Statistics
| General | ||||
|---|---|---|---|---|
| Species Numbers | 10 | |||
| Map Numbers | 153 in total | |||
| Compound Numbers | 1427 on the maps, 1506 in the database | |||
| Reaction Numbers | 1434 on the maps, 1434 in the database | |||
| Genes | ||||
| Arabidopsis thaliana | 2610 on the maps, 33518 in the database (TAIR9) | |||
| Oryza sativa | 3082 on the maps, 34780 in the database (RAP-DB build 5 locus) | |||
| Oryza sativa [RAP-DB transcript] | 3928 on the maps, 42057 in the database (RAP-DB build 5 transcripts) | |||
| Solanum lycopersicum (Tomato) | 1329 on the maps, 10038 in the database (Affymetrix Tomato GeneChip probes) | |||
| Lotus japonicus | 3302 on the maps, 43051 in the database (miyakogusa.jp annotations) | |||
| Glycine max | 1725 on the maps, 60943 in the database (Affymetrix Soybean GeneChip probes) | |||
| Hordeum vulgare | 742 on the maps, 22770 in the database (Affymetrix Barley1 GeneChip probes) | |||
| Populus trichocarpa | 2465 on the maps, 61251 in the database (Affymetrix Popular GeneChip probes) | |||
| Triticum aestivum | 921 on the maps, 61115 in the database (Affymetrix Wheat GeneChip probes) | |||
| Vitis vinifera | 660 on the maps, 16436 in the database (Affymetrix Vitis vinifera GeneChip probes) | |||
| Zea mays | 551 on the maps, 17555 in the database (Affymetrix Maize GeneChip probes) | |||
| Correlation Data (gene-to-gene) | ||||
| Arabidopsis thaliana | Ath: ATTED-II AthGeneCor_v3 (1388 chips) PCC >= 0.6 | |||
| Ath: ATTED-II AthGeneCor_v3 (1388 chips) PCC >= 0.795 (top 5 x genes) | ||||
| Ath: ATTED-II AthGeneCor_v3 (1388 chips) PCC <= -0.6 | ||||
| Ath: ATTED-II hormones (236 chips) PCC >= 0.817 (top 5 x genes)* | ||||
| Ath: ATTED-II tissues (237 chips) PCC >= 0.916 (top 5 x genes)* | ||||
| Ath: ATTED-II stresses (298 chips) PCC >= 0.739 (top 5 x genes)* | ||||
| Ath: ATTED-II c4.1 (1388 chips) MR <= 100 | ||||
| Ath: CoP (5257 chips) CCC Co-expressed Genes | ||||
| Oryza sativa | Osa: ATTED-II c1.0 (208 chips) MR <= 100 | |||
| Osa: CoP (432 chips) CCC Co-expressed Genes | ||||
| Solanum lycopersicum | Sly: MiBASE (50 chips) MR <= 100 (and PCC >= 0.6) | |||
| Glycine max | Gma: CoP (2994 chips) CCC Co-expressed Genes | |||
| Hordeum vulgare | Hvu: CoP (403 chips) CCC Co-expressed Genes | |||
| Populus trichocarpa | Ptr: CoP (95 chips) CCC Co-expressed Genes | |||
| Triticum aestivum | Tae: CoP (368 chips) CCC Co-expressed Genes | |||
| Vitis vinifera | Vvi: CoP (210 chips) CCC Co-expressed Genes | |||
| Zea mays | Zma: CoP (263 chips) CCC Co-expressed Genes | |||
| Correlation Data (metabolite-to-metabolite) | ||||
| Arabidopsis thaliana | Demo data - from time course exps. of drug treated Ath cells | |||
| Cell suspension cultures of Arabidopsis thaliana (T87) was treated by a drug and sampled at 17 different time points. Metabolome data were obtained by GC-MS and CE-MS and Pearson's correlation coefficients of co-accumulation levels between identified metabolites were calculated. | ||||
| PCC: Pearson's Correlation Coefficient CCC: Cosign theta Correlation Coefficient MR: Mutual Rank Co-expressed Genes: Gene-to-gene relationships evaluated as significant co-expressions in CoP top 5 x genes: The threshold of PCC was determined so that one gene correlates 5 other genes on the maps in average. * The correlation data calculated from selected experimental conditions (hormones, tissues, and stresses) were kindly provided by Dr. Obayashi and no longer available on ATTED-II. |
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| Gene and Probe Infromation | ||||
| Species | Gene ID | Probe ID / Sample | Array Type | Abbr. |
| Arabidopsis thaliana | AGI codes from TAIR9 | Same as Gene ID / At1g12345 | AGI codes | Ath |
| Oryza sativa | RAP-DB build 5 locus | Same as Gene ID Affymetrix Rice GeneChip probe ID |
RAP-DB locus |
Osa |
| Oryza sativa [RAP-DB transcript] | RAP-DB build 5 transcripts | Same as Gene ID / Os01t0136100-01 | RAP5 transcript | OsaT |
| Solanum lycopersicum (Tomato) | Affymetrix Tomato GeneChip probes | Same as Gene ID / Les.1020.2.A1_at | Affymetrix | Sly |
| Lotus japonicus | miyakogusa.jp annotations | Same as Gene ID / chr1.CM0001.10.nd, LjSGA_086535.1 |
Kazusa ID | Lja |
| Glycine max | Affymetrix Soybean GeneChip probes | Same as Gene ID / Gma.10049.1.A1_at | Affy Soybean | Gma |
| Hordeum vulgare | Affymetrix Barley1 GeneChip probes | Same as Gene ID / AB011264_at | Affy Barley1 | Hvu |
| Populus trichocarpa | Affymetrix Poplar GeneChip probes | Same as Gene ID / Ptp.1009.1.A1_at | Affy Poplar | Ptr |
| Triticum aestivum | Affymetrix Wheat GeneChip probes | Same as Gene ID / Ta.10015.2.S1_at | Affy Wheat | Tae |
| Vitis vinifera | Affymetrix Vitis vinifera GeneChip probes | Same as Gene ID / 1606470_at | Affy Vitis vinifera | Vvi |
| Zea mays | Affymetrix Maize GeneChip probes | Same as Gene ID / Zm.10043.1.A1_at | Affy Maize | Zma |
| The gene information file and probe information file for each species are available from "Download" function after log-in. Check on "Information" for Data Type and press "Search" button. Then all the information files used in the KaPPA-View4 system will be listed. Please see the files named Abbr_geneInfo_DATE.csv for gene information (File Type: Gene) and Abbr_featureGene_DATE.csv for probe information (File Type: Feature).Quantitative gene expression data should be described with the proper probe IDs and should be uploaded as corresponding Array Type. | ||||