GRASSIUS 2.0: A gene regulatory information knowledgebase for maize and other grasses
Grass species, which include the major cereal crops maize, wheat, rice, and sugarcane, are an integral part of our global agriculture and source of food and energy for a growing world population. GRASSIUS was established as a knowledgebase for transcription factors (TFs) and coregulators (CoRegs) in...
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| Format: | Article |
| Language: | English |
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Elsevier
2024-12-01
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| Series: | Current Plant Biology |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2214662824000781 |
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| author | John Gray Yi-Hsuan Chu Ankita Abnave Fabio Gomez Cano Yun Sun Lee Sarah Percival Nan Jiang Erich Grotewold |
| author_facet | John Gray Yi-Hsuan Chu Ankita Abnave Fabio Gomez Cano Yun Sun Lee Sarah Percival Nan Jiang Erich Grotewold |
| author_sort | John Gray |
| collection | DOAJ |
| description | Grass species, which include the major cereal crops maize, wheat, rice, and sugarcane, are an integral part of our global agriculture and source of food and energy for a growing world population. GRASSIUS was established as a knowledgebase for transcription factors (TFs) and coregulators (CoRegs) in maize and several other species in the grass family. TFs are a primary component of the gene regulatory networks (GRNs) and the underlying gene regulatory grids (GRGs) that govern all aspects of plant growth and metabolism. GRASSIUS is the source for all information pertaining to the maize TFome collection, which serves as a powerful resource for the discovery of GRNs in maize and other cereals [1,2]. Here we describe the release of the GRASSIUS 2.0 knowledgebase (www.grassius.org) with updated data, query, and tool features, as well as the ability to expand to accommodate future datasets. The membership and annotation of all TF and CoReg families has been updated and revised to include gene models from v3, v4, and v5, of the maize B73 genome and recent genome versions of rice, sorghum, Brachypodium, and sugarcane. A translation tool enables cross referencing of Gene IDs between versions of the maize genome. Protein-DNA interactions (PDIs) have been added incorporating results derived from various gene- and TF-centered PDI discovery tools and visualized through a new web-based interface. A filtering tools permits the selection and visualization of PDIs within a ± 2 kb distance from the transcriptional start site (TSS) of a gene of interest. A new BLAST (Basic Local Alignment Search Tool) tool facilitates searching of the maize TFome as well as v3, v4, and v5 TF gene model sets. Lastly, we describe the methodology used to implement GRASSIUS 2.0 which can guide others in developing and updating similar plant gene regulatory knowledgebases. |
| format | Article |
| id | doaj-art-211fdb3781e14829bd01ffbe7f4ba25a |
| institution | OA Journals |
| issn | 2214-6628 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Current Plant Biology |
| spelling | doaj-art-211fdb3781e14829bd01ffbe7f4ba25a2025-08-20T01:59:01ZengElsevierCurrent Plant Biology2214-66282024-12-014010039610.1016/j.cpb.2024.100396GRASSIUS 2.0: A gene regulatory information knowledgebase for maize and other grassesJohn Gray0Yi-Hsuan Chu1Ankita Abnave2Fabio Gomez Cano3Yun Sun Lee4Sarah Percival5Nan Jiang6Erich Grotewold7Department of Molecular, Cellular, and Developmental Biology, University of Toledo, Toledo, OH 43606, USA; Corresponding author.Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USAMolecular Biology Graduate Program, University of Toledo, Toledo, OH 43606, USADepartment of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USADepartment of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USAComputational Mathematics, Science and Engineering Department, Michigan State University, East Lansing, MI 48824, USADepartment of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USADepartment of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USAGrass species, which include the major cereal crops maize, wheat, rice, and sugarcane, are an integral part of our global agriculture and source of food and energy for a growing world population. GRASSIUS was established as a knowledgebase for transcription factors (TFs) and coregulators (CoRegs) in maize and several other species in the grass family. TFs are a primary component of the gene regulatory networks (GRNs) and the underlying gene regulatory grids (GRGs) that govern all aspects of plant growth and metabolism. GRASSIUS is the source for all information pertaining to the maize TFome collection, which serves as a powerful resource for the discovery of GRNs in maize and other cereals [1,2]. Here we describe the release of the GRASSIUS 2.0 knowledgebase (www.grassius.org) with updated data, query, and tool features, as well as the ability to expand to accommodate future datasets. The membership and annotation of all TF and CoReg families has been updated and revised to include gene models from v3, v4, and v5, of the maize B73 genome and recent genome versions of rice, sorghum, Brachypodium, and sugarcane. A translation tool enables cross referencing of Gene IDs between versions of the maize genome. Protein-DNA interactions (PDIs) have been added incorporating results derived from various gene- and TF-centered PDI discovery tools and visualized through a new web-based interface. A filtering tools permits the selection and visualization of PDIs within a ± 2 kb distance from the transcriptional start site (TSS) of a gene of interest. A new BLAST (Basic Local Alignment Search Tool) tool facilitates searching of the maize TFome as well as v3, v4, and v5 TF gene model sets. Lastly, we describe the methodology used to implement GRASSIUS 2.0 which can guide others in developing and updating similar plant gene regulatory knowledgebases.http://www.sciencedirect.com/science/article/pii/S2214662824000781MaizeRiceKnowledgebaseDatabaseTranscription factorCoregulator |
| spellingShingle | John Gray Yi-Hsuan Chu Ankita Abnave Fabio Gomez Cano Yun Sun Lee Sarah Percival Nan Jiang Erich Grotewold GRASSIUS 2.0: A gene regulatory information knowledgebase for maize and other grasses Current Plant Biology Maize Rice Knowledgebase Database Transcription factor Coregulator |
| title | GRASSIUS 2.0: A gene regulatory information knowledgebase for maize and other grasses |
| title_full | GRASSIUS 2.0: A gene regulatory information knowledgebase for maize and other grasses |
| title_fullStr | GRASSIUS 2.0: A gene regulatory information knowledgebase for maize and other grasses |
| title_full_unstemmed | GRASSIUS 2.0: A gene regulatory information knowledgebase for maize and other grasses |
| title_short | GRASSIUS 2.0: A gene regulatory information knowledgebase for maize and other grasses |
| title_sort | grassius 2 0 a gene regulatory information knowledgebase for maize and other grasses |
| topic | Maize Rice Knowledgebase Database Transcription factor Coregulator |
| url | http://www.sciencedirect.com/science/article/pii/S2214662824000781 |
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