RICECHIP.ORG: Support for Annotation & Functional Analysis of the Oryza sativa (Rice) Genome

External Oryza Resources:

RGAP/Michigan State University:
  RGAP Rice Annotation Project
  WEB BLAST

IRGSP International Rice Genome
    Sequencing Project
  RGP Rice Genome Project
  RAP-DB Rice Annotation Project
  ID Converter converts TIGR & IRGSP loci
  RiceXPro expression database

Gramene & Other Integrators:
  Pathway Tools Query Page
  Genome Browser Chromosomes
  FeatureView Genes/Features   IC4R Information Commons for Rice

Functional Categorization sites:
  RiceCyc Metabolic Pathways - Gramene
  RiceFREND - Platform for retrieving coexpressed gene networks
  RiceNet v2 Gene Network Analysis
  TFDB Transcription Factors - Grassius
  DRTF Transcription Factors - Beijing
  RTFD Transcription Factors - Potsdam
  CAZY Carbohydrate Active Enzymes
  ChromDB Chromatin Database
  RepeatMasker Retros & Repeats
  Retroryza Retrotransposon Families
  Rice MPSS Rice mRNA and small RNA
  PO Plant Ontology
  TARGeT: Tree Analysis of Related
    Genes and Transposons
  Yale Rice Cellular Expression Profiling
  CSRDB Cereal small RNAs Database

KEGG - Kyoto Encyclopedia of Genes
     and Genomes

KOME - Knowledge-based Oryza
    Molecular biological Encyclopedia

Korea Rice Genome Database

NCBI (& GenBank):
  Genome viewer
  Genomic sequences
  cDNA sequences
  EST sequences
  STS sequences
  GSS sequences
  HTG sequences
  GEO Gene Expression Omnibus

OsGDB Oryza sativa Genome Database

Oryzabase Integrated Rice Science Database

PlantPAN Plant Promoter Analysis Navigator

PLEXdb (Plant Expression Database)
  RicePLEX
  Rice experimental databases
  Rice 57K annotation

Rice Array Database (RAD)

MGOS Magnaporthe Grisea Oryza Sativa
    Interaction Database

OMAP Oryza Map Alignment Project

Educational Information:
  International Rice Research Institute IRRI
  International Rice Research Notes (IRRN)
  IRRI Training Program - tutorials
  Rice in Wikipedia
  History of rice cultivation - domestication
  Introduction to Rice - Wayne Armstrong
  IRRI Rice Morphology - training program
  Anatomy Atlas - Virtual Crops® site
  Rice in Cal's POTW - brief growing info
  What Makes Your Cereal Go Snap, Crackle, and Pop?

Internal Onsite Resources:

Enter a Search Phrase:
 (e.g. ribosomal protein)
Enter Osa1 Gene Model:
 (e.g. LOC_Os05g49420.1)
Enter an AFFY Probe Set ID:
 (e.g. Os.19553.1.S1_at)

Lexicon to Osa1 primary descriptions in the RGAP (v7) annotation (with number of matches in Affy and genome).

External 57K GeneChipTM Resources:

AFFYMETRIX selected resources: NCBI GEO (Gene Expression Omnibus) Site GPL2025 platform datasets, currently consisting of 187 series, ~3042 datasets. Last new series added: 3 March 2016
 

Some Papers Using the Affymetrix 57K Rice Genome GeneChipTM:

  1. Qiu D, Xiao J, Xie W, Liu H, Li X, Xiong L, Wang S (2008) Rice Gene Network Inferred from Expression Profiling of Plants Overexpressing OsWRKY13, a Positive Regulator of Disease Resistance. Mol Plant 1538-1551. (15 April 2008)
  2. Batista R, Saibo N, Lourenço T, Oliveira MM. (2008) Microarray analyses reveal that plant mutagenesis may induce more transcriptomic changes than transgene insertion. Proc Natl Acad Sci USA 105(9):3640-3645. (26 February 2008)
  3. Swarbrick PJ, Huang K, Liu G, Slate J et al. (2008) Global patterns of gene expression in rice cultivars undergoing a susceptible or resistant interaction with the parasitic plant Striga hermonthica. New Phytol 179: 515-529 (28 June 2008)
  4. Yang B, Sugio A, Zhu T, White FF (2007) Two type III effector genes of Xanthomonas oryzae pv. oryzae control the induction of the host genes OsTFIIA?1 and OsTFX1 during bacterial blight of rice. Proc Natl Acad Sci USA 104: 10720-10725. (11 June 2007) (custom Affy microarray chip)

*The Affymetrix 57K Rice Genome GeneChipTM has 57,381 probe sets (including 187 control probe sets); it has also been called the 51K chip, in reference to the 51,279 transcripts that Affymetrix used to construct the chip. Of these, 54,168 probe sets represent the O. sativa japonica cultivar group and 1,347 represent the O. sativa indica cultivar group.


Rice diversity, courtesy IRRI image collection