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| #LINK | |||
| #lang | en | ||
| #attribution_name | GenoCon | ||
| #attribution_url | http://atted.jp/download.shtml | ||
| #license | http://creativecommons.org/publicdomain/zero/1.0/deed.ja | ||
| #file_name | tooltip_DataTable | ||
| #download_from | http://linkdata.org/work/rdf1s734i | ||
| #namespace | Work | http://linkdata.org/work/ | |
| #property | explanation | URL | Work Name |
| #object_type_xsd | string | string | string |
| #property_context | Assertion | Assertion | Assertion |
| AtGenExpress | Developmental Arabidopsis thaliana microarray measurements. AtGenExpress is a high-throughput database which includes microarray measurements of gene expression in several conditions. The Developmental Series includes measurements from the main tissue organs of the plants. Gene expression data from AtGenExpress was taken in triplicate, and we use the median value. Expression data was used as log-transformed absolute expression values. | Work:rdf1s456i | AtGenExpress |
| AtGenExpress_median | Developmental Arabidopsis thaliana microarray measurements. AtGenExpress is a high-throughput database which includes microarray measurements of gene expression in several conditions. The Developmental Series includes measurements from the main tissue organs of the plants. Gene expression data from AtGenExpress was taken in triplicate, and we use the median value. Expression data was used as log-transformed absolute expression values. | Work:rdf1s460i | AtGenExpress |
| AtGenExpress_mean | Developmental Arabidopsis thaliana microarray measurements. AtGenExpress is a high-throughput database which includes microarray measurements of gene expression in several conditions. The Developmental Series includes measurements from the main tissue organs of the plants. Gene expression data from AtGenExpress was taken in triplicate, and we use the mean value. Expression data was used as log-transformed absolute expression values. | Work:rdf1s785i | AtGenExpress |
| DIURNAL | Circadian Arabidopsis thaliana microarray measurements. The DIURNAL project is a microarray gene expression database which was collected over two days (44 hours) at four hour intervals in various growth conditions. These measurements are made on 7-9 day old seedlings, and show gene expression levels across the whole plant. For DIURNAL gene expression data, we calculated the Phase of each data by non-linear best fit to a sine wave with a 24 hour period, and similarly calculated the Amplitude. Visually checking the 1000 largest amplitude genes showed a good fit in all cases, though a few genes clearly deviated from sinusoidal behavior. All had a major period of 24 hours. | Work:rdf1s461i | DIURNAL |
| ATTED | The ATTED-II database uses gene co-expression analysis of the AtGenExpress data to predict functional 7 base-pair motifs in promoters. Motifs identified within a promoter region 200 bp upstream of the transcription start site. | Work:rdf1s458i | ATTED-II |
| PPDB | The Plant Promoter Database (PPDB) uses word frequency analysis to identify 8 base-pair motifs in promoters. Motifs are categorized as TATA-box, Y-patch (a CT-rich region often found in plant TATA box promoters), the initiator near the transcription start site, and cis-regulatory motifs. The regulatory motifs are a group of 308 8 base-pair sequences which are used to represent regulatory sites. PPDB also deposits the data of transcription start sites (TSSs) detected by the CT-MPSS method, a combination of cap trapper (CT), a reliable method for preparing the 5' end of full-length cDNA, and massively parallel signature sequencing (MPSS), which enables ultra-parallel sequencing in a considerably shorter time and at lower cost than conventional sequencing methods. | Work:rdf1s459i | PPDB (Plant Promoter Database) |
| PLACE | Motifs in the PLACE (Plant Cis-acting Regulatory DNA Elements) database were curated from literature sources. http://www.dna.affrc.go.jp/PLACE/ | - | PLACE (Plant Cis-acting Regulatory DNA Elements) database |
| COL_LDHH | The data are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h). | Work:rdf1s457i | DIURNAL fitted up with sine wave |
| COL_SD | The data are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition of short day light, that is, Light (8h) Dark (16h). | Work:rdf1s457i | DIURNAL fitted up with sine wave |
| DD_DDHC | The data are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Dark (12h) Dark (12h) / Hot (12h) / Cold (12h), and subjected to Dark (24h). | Work:rdf1s457i | DIURNAL fitted up with sine wave |
| LDHC | The data are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Dark (12h) / Hot (12h) / Cold (12h). | Work:rdf1s457i | DIURNAL fitted up with sine wave |
| LDHH_SM | The data are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h), by using the Smith method. | Work:rdf1s457i | DIURNAL fitted up with sine wave |
| LDHH_ST | The data are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h), by using the Stitt method. | Work:rdf1s457i | DIURNAL fitted up with sine wave |
| LER_SD | The data are associated with the Arabidopsis Ler (Landsberg-ereta) strain, grown under the circadian condition of short day light, that is, Light (8h) Dark (16h). | Work:rdf1s457i | DIURNAL fitted up with sine wave |
| LIGHT5_HIF138_13 | The data are associated with the Arabidopsis hif138-13 (HETEROGENOUS INBRED FAMILY 138-13) strain, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h). | Work:rdf1s457i | DIURNAL fitted up with sine wave |
| LIGHT5_HIF138_8 | The data are associated with the Arabidopsis hif138-8 (HETEROGENOUS INBRED FAMILY 138-8) strain, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h). | Work:rdf1s457i | DIURNAL fitted up with sine wave |
| LIGHT5_znknOX | The data are associated with the Arabidopsis tsp-ox (hif138-8) (TANDEM ZINCKNUCKLE PROTEIN-ox) strain, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h). | Work:rdf1s457i | DIURNAL fitted up with sine wave |
| LL12_LDHH | The data are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Light (12h) / Hot (24h), and subjected to Light (24h) by the Kay method. | Work:rdf1s457i | DIURNAL fitted up with sine wave |
| LL23_LDHH | The data are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Light (12h) / Hot (24h), and subjected to Light (24h) by the Miller method. | Work:rdf1s457i | DIURNAL fitted up with sine wave |
| LLHC | The data are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Light (12h) / Hot (12h) / Cold (12h). | Work:rdf1s457i | DIURNAL fitted up with sine wave |
| LL_LDHC | The data are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Dark (12h) / Hot (12h) / Cold (12h), and subjected to Light (24h). | Work:rdf1s457i | DIURNAL fitted up with sine wave |
| LL_LLHC | The data are associated with the Arabidopsis Columbia strain 0, grown under the circadian condition Light (12h) Light (12h) / Hot (12h) / Cold (12h), and subjected to Light (24h). | Work:rdf1s457i | DIURNAL fitted up with sine wave |
| lhyox_SD | The data are associated with the Arabidopsis lhy (lhy-ox) (LATE ELONGATED HYPOCOTYL) strain, grown under the circadian condition of short day light, that is, Light (8h) Dark (16h). | Work:rdf1s457i | DIURNAL fitted up with sine wave |
| longday | The data are associated with the Arabidopsis Ler strain, grown under the circadian condition of long day light, that is, Light (16h) Dark (8h) by using the Kay method. | Work:rdf1s457i | DIURNAL fitted up with sine wave |
| lux_2_LDHH | The data are associated with the Arabidopsis lux-2 (LUX ARRHYTHMO-2) strain, grown under the circadian condition Light (12h) Dark (12h) / Hot (24h). | Work:rdf1s457i | DIURNAL fitted up with sine wave |
| phyB9_SD | The data are associated with the Arabidopsis phyB9 (PHYTOCHROME B-9) strain, grown under the circadian condition of short day light, that is, Light (8h) Dark (16h). | Work:rdf1s457i | DIURNAL fitted up with sine wave |
| shortday | The data are associated with the Arabidopsis Ler strain, grown under the circadian condition of short day light, that is, Light (8h) Dark (16h) by using the Kay method. | Work:rdf1s457i | DIURNAL fitted up with sine wave |
| DIURNAL_normalized | Expression data from DIURNAL is used as values normalized to the mean of all 12 timepoints for a given growth condition. | Work:rdf1s370i | DIURNAL normalized |
| AtGenExpress_normalized | Expression data from AtGenExpress is used as values normalized to the mean of all experiments for the AtGenExpress data. | Work:rdf1s369i | AtGenExpress normalized |
| Flowering | This collection of Gene Expression Properties are associated with flowering tissues. | Work:rdf1s220i | Developmental conditions |
| Fruit_Seeds | This collection of Gene Expression Properties are associated with fruit and seed tissues. | Work:rdf1s220i | Developmental conditions |
| Leaf | This collection of Gene Expression Properties are associated with leaf tissues. | Work:rdf1s220i | Developmental conditions |
| Root | This collection of Gene Expression Properties are associated with root tissues. | Work:rdf1s220i | Developmental conditions |
| Seedling | This collection of Gene Expression Properties are associated with seedling tissues. | Work:rdf1s220i | Developmental conditions |
| Stem | This collection of Gene Expression Properties are associated with stem tissues. | Work:rdf1s220i | Developmental conditions |
| Whole_Plant | This collection of Gene Expression Properties are associated with whole plant body parts. | Work:rdf1s220i | Developmental conditions |
Koro_Nishikata
Robert Cox
