Contact

Link and Publish your data

to the Linked Open Data Community

Linkdata Work Information

PromoterCAD Beginning Tutorial 1 - Tooltip Information - new

1

value

useful
0
Loading...



Select a file name to see the detais.
   
#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/rdf1s591i
#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
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)
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_normalize Expression data from DIURNAL is used as values normalized to the mean of all 12 timepoints for a given growth condition.
AtGenExpress_normalize 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
* Row count is limited to 100.