Reactome: A Curated Pathway Database

Release Summary

Gramene Release 56b (Plant Reactome Release 15)

In Gramene Release 56b (PR r15), we have added 22 newly curated pathways, 3 updated pathways, 8 newly projected species, and gene interaction data to Plant Reactome.

Interactor Overlays

Users can display gene-gene interaction data on Plant Reactome pathways either by choosing a publicly-available dataset under “Interactor Overlay”, or by uploading a dataset of their choice. This feature can aid researchers by extending the network of known complexes and pathways with candidate proteins. The Plant Reactome team has specifically provided locally-hosted interaction data for A. thaliana (courtesy of the Planteome project). This data can be viewed by selecting “Plant Interactome” on the Interactor Overlay panel and A. thaliana on the species selector.

circadian_AT_interactions_2

    circadian_AT_interactions_4

Expanded Reference Species Gene Name listings

Additional and alternate O. sativa gene names are now visible under the Molecules tab when viewing rice pathways.

Pathway Curation

This release contains 22 newly curated and 3 revised pathways from reference species rice (O. sativa). The hierarchical list of pathways has been updated accordingly.

Newly curated pathways:

  • Reproductive structure development
  • Anther and pollen Development
  • Vegetative structure development
  • Primary root development
  • Response to submergence
  • Underwater shoot and internode elongation
  • Response to phosphate deficiency
  • Photorespiration
  • Ureide biosynthesis
  • Beta-alanine betaine biosynthesis
  • Proline biosynthesis V from arginine
  • Phospholipid biosynthesis I
  • Sphingolipid metabolism
  • Response to iron deficiency
  • Mugineic acid biosynthesis
  • Iron uptake and transport in root vascular system
  • Proline degradation
  • Glutamate degradation
  • Phenylalanine degradation III
  • Lysine degradation II
  • Threonine degradation

Revised pathways:

  • Cardiolipin biosynthesis
  • Ent-kaurene biosynthesis
  • Responses to stimuli

Pathway Projections

The Plant Reactome has expanded gene homology-based pathway projections to 74 plant species. Newly projected species include garden cucumber (Cucumis sativus), white yam (Dioscorea rotundata), sunflower (Helianthus annuus), white jute (Corchorus capsularis), blue lupin (Lupinus angustifolius), coyote tobacco (Nicotiana attenuata), Irish moss (Chondrus crispus), and an extremophilic unicellular species of red algae Galdieria sulphuraria (capable of photosynthesis as well as heterotrophic growth by utilizing ~50 different extracellular carbon sources). In addition, we have revised pathway projections (converted from Inparanoid to Compara orthology) for three species: a wild South American cotton (Gossypium raimondii), cassava (Manihot esculenta), and common bean (Phaseolus vulgaris). Notable updated Compara orthology data has been kindly provided by Ensembl for updated species.

Visit the Download page to access the updated data files associated with pathways, reactions, gene products, metabolites and external reference sources such as ChEBI, Ensembl, and UniProt.

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 Homology method
Oryza sativa japonica 264^ 1168 1384 Ensembl Gramene Curated Reference
Aegilops tauschii 202 489 889 Ensembl Gramene Compara
Amborella trichopoda 213 538 647 Ensembl Gramene Compara
Arabidopsis lyrata 213 544 1040 Ensembl Gramene Compara
Arabidopsis thaliana 214 551 1027 Ensembl Gramene Compara
Arachis duranensis 218 529 825 PeanutBase Inparanoid
Arachis ipaensis 216 535 847 PeanutBase Inparanoid
Beta vulgaris 212 540 745 Ensembl Gramene Compara
Brachypodium distachyon 208 561 926 Ensembl Gramene Compara
Brassica napus 212 539 2953 Ensembl Gramene Compara
Brassica oleracea 214 539 1531 Ensembl Gramene Compara
Brassica rapa 211 543 1555 Ensembl Gramene Compara
Cajanus cajan 218 547 1097 LegumeInfo Inparanoid
Capsicum annuum 217 529 1047 PMID: 24441736 Inparanoid
Chlamydomonas reinhardtii 161 317 264 Ensembl Gramene Compara
Chondrus crispus 134 230 194 Ensembl Gramene Compara
Cicer arietinum 219 544 1306 NCBI Inparanoid
Citrus sinensis 218 541 2176 Phytozome Inparanoid
Coffea canephora 218 542 949 PMID:25190796 Inparanoid
Corchorus capsularis 210 526 756 Ensembl Gramene Compara
Cucumis sativus 211 536 810 Ensembl Gramene Compara
Cyanidioschyzon merolae 135 242 182 Ensembl Gramene Compara
Dioscorea rotundata 203 451 563 Ensembl Gramene Compara
Erythranthe guttata 204 492 659 Phytozome Inparanoid
Eucalyptus grandis 206 491 690 Phytozome Inparanoid
Fragaria vesca 218 522 905 Phytozome Inparanoid
Galdieria sulphuraria 139 257 207 Ensembl Gramene Compara
Glycine max 214 542 1911 Ensembl Gramene Compara
Gossypium raimondii 213 551 1382 Ensembl Gramene Compara
Helianthus annuus 212 533 1496 Ensembl Gramene Compara
Hordeum vulgare 213 534 925 Ensembl Gramene Compara
Jatropha curcas 204 483 526 KDRI (Kazusa) Inparanoid
Leersia perrieri 216 554 917 Ensembl Gramene Compara
Lupinus angustifolius 183 379 593 Ensembl Gramene Compara
Malus domestica 216 526 1811 PMID: 20802477 Inparanoid
Manihot esculenta 215 549 1207 Ensembl Gramene Compara
Medicago truncatula 210 538 1183 Ensembl Gramene Compara
Musa acuminata 207 506 1172 Ensembl Gramene Compara
Nicotiana attenuata 205 461 684 Ensembl Gramene Compara
Oryza australiensis * 213 502 1527 OMAP/OGE Inparanoid
Oryza barthii 214 565 948 Ensembl Gramene Compara
Oryza brachyantha 215 563 922 Ensembl Gramene Compara
Oryza glaberrima 218 560 947 Ensembl Gramene Compara
Oryza glumaepatula 218 571 962 Ensembl Gramene Compara
Oryza longistaminata * 213 538 825 Ensembl Gramene Compara
Oryza meridionalis 209 506 817 Ensembl Gramene Compara
Oryza meyeriana var. granulata 217 523 3155 OMAP/OGE Inparanoid
Oryza minuta * 218 532 1845 OMAP/OGE Inparanoid
Oryza nivara 214 570 953 Ensembl Gramene Compara
Oryza officinalis * 215 533 1686 OMAP/OGE Inparanoid
Oryza punctata 213 566 968 Ensembl Gramene Compara
Oryza rufipogon 216 573 968 Ensembl Gramene Compara
Oryza sativa aus subgroup 169 255 320 PMID: 24578372 Inparanoid
Oryza sativa Indica Group 220 586 1049 Ensembl Gramene Compara
Ostreococcus lucimarinus 144 294 239 Ensembl Gramene Compara
Phaseolus vulgaris 214 548 1052 Ensembl Gramene Compara
Phoenix dactylifera 211 508 995 PMID: 23917264 Inparanoid
Physcomitrella patens 199 471 928 Ensembl Gramene Compara
Picea abies 213 491 1183 Congenie Inparanoid
Pinus taeda 202 438 1140 TreeBase Inparanoid
Populus trichocarpa 213 554 1305 Ensembl Gramene Compara
Prunus persica 214 552 929 Ensembl Gramene Compara
Selaginella moellendorffii 209 514 1170 Ensembl Gramene Compara
Setaria italica 212 566 1017 Ensembl Gramene Compara
Solanum lycopersicum 213 545 1012 Ensembl Gramene Compara
Solanum tuberosum 207 527 964 Ensembl Gramene Compara
Sorghum bicolor 214 572 1001 Ensembl Gramene Compara
Synechocystis pcc6803 147 299 217 Jaiswal Inparanoid
Theobroma cacao 214 554 874 Ensembl Gramene Compara
Trifolium pratense 214 538 964 Ensembl Gramene Compara
Triticum aestivum 214 570 3189 Ensembl Gramene Compara
Triticum turgidum * 216 545 2482 PMID: 23800085 Inparanoid
Triticum urartu 203 497 811 Ensembl Gramene Compara
Vitis vinifera 212 539 875 Ensembl Gramene Compara
Zea mays 211 552 1256 Ensembl Gramene Compara

NOTES:

  • 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.
  • The Plant Reactome increasingly includes curated regulatory and developmental pathways, which require more reference DNA and RNA sequence elements, in addition to the traditional protein-coding elements. These sequence elements are not included in Reactome orthoinference at this time, although we are actively working to enhance the projection process to include these elements on projected pathways in future releases.