Reactome: A Curated Pathway Database

Release Summary

Release 53

Pathways:  The Plant Reactome underwent a major software, user interface and functionality upgrade: 

  • Upgraded to the Reactome v3.3 platform, which includes a new Neo4j graph database and a new Fireworks hierarchical graph display of pathways
  • Improved visualization of uploaded Omics data, capabilities to import gene-gene interaction data from external resources for overlaying on pathway diagram and including them in analysis, and comparative pathway analysis between the reference and projected species.
  • Supports display of gene expression profiles in the context of pathways accessed remotely from the EMBL-EBI gene expression ATLAS.
  • Added ContentService and AnalysisService data APIs that allow direct RESTful access to Plant Reactome data.
  • Implemented DiagramJs and FireworksJs graphical widget APIs for users to embed interactive pathway navigation in their web sites.
  • Implemented a revised Solr Search data index and search results layout.
  • All data objects carry stable IDs for cross-referencing.
  • Plant Reactome data and diagrams are now integrated with Gramene‚Äôs new search interface.

Pathway Curation

Revision made to set the top-level pathways as Cellular Processes, Circadian Rhythm, Metabolism & Regulation, Response to Stress, and Inflorescence Development (for Fireworks utility).

Pathway Projection Statistics and Status (update/new)

  • * 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
Species Pathways Reactions Gene Products Sequence source Outgoing Link Homology method
Oryza sativa japonica 241^ 1069 1263 Ensembl Gramene Uniprot Curated Reference
Aegilops tauschii 200 498 925 Ensembl Gramene Ensembl Gramene Compara
Amborella trichopoda 207 530 677 Ensembl Gramene Ensembl Gramene Compara
Arabidopsis lyrata 205 536 1064 Ensembl Gramene Ensembl Gramene Compara
Arabidopsis thaliana 205 539 1069 Ensembl Gramene TAIR Compara
Arachis duranensis 212 542 847 PeanutBase PeanutBase Inparanoid
Arachis ipaensis 210 546 862 PeanutBase PeanutBase Inparanoid
Beta vulgaris 211 553 783 Ensembl Gramene Ensembl Gramene Compara
Brachypodium distachyon 204 562 970 Ensembl Gramene Ensembl Gramene Compara
Brassica napus 212 555 3276 Ensembl Gramene Ensembl Gramene Compara
Brassica oleracea 204 526 1613 Ensembl Gramene Ensembl Gramene Compara
Brassica rapa 204 534 1639 Ensembl Gramene Ensembl Gramene Compara
Cajanus cajan 213 550 1103 LegumeInfo LegumeInfo Inparanoid
Capsicum annuum 213 536 1077 PMID: 24441736 N/A Inparanoid
Chlamydomonas reinhardtii 145 296 242 Ensembl Gramene Ensembl Gramene Compara
Cicer arietinum 214 554 1307 NCBI NCBI Inparanoid
Citrus sinensis 213 552 2210 Phytozome Phytozome Inparanoid
Coffea canephora 214 556 994 PMID:25190796 N/A Inparanoid
Cyanidioschyzon merolae 123 217 166 Ensembl Gramene Ensembl Gramene Compara
Eucalyptus grandis 206 535 886 Phytozome Phytozome Inparanoid
Fragaria vesca 214 536 951 Phytozome Phytozome Inparanoid
Glycine max 205 531 1961 Ensembl Gramene Ensembl Gramene Compara
Gossypium raimondii 213 558 1541 Phytozome Phytozome Inparanoid
Hordeum vulgare 202 500 808 Ensembl Gramene Ensembl Gramene Compara
Jatropha curcas 203 524 624 KDRI (Kazusa) KDRI (Kazusa) Inparanoid
Leersia perrieri 211 560 951 Ensembl Gramene Ensembl Gramene Compara
Malus domestica 211 535 1897 PMID: 20802477 Phytozome Inparanoid
Manihot esculenta 207 534 1096 Phytozome Phytozome Inparanoid
Medicago truncatula 206 528 1198 Ensembl Gramene Ensembl Gramene Compara
Mimulus guttatus 205 537 766 Phytozome Phytozome Inparanoid
Musa acuminata 204 518 1260 Ensembl Gramene Ensembl Gramene Compara
Oryza australiensis * 210 518 1628 OMAP/OGE N/A Inparanoid
Oryza barthii 211 570 988 Ensembl Gramene Ensembl Gramene Compara
Oryza brachyantha 211 561 935 Ensembl Gramene Ensembl Gramene Compara
Oryza glaberrima 213 564 1003 Ensembl Gramene Ensembl Gramene Compara
Oryza glumaepatula 213 572 1013 Ensembl Gramene Ensembl Gramene Compara
Oryza granulata * 212 534 2941 OMAP/OGE N/A Inparanoid
Oryza kasalath 173 258 325 PMID: 24578372 N/A Inparanoid
Oryza longistaminata * 210 557 869 Ensembl Gramene Ensembl Gramene Compara
Oryza meridionalis 204 520 869 Ensembl Gramene Ensembl Gramene Compara
Oryza minuta * 213 541 1851 OMAP/OGE N/A Inparanoid
Oryza nivara 209 576 1015 Ensembl Gramene Ensembl Gramene Compara
Oryza officinalis * 211 546 1616 OMAP/OGE N/A Inparanoid
Oryza punctata 209 568 1002 Ensembl Gramene Ensembl Gramene Compara
Oryza rufipogon 211 578 1025 Ensembl Gramene Ensembl Gramene Compara
Oryza sativa Indica 214 589 1083 Ensembl Gramene Ensembl Gramene Compara
Ostreococcus lucimarinus 135 279 230 Ensembl Gramene Ensembl Gramene Compara
Phaseolus vulgaris 215 558 1068 Phytozome Phytozome Inparanoid
Phoenix dactylifera 207 522 1000 PMID: 23917264 N/A Inparanoid
Physcomitrella patens 194 480 986 Ensembl Gramene Ensembl Gramene Compara
Picea abies 207 501 1215 Congenie Congenie Inparanoid
Pinus taeda 197 456 1160 TreeBase N/A Inparanoid
Populus trichocarpa 206 539 1320 Ensembl Gramene Ensembl Gramene Compara
Prunus persica 206 538 888 Ensembl Gramene Ensembl Gramene Compara
Selaginella moellendorffii 199 498 1241 Ensembl Gramene Ensembl Gramene Compara
Setaria italica 209 566 1059 Ensembl Gramene Ensembl Gramene Compara
Solanum lycopersicum 208 535 1069 Ensembl Gramene Ensembl Gramene Compara
Solanum tuberosum 205 514 1023 Ensembl Gramene Ensembl Gramene Compara
Sorghum bicolor 210 569 1025 Ensembl Gramene Ensembl Gramene Compara
Synechocystis pcc6803 148 312 264 Jaiswal MicrobeDB Inparanoid
Theobroma cacao 209 543 866 Ensembl Gramene Ensembl Gramene Compara
Trifolium pratense 208 540 1006 Ensembl Gramene Ensembl Gramene Compara
Triticum aestivum 210 571 3276 Ensembl Gramene Ensembl Gramene Compara
Triticum turgidum * 213 553 2522 PMID: 23800085 N/A Inparanoid
Triticum urartu 205 509 843 Ensembl Gramene Ensembl Gramene Compara
Vitis vinifera 202 528 928 Ensembl Gramene Ensembl Gramene Compara
Zea mays 209 563 1269 Ensembl Gramene MaizeGDB Compara

NOTE: The pathway counts for both reference and projected species include a few organizational “container” names, such as “Hormone biosyntheses” and “Metabolism”. Additionally, the bulk of the projected pathways occur in the areas of metabolic and regulatory function, whereas the rice reference data set has additional pathways related to cell cycle functions. We are not currently using these additional pathways as a source for orthology projection.