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Table 2 Summary of databases for expression analysis of rice genes

From: The Rice Oligonucleotide Array Database: an atlas of rice gene expression

Database Platform Expression type Co-expression Output type Other features Reference
ROAD - Affymetrix    - Heatmap - Single/multiple-platform probe search This study
- Agilent 22K/44K - Anatomy - Whole dataset - Line plot - GO/KO enrichment analysis
- NSF 20K/45K - Development - Biotic stress - Bar plot - Meta-profiling analyses for both Affymetrix and Agilent 44K
- BGI/Yale - Individual dataset - Abiotic stress - Network - Accept gene list and bulk download
    - Table  
PLEXdb - Affymetrix - Individual dataset - N/A - Heatmap - Identify probes of homologs between different species (Dash et al.[2012])
    - Line plot - Rice and 15other plant species
    - Bar plot  
    - Table  
Genevestigator - Affymetrix - Anatomy - N/A - Scatter plot - Bi/hierarchical clustering (Hruz et al.[2008])
  - Development   - Heatmap - Accept gene list
  - Perturbations    - Result export is prohibited
  - Neoplasms    - Rice and 14 other organisms
  - Individual dataset    
RiceXPro - Agilent 44K - Anatomy - Anatomy - Heatmap - Provide useful web links for other analyses such as Rice TOGO, SALAD, RAP-DB (Sato et al.[2011])
  - Development of leaf - Development - Bar plot - Hierarchical clustering
  - Root cell-type anatomy of leaf - Line plot - T-test and fold change (FC) analysis
     - Accept gene list
BAR - Affymetrix - Individual dataset - N/A - Electronic fluorescent pictograph - Rice and 6 other plant species (Toufighi et al.[2005])
    - Table  
gAtlas in RiceGE - Affymetrix - Whole dataset - N/A - Bar plot - Filter option to select specific Dataset (Jung et al.[2011])
- RMOS     
RiceNet in PlaNet - Affymetrix - Whole dataset - Whole dataset - Line plot - Mapman ontology analysis (Mutwil et al.[2011])
    - Network - Provide phenotypes in Tos17 insertion mutant lines
    - Table - Provide cluster network and node vicinity network separately
OryzaExpress - Affymetrix - Whole dataset - Whole dataset - Line plot - Diverse options for developing co- expression network (CA, PCC, MR and PAC) (Hamada et al.[2011])
- Agilent 22K    - Bar plot - Predicted orthologs and networks in Arabidopsis
    - Network - 11 options to display data in network
    - Table  
Gene Co-expression Network Browser - Affymetrix - N/A - Whole dataset - Network - 45 gene modules (Ficklin et al.[2010])
     - 76 enriched co-functional clusters
     - GO/KO/IPR enrichment analysis
- 6 options to display data in network
- Rice and maize
  1. Note: Hyperlinks for the mentioned databases are as followings: ROAD (Rice Oligonucleotide Array Database),http://www.ricearray.org/; PLEXdb (Plant Expression Database),http://www.plexdb.org/; Genevestigator,https://www.genevestigator.com/gv/; RiceXPro,http://ricexpro.dna.affrc.go.jp/; BAR (The Bio-Array Resource for Plant Biology),http://bar.utoronto.ca/; gAtlas in RiceGE (Rice Functional Genomic Express Database),http://signal.salk.edu/cgi-bin/RiceGE?JOB=APPENDIX&QUERY=GeneAtlas; RiceNet in PlaNet,http://aranet.mpimp-golm.mpg.de/ricenet; OryzaExpress,http://bioinf.mind.meiji.ac.jp/OryzaExpress/; Gene Co-expression Network Browser,http://www.clemson.edu/genenetwork/.