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Planteome Gene Annotation Enrichment Analysis

Botong Qu, Jaden Diefenbaugh, Eugene Zhang, Justin Elser, Pankaj Jaiswal, Seth Carbon, Christopher J. Mungall
2016 International Conference on Biomedical Ontology  
Annotation enrichment analysis of a gene list helps biologists to identify the potential biological functions associated with it.  ...  We introduce a tool to help biologists to find out these terms based on the expanding ontology database of the Planteome project.  ...  To assist this analysis process, we provide a gene annotation enrichment analysis tool which uses Fisher's exact and chi-squared methods to statistically analyze all annotation data.  ... 
dblp:conf/icbo/QuDZEJCM16 fatcat:luz4upyy3jc47d3skzap7e6mba

The Planteome Project

Laurel Cooper, Austin Meier, Justin Elser, Justin Preece, Xu Xu, Ryan Kitchen, Botong Qu, Eugene Zhang, Sinisa Todorovic, Pankaj Jaiswal, Marie-Angélique Laporte, Elizabeth Arnaud (+5 others)
2016 International Conference on Biomedical Ontology  
Analysis and annotation tools are being developed to facilitate studies of plant traits, phenotypes, diseases, gene function and expression and genetic diversity data across a wide range of plant species  ...  The Planteome project ( develops and hosts a suite of reference ontologies for plants associated with a growing corpus of genomics data.  ...  ACKNOWLEDGMENT Funding for the Planteome project is provided by the National Science Foundation award IOS #1340112  ... 
dblp:conf/icbo/CooperMEPXKQZTJ16 fatcat:nurcyvvylbaalod6qjjjtglf7m

The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics

Laurel Cooper, Austin Meier, Marie-Angélique Laporte, Justin L Elser, Chris Mungall, Brandon T Sinn, Dario Cavaliere, Seth Carbon, Nathan A Dunn, Barry Smith, Botong Qu, Justin Preece (+7 others)
2017 Nucleic Acids Research  
The Planteome project is developing a plant gene annotation platform; Planteome Noctua, to facilitate community engagement.  ...  The Planteome project ( provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes.  ...  ACKNOWLEDGEMENTS We would like to thank all the collaborating databases and projects (listed in Tables 4 and 5 ) who contributed annotated data to the Planteome database and all the projects and genomics  ... 
doi:10.1093/nar/gkx1152 pmid:29186578 pmcid:PMC5753347 fatcat:7hbnerl4uvf47c6ikf2m3sm6se

The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species

Ramona L. Walls, Laurel Cooper, Justin Elser, Maria Alejandra Gandolfo, Christopher J. Mungall, Barry Smith, Dennis W. Stevenson, Pankaj Jaiswal
2019 Frontiers in Plant Science  
, image analysis, and comparative development and evolution.  ...  Although many genes appear to be active throughout embryo development, we identified a small set of uniquely expressed genes for each stage of embryo development and also between the two species.  ...  ACKNOWLEDGMENTS We would like to thank all the collaborating databases and projects that have contributed annotated data to the Planteome database and all the genomics platforms that have adopted the Plant  ... 
doi:10.3389/fpls.2019.00631 pmid:31214208 pmcid:PMC6558174 fatcat:66ha5uhgunh4bl666zq7sniwqa

The Plant Ontology™Consortium and Plant Ontologies

The Plant Ontology Consortium
2002 Comparative and Functional Genomics  
The Plant Ontology™Consortium is expanding the paradigm of the Gene Ontology™Consortium (  ...  As a result, TO is being enriched with well defined crop-specific terms of Crop Ontology and Planteome can integrate additional data annotated in a unified way by the breeding and the genetic communities  ...  The Planteome project ( aims to support comparative plant biology, and provides integrated access to annotated datasets generated by inter and intraspecific comparative analysis of transcriptomes  ... 
doi:10.1002/cfg.154 pmid:18628842 pmcid:PMC2447263 fatcat:kpwbd7nmxjfyldwpgmvhz5pfcu

Improving Publication Pipeline with Automated Biological Entity Detection and Validation Service

Weijia Xu, Amit Gupta, Pankaj Jaiswal, Crispin Taylor, Patti Lockhart, Jennifer Regala
2019 Data and Information Management  
annotations.  ...  Through the web interface, the authors can make additional annotations and corrections to the current results.  ...  The Planteome project ( provides a suite of references and species-specific ontologies for plants and annotations to genes and phenotypes.  ... 
doi:10.2478/dim-2019-0003 fatcat:w4swautdkbefti3gfy4scsle5u

The sugarcane mitochondrial genome: assembly, phylogenetics and transcriptomics

Dyfed Lloyd Evans, Thandekile Thandiwe Hlongwane, Shailesh V. Joshi, Diego M. Riaño Pachón
2019 PeerJ  
The mitogenome was exhaustively annotated using BLAST and transcript datasets were mapped with HISAT2 prior to analysis with the Integrated Genome Viewer.  ...  Transcriptomic and spliceosomal analyses reveal that the two chromosomes of the sugarcane mitochondrion are combined at the transcript level and that splice sites occur more frequently within gene coding  ...  The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.  ... 
doi:10.7717/peerj.7558 pmid:31579570 pmcid:PMC6764373 fatcat:b2zb3vlo4behzlaqevpuvj5x6y

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 integrates ontology-based protein structure–function annotation; information on genetic, epigenetic, expression, and phenotypic diversity; and gene functional annotations extracted from plant-focused  ...  The Reactome platform facilitates comparison between reference and projected pathways, gene expression analyses and overlays of genegene interactions.  ...  Marco and David Micklos (MaizeCode Project) for jointly running the maize gene structural annotation jamborees.  ... 
doi:10.1093/nar/gkaa979 pmid:33170273 fatcat:atundz637bfalivwtye3vb3twe

ACT: A tool for gene coexpression analysis in Arabidopsis thaliana

Vasileios L. Zogopoulos, Georgia Saxami, Apostolos Malatras, Antonia Angelopoulou, Chih-Hung Jen, William J. Duddy, Gerasimos Daras, Polydefkis Hatzopoulos, David R. Westhead, Ioannis Michalopoulos
2021 iScience  
ACT was developed to present subclades of coexpressed genes, as well as to perform gene set enrichment analysis, being unique in revealing enriched transcription factors targeting coexpressed genes.  ...  Arabidopsis Coexpression Tool (ACT), a gene coexpression analysis web tool for Arabidopsis thaliana, identifies genes which are correlated to a driver gene.  ...  Enrichment categories include gene ontologies from Gene Ontology (Gene Ontology Consortium, 2021), plant ontologies from Planteome (Cooper et al., 2018) , biological pathways from KEGG Pathways (Kanehisa  ... 
doi:10.1016/j.isci.2021.102848 fatcat:pocfjgr6jrfspildqormrjhhfy

Plant Reactome: a resource for plant pathways and comparative analysis

Sushma Naithani, Justin Preece, Peter D'Eustachio, Parul Gupta, Vindhya Amarasinghe, Palitha D. Dharmawardhana, Guanming Wu, Antonio Fabregat, Justin L. Elser, Joel Weiser, Maria Keays, Alfonso Munoz-Pomer Fuentes (+4 others)
2016 Nucleic Acids Research  
The database provides intuitive bioinformatics tools for the visualization, analysis and interpretation of pathway knowledge to support genome annotation, genome analysis, modeling, systems biology, basic  ...  These reference annotations were used to project pathways for 62 model, crop and evolutionarily significant plant species based on gene homology.  ...  PATHWAY ANALYSIS TOOLS Moving beyond differential gene expression, ontologybased enrichment and genome annotations, researchers are often looking for ways to analyze their data for making inferences and  ... 
doi:10.1093/nar/gkw932 pmid:27799469 pmcid:PMC5210633 fatcat:uxqy23gd4newjholwhkbbtmoju

Genetic and Genomic Resources for Soybean Breeding Research

Jakob Petereit, Jacob I. Marsh, Philipp E. Bayer, Monica F. Danilevicz, William J. W. Thomas, Jacqueline Batley, David Edwards
2022 Plants  
Variable gene families were more diverse and had a higher rate of positive selection compared to core genes, and they were also enriched for abiotic and biotic stress response annotation.  ...  Of these genes, 7% were variable and enriched for annotations associated with the regulation of immune and defense responses, signaling and plant development [74] .  ... 
doi:10.3390/plants11091181 pmid:35567182 pmcid:PMC9101001 fatcat:qylsh3qqtrfitllo5zsajzr6o4

AgroPortal: A vocabulary and ontology repository for agronomy

Clément Jonquet, Anne Toulet, Elizabeth Arnaud, Sophie Aubin, Esther Dzalé Yeumo, Vincent Emonet, John Graybeal, Marie-Angélique Laporte, Mark A. Musen, Valeria Pesce, Pierre Larmande
2018 Computers and Electronics in Agriculture  
A B S T R A C T Many vocabularies and ontologies are produced to represent and annotate agronomic data.  ...  We offer a portal that features ontology hosting, search, versioning, visualization, comment, and recommendation; enables semantic annotation; stores and exploits ontology alignments; and enables interoperation  ...  The domain has seen success stories such as the Gene Ontology (Ashburner et al., 2000) , widely used to annotate genes and their products.  ... 
doi:10.1016/j.compag.2017.10.012 fatcat:tsvou7l42bg5hn6cw43ogtj2je

Cyberinfrastructure to Improve Forest Health and Productivity: The Role of Tree Databases in Connecting Genomes, Phenomes, and the Environment

Jill L. Wegrzyn, Margaret A. Staton, Nathaniel R. Street, Dorrie Main, Emily Grau, Nic Herndon, Sean Buehler, Taylor Falk, Sumaira Zaman, Risharde Ramnath, Peter Richter, Lang Sun (+6 others)
2019 Frontiers in Plant Science  
They provide frameworks to view and update annotations for complex genomes, interrogate systems level expression profiles, curate data for comparative genomics, and perform real-time analysis with genotype  ...  These repositories represent integrated cyberinfrastructure that support cross-site queries and analysis in web-based environments.  ...  enrichment tests for Gene Ontology (Ashburner et al., 2000) , Pfam (Finn et al., 2010) , genome synteny browsing alongside sequence similarity searching.  ... 
doi:10.3389/fpls.2019.00813 pmid:31293610 pmcid:PMC6603172 fatcat:vpbwpe3sg5f3hmnzboiwaxanga

Plant Reactome: a knowledgebase and resource for comparative pathway analysis

2019 Nucleic Acids Research  
In addition to browsing plant pathways, users can upload and analyze their omics data, such as the gene-expression data, and overlay curated or experimental gene-gene interaction data to extend pathway  ...  The curation team actively engages researchers and students on gene and pathway curation by offering workshops and online tutorials.  ...  set enrichment analysis (GSEA).  ... 
doi:10.1093/nar/gkz996 pmid:31680153 pmcid:PMC7145600 fatcat:ykzfjhf4hvgs7keopndswr5req

Hierarchical Canonical Correlation Analysis Reveals Phenotype, Genotype, and Geoclimate Associations in Plants

Raphael Petegrosso, Tianci Song, Rui Kuang
2020 Plant Phenomics  
In particular, we propose a novel method called hierarchical canonical correlation analysis (HCCA) to combine mutations, gene expressions, and DNA methylations with geoclimatic features for informative  ...  using advanced canonical correlation analysis (CCA).  ...  Hierarchical Enrichment Analysis Detects More Relevant Gene-Geoclimate Associations.  ... 
doi:10.34133/2020/1969142 pmid:33313545 pmcid:PMC7706319 fatcat:7hrnl7re6zh5zjfpkghquxkxvy
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