Oryza sativa

Organism Details
Common Name Rice
Genus Oryza
Species sativa
Abbreviation O.sativa
Description

Rice is one of the most important staple crops and serves as the model species for the Poaceae family of grasses.  It is rich in both genomic and genetic resources.  This site provides several co-expression networks for rice derived from publicly available samples using the Affymetrix GeneChip Rice Genome array.   Genetic data from mutational studies, QTLs and GWAS have been incorporated to help explore the multi-functional behavior of genes.

Click "Networks" in the "Resources" menu to the right to view a list of all networks for this species. In summary, the following networks are available:

  • The rice global gene co-expression network v1.0
  • Rice K25 GIL-collection--a set of 22 networks built from pre-clustering of input samples.
Source Data

Information and data required to construct the networks for this species can be found at the following locations:

Publications

Details about the networks presented for this species are found in the following publications:

Genomic/Genetic Data Summary
The following genomic and genetic data types are currently present for this organism.
Feature Type Count
Chromosomes 12
Genes 57,840
SNPs 1,976,280
InDel 165,248
MNP 0
QTLs 8,646
Networks
The following network are available for this species. Click on a network for further details and exploration.
Network Name Network Type Module Count Edge Count Node Count Average Degree <k>
OsGlobal-v1.0 co-expression 30 32,820 2,257 29.08
OsK25v1.0_G0002 co-expression 569 14,507 1,233 23.53
OsK25v1.0_G0003 co-expression 676 31,700 1,549 40.93
OsK25v1.0_G0005 co-expression 290 12,615 790 31.94
OsK25v1.0_G0006 co-expression 355 35,915 817 87.92
OsK25v1.0_G0007 co-expression 370 7,132 939 15.19
OsK25v1.0_G0008 co-expression 476 14,037 1,302 21.56
OsK25v1.0_G0009 co-expression 173 2,350 621 7.57
OsK25v1.0_G0011 co-expression 397 7,123 752 18.94
OsK25v1.0_G0012 co-expression 522 23,771 1,284 37.03
OsK25v1.0_G0013 co-expression 150 1,198 327 7.33
OsK25v1.0_G0014 co-expression 330 4,389 883 9.94
OsK25v1.0_G0015 co-expression 256 7,541 487 30.97
OsK25v1.0_G0016 co-expression 129 997 435 4.58
OsK25v1.0_G0017 co-expression 194 7,176 539 26.63
OsK25v1.0_G0018 co-expression 216 6,362 547 23.26
OsK25v1.0_G0019 co-expression 234 2,184 778 5.61
OsK25v1.0_G0020 co-expression 260 2,888 651 8.87
OsK25v1.0_G0021 co-expression 24 118 83 2.84
OsK25v1.0_G0022 co-expression 279 4,936 879 11.23
OsK25v1.0_G0023 co-expression 302 32,787 800 81.97
OsK25v1.0_G0024 co-expression 325 2,757 769 7.17
OsK25v1.0_G0025 co-expression 135 1,400 408 6.86

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