Release Notes 48b (November 2015)
Website
See also legacy data in the Gramene's Archive.
Genomes Release Notes
Pathway Release Notes
Plant Reactome
The Plant Reactome database has expanded gene homology-based pathway projections to 58 plant species (previous Gramene release 47 included pathway projections for 33 plant species). Notable newly projected species include wild ancestors of peanut, common bean (Phaseolus), chickpea, pigeonpea, cacao, Brassica oleracea, capsicum pepper, sweet orange, coffee, cotton, grape, date palm, Triticum turgidum (wheat BB), basal angiosperm Amborella, the gymnosperms Norway spruce and Loblolly pine, lower plants Physcomitrella and Selaginella, and green algae Chlamydomonas. In addition, we have added two new hormone signaling pathways and revised three previously curated pathways. Please take a note of the following pathway statistics and status table for more details.
The Plant Reactome database continues to provide the following features:
- Tutorial for users via our YouTube Channel
- Data analysis tools
- Diagram overlay visualization of gene lists, Uniprot IDs (O. sativa japonica only), compound identifiers, and/or -omics expression data
- Inter-species pathway comparison
- Advanced search features built on the Apache Solr platform
RESTful API for programmatic access to Plant Reactome data
Newly curated hormone signaling pathways
- O. sativa Salicylic acid signaling
- O. sativa Jasmonic acid signaling
Updated pathways
- O. sativa Salicylic acid biosynthesis
- O. sativa Brassinosteroid signaling
- O. sativa Strigolactone signaling
Pathway Projection Statistics and Status (update/new)
Notes:
- *data from sequenced transcriptomes
- ^ projections currently exclude cell-cycle pathways and annotations
- Planteome Inparanoid data was kindly provided by the Planteome project
- When available the outgoing links from gene product IDs mapped to reactions are always hyperlinked to respective entries in collaborator databases/online resources
- The latest projection statistics are also available from the Plant Reactome website.
| Species | Pathways | Reactions | Gene Products | Sequence source | Outgoing Link | Homology method | Status |
|---|---|---|---|---|---|---|---|
| Oryza sativa japonica | 241^ | 1069 | 955 | Ensembl Gramene | Uniprot | Curated Reference | Updated |
| Aegilops tauschii | 178 | 458 | 731 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara | Updated |
| Amborella trichopoda | 185 | 483 | 554 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara | New |
| Arabidopsis lyrata | 183 | 485 | 826 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara | New |
| Arabidopsis thaliana | 183 | 489 | 818 | Ensembl Gramene | TAIR | Ensembl Compara | Updated |
| Arachis duranensis | 191 | 512 | 738 | PeanutBase | PeanutBase | Planteome Inparanoid | New |
| Arachis ipaensis | 189 | 516 | 748 | PeanutBase | PeanutBase | Planteome Inparanoid | New |
| Brachypodium distachyon | 182 | 505 | 738 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara | Updated |
| Brassica oleracea | 182 | 476 | 1231 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara | New |
| Brassica rapa | 182 | 485 | 1242 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara | Updated |
| Cajanus cajan | 192 | 519 | 942 | LegumeInfo | LegumeInfo | Planteome Inparanoid | New |
| Capsicum annuum | 193 | 505 | 937 | PMID: 24441736 | N/A | Planteome Inparanoid | New |
| Chlamydomonas reinhardtii | 138 | 287 | 224 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara | New |
| Cicer arietinum | 193 | 522 | 1091 | NCBI | NCBI | Planteome Inparanoid | New |
| Citrus sinensis | 193 | 522 | 1920 | Phytozome | Phytozome | Planteome Inparanoid | New |
| Coffea canephora | 193 | 524 | 873 | PMID:25190796 | N/A | Planteome Inparanoid | New |
| Cyanidioschyzon merolae | 116 | 214 | 157 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara | New |
| Fragaria vesca | 193 | 508 | 846 | Phytozome | Phytozome | Planteome Inparanoid | New |
| Glycine max | 183 | 481 | 1511 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara | Updated |
| Gossypium raimondii | 192 | 526 | 1305 | Phytozome | Phytozome | Planteome Inparanoid | New |
| Hordeum vulgare | 180 | 450 | 630 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara | Updated |
| Leersia perrieri | 189 | 503 | 718 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara | Updated |
| Malus domestica | 190 | 504 | 1667 | PMID: 20802477 | Phytozome | Planteome Inparanoid | New |
| Medicago trunculata | 184 | 479 | 949 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara | Updated |
| Musa acuminata | 182 | 472 | 958 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara | Updated |
| Oryza australiensis * | 189 | 488 | 1357 | OMAP/OGE | N/A | Planteome Inparanoid | Updated |
| Oryza barthii | 189 | 514 | 749 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara | Updated |
| Oryza brachyantha | 189 | 505 | 708 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara | Updated |
| Oryza glaberrima | 191 | 514 | 762 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara | Updated |
| Oryza glumaepatula | 191 | 516 | 758 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara | Updated |
| Oryza granulata * | 191 | 504 | 2372 | OMAP/OGE | N/A | Planteome Inparanoid | Updated |
| Oryza kasalath | 154 | 247 | 287 | PMID: 24578372 | N/A | Planteome Inparanoid | Updated |
| Oryza longistaminata * | 193 | 512 | 1146 | OMAP/OGE | N/A | Planteome Inparanoid | Updated |
| Oryza meridionalis | 183 | 468 | 652 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara | Updated |
| Oryza minuta * | 192 | 510 | 1594 | OMAP/OGE | N/A | Planteome Inparanoid | Updated |
| Oryza nivara | 187 | 522 | 762 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara | Updated |
| Oryza officinalis * | 190 | 518 | 1363 | OMAP/OGE | N/A | Planteome Inparanoid | Updated |
| Oryza punctata | 187 | 513 | 754 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara | Updated |
| Oryza rufipogon | 189 | 522 | 770 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara | Updated |
| Oryza sativa indica | 192 | 531 | 814 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara | Updated |
| Ostreococcus lucimarinus | 129 | 272 | 214 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara | New |
| Phaseolus vulgaris | 194 | 528 | 909 | Phytozome | Phytozome | Planteome Inparanoid | New |
| Phoenix dactylifera | 187 | 493 | 860 | PMID: 23917264 | N/A | Planteome Inparanoid | New |
| Physcomitrella patens | 171 | 434 | 829 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara | New |
| Picea abies | 187 | 474 | 1067 | Congenie | Congenie | Planteome Inparanoid | Updated |
| Pinus taeda | 176 | 430 | 1046 | TreeBase | N/A | Planteome Inparanoid | Updated |
| Populus trichocarpa | 184 | 489 | 1030 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara | Updated |
| Prunus persica | 184 | 488 | 713 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara | Updated |
| Selaginella moellendorffii | 177 | 460 | 1031 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara | New |
| Setaria italica | 187 | 509 | 826 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara | Updated |
| Solanum lycopersicum | 186 | 487 | 860 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara | Updated |
| Solanum tuberosum | 183 | 467 | 828 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara | Updated |
| Sorghum bicolor | 188 | 514 | 791 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara | Updated |
| Theobroma cacao | 187 | 491 | 689 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara | New |
| Triticum aestivum | 188 | 511 | 1862 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara | Updated |
| Triticum turgidum * | 192 | 522 | 2268 | PMID: 23800085 | N/A | Planteome Inparanoid | New |
| Triticum urartu | 183 | 466 | 664 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara | Updated |
| Vitis vinifera | 180 | 476 | 732 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara | Updated |
| Zea mays | 186 | 506 | 925 | Ensembl Gramene | MaizeGDB | Ensembl Compara | Updated |
"Cyc" Pathways
- BioCyc-based pathway databases on Pathway Tools ver. 19.0 are available from a virtual server hosted at iPlant.
- Summary tables for the Cyc pathway databases created by Gramene can be seen in release 46 notes.
Ontologies Release Notes
No updates in this release. Last update done in release 31 (May 2010). A summary of ontologies data was last provided in release 46.
Infrastructure
Web Services
Gramene's web services page documents many ways to directly connect to and analyze our databases.
Programmatic access to Gramene is now available through the RESTful Ensembl API.
Public MySQL Server
Our partner Ensembl Genomes offer a public, read-only MySQL server with copies of the species-specific and comparative genomic databases that we use. To use this with the mysql command-line client:
$ mysql -hmysql-eg-publicsql.ebi.ac.uk -P4157 -uanonymous
Please note that the versioning scheme used at this public database differs from ours; Gramene's release 48_82 is set as version 29_82.
Gramene currently a legacy public, read-only MySQL server for release 40 of our databases. You can connect to the host "gramenedb.gramene.org" with the password "gramene," e.g.:
mysql -hgramenedb.gramene.org -pgramene
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