Website and coding updates:
The Plant Reactome web site front-end has been redesigned and re-implemented on the Joomla Content Management System. Hosted interaction data is now accompanied by a confidence score (where available), which enables a threshold filter to be applied in the Pathway Browser when viewing the interactor overlay. The latest Plant Reactome pathway data has been re-indexed and made available via Gramene search.
Analytical Tools:
Currently, Plant Reactome supports researchers with the following analytical tools:
- - Search for gene/protein, metabolites, pathways
- Upload and analyze gene-expression data on plant pathways
- Upload and analyze gene-gene interaction data on plant pathways
- Compare reference rice pathways with pathways from any of 78 projected species currently hosted by Plant Reactome.
Curation of reference rice pathways:
In Gramene Release 59, we have added 14 newly curated pathways and 2 "container" pathways, and updated 2 other existing pathways, resulting in a total of 280 reference rice pathways.
New Pathways:
- Tricin biosynthesis
- Lycopene catabolism
- Oryzalyde A biosynthesis
- Abscisic acid homeostasis
- Reactive oxygen species (ROS) homeostasis
- Generation of superoxide radicals
- Removal of superoxide radicals
- Valine degradation
- Cysteine degradation
- Recognition of fungal and bacterial pathogens and immunity response
- Reproductive meristem phase change
- Flower development
- Floral bract development
- Seed development
Example of recently curated rice pathway:
Updated/renamed pathways:
- - Secondary metabolism
- Hormone signaling, transport, and metabolism
Pathway Projection Statistics:
We have extended orthology-based pathway projections for 4 new species:Daucus carota(carrot),Vigna radiata (mung bean), Vigna angularis (adzuki bean) and Triticum dicoccoides (Emmer wheat). Plant Reactome now hosts pathway projections for 78 species ranging from unicellular autotrophs to higher plants. In addition, we have revised pathways forTriticum aestivum (bread wheat), based on its recent genome update (IWGSC RefSeq v1.0).
- *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
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Species
Pathways
Reactions
Genes
Sequence Source
Homology Method
Oryza sativa
280
1228
1607
UniProt
Curated Reference
Aegilops tauschii
211
513
922
Ensembl Gramene
Compara
Amborella trichopoda
219
550
660
Ensembl Gramene
Compara
Arabidopsis lyrata
226
560
1042
Ensembl Gramene
Compara
Arabidopsis thaliana
225
565
1016
Ensembl Gramene
Compara
Arachis duranensis
233
585
982
PeanutBase
Inparanoid
Arachis ipaensis
230
570
911
PeanutBase
Inparanoid
Beta vulgaris
224
556
750
Ensembl Gramene
Compara
Brachypodium distachyon
221
587
981
Ensembl Gramene
Compara
Brassica napus
227
561
3106
Ensembl Gramene
Compara
Brassica oleracea
224
550
1583
Ensembl Gramene
Compara
Brassica rapa
225
557
1571
Ensembl Gramene
Compara
Cajanus cajan
233
609
1315
LegumeInfo
Inparanoid
Capsicum annuum
232
561
1159
PMID: 24441736
Inparanoid
Chlamydomonas reinhardtii
164
316
260
Ensembl Gramene
Compara
Chondrus crispus
131
198
172
Ensembl Gramene
Compara
Cicer arietinum
231
572
1416
NCBI
Inparanoid
Citrus sinensis
230
569
2287
Phytozome
Inparanoid
Coffea canephora
230
567
1003
PMID:25190796
Inparanoid
Corchorus capsularis
222
529
762
Ensembl Gramene
Compara
Cucumis sativus
224
556
808
Ensembl Gramene
Compara
Cyanidioschyzon merolae
130
186
159
Ensembl Gramene
Compara
Daucus carota
224
535
1015
Ensembl Gramene
Compara
Dioscorea rotundata
215
458
567
Ensembl Gramene
Compara
Erythranthe guttata
206
497
664
Phytozome
Inparanoid
Eucalyptus grandis
208
496
714
Phytozome
Inparanoid
Fragaria vesca
230
545
964
Phytozome
Inparanoid
Galdieria sulphuraria
132
226
182
Ensembl Gramene
Compara
Glycine max
226
574
1909
Ensembl Gramene
Compara
Gossypium raimondii
227
568
1402
Ensembl Gramene
Compara
Helianthus annuus
223
547
1467
Ensembl Gramene
Compara
Hordeum vulgare
224
562
983
Ensembl Gramene
Compara
Jatropha curcas
206
488
539
KDRI (Kazusa)
Inparanoid
Leersia perrieri
227
586
938
Ensembl Gramene
Compara
Lupinus angustifolius
188
387
572
Ensembl Gramene
Compara
Malus domestica
228
551
1920
PMID: 20802477
Inparanoid
Manihot esculenta
226
566
1167
Ensembl Gramene
Compara
Medicago truncatula
222
556
1112
Ensembl Gramene
Compara
Musa acuminata
214
532
1175
Ensembl Gramene
Compara
Nicotiana attenuata
216
457
667
Ensembl Gramene
Compara
Oryza australiensis *
224
523
1613
OMAP/OGE
Inparanoid
Oryza barthii
228
603
997
Ensembl Gramene
Compara
Oryza brachyantha
226
592
963
Ensembl Gramene
Compara
Oryza glaberrima
232
600
1001
Ensembl Gramene
Compara
Oryza glumaepatula
230
605
1002
Ensembl Gramene
Compara
Oryza longistaminata *
225
561
855
Ensembl Gramene
Compara
Oryza meridionalis
222
541
870
Ensembl Gramene
Compara
Oryza meyeriana var. granulata
229
546
3306
OMAP/OGE
Inparanoid
Oryza minuta *
230
565
1979
OMAP/OGE
Inparanoid
Oryza nivara
227
612
1004
Ensembl Gramene
Compara
Oryza officinalis *
227
556
1771
OMAP/OGE
Inparanoid
Oryza punctata
226
590
1001
Ensembl Gramene
Compara
Oryza rufipogon
227
610
1020
Ensembl Gramene
Compara
Oryza sativa aus subgroup
180
268
345
PMID: 24578372
Inparanoid
Oryza sativa Indica Group
233
627
1083
Ensembl Gramene
Compara
Ostreococcus lucimarinus
144
230
203
Ensembl Gramene
Compara
Phaseolus vulgaris
226
564
1012
Ensembl Gramene
Compara
Phoenix dactylifera
224
534
1037
PMID: 23917264
Inparanoid
Physcomitrella patens
202
464
958
Ensembl Gramene
Compara
Picea abies
226
508
1249
Congenie
Inparanoid
Pinus taeda
215
460
1187
TreeBase
Inparanoid
Populus trichocarpa
225
559
1300
Ensembl Gramene
Compara
Prunus persica
226
570
892
Ensembl Gramene
Compara
Selaginella moellendorffii
203
470
1113
Ensembl Gramene
Compara
Setaria italica
226
596
1069
Ensembl Gramene
Compara
Solanum lycopersicum
223
558
1005
Ensembl Gramene
Compara
Solanum tuberosum
217
528
942
Ensembl Gramene
Compara
Sorghum bicolor
227
605
1043
Ensembl Gramene
Compara
Synechocystis pcc6803
152
304
221
Jaiswal
Inparanoid
Theobroma cacao
227
564
866
Ensembl Gramene
Compara
Trifolium pratense
223
559
951
Ensembl Gramene
Compara
Triticum aestivum
228
612
3469
Ensembl Gramene
Compara
Triticum dicoccoides
225
593
2065
Ensembl Gramene
Compara
Triticum turgidum *
228
573
2620
PMID: 23800085
Inparanoid
Triticum urartu
216
513
842
Ensembl Gramene
Compara
Vigna angularis
222
548
956
Ensembl Gramene
Compara
Vigna radiata
223
563
1026
Ensembl Gramene
Compara
Vitis vinifera
224
563
900
Ensembl Gramene
Compara
Zea mays
224
589
1312
Ensembl Gramene
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.
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.