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 |