TrEMBL and PIR protein database activities have united to form the Universal Protein Knowledgebase (UniProt), which is to provide a comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and query interfaces.
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KEGG: new perspectives on genomes, pathways, diseases and drugs
TL;DR: The content has been expanded and the quality improved irrespective of whether or not the KOs appear in the three molecular network databases, and the newly introduced addendum category of the GENES database is a collection of individual proteins whose functions are experimentally characterized and from which an increasing number of KOs are defined.
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Evaluation: from Precision, Recall and F-measure to ROC, Informedness, Markedness and Correlation
TL;DR: E elegant connections between the concepts of Informedness, Markedness, Correlation and Significance as well as their intuitive relationships with Recall and Precision are demonstrated.
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Comparison of the predicted and observed secondary structure of T4 phage lysozyme.
TL;DR: Although empirical predictions based on larger numbers of known protein structure tend to be more accurate than those based on a limited sample, the improvement in accuracy is not dramatic, suggesting that the accuracy of current empirical predictive methods will not be substantially increased simply by the inclusion of more data from additional protein structure determinations.
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Accelerated Profile HMM Searches
TL;DR: An acceleration heuristic for profile HMMs, the “multiple segment Viterbi” (MSV) algorithm, which computes an optimal sum of multiple ungapped local alignment segments using a striped vector-parallel approach previously described for fast Smith/Waterman alignment.