"TENOR (Transcriptome ENcyclopedia Of Rice)" is a database to privide transcriptional activity on the rice genome at the nucleotide level based on the RNA-Seq data under 140 environmental stresses and plant hormone treated conditions. As well as expression profiles, information of cis-regulatory elements in promoter regions and co-expressed transcript are provided for each transcript.
The rice (Oryza sativa L. ssp. japonica cv. Nipponbare) seedlings were used for all experiments. All samples were hydroponically grown at 28ºC temperatures, 16h-light/8h-dark cycle with the light period from 6:00 A.M. to 10:00 P.M., and 70-80% relative humidity. 0h (control) samples were harvested at 9:00 A.M.
|Treatments||Tissue||Time points||Developmental stage of 0h samples||Medium|
|High salinity (150mM NaCl)1||Shoot/Root||O||O||7 days after germination||distilled water|
|High phosphate (3 mM KH2PO4)2||Shoot/Root||O||O||O||O||O (only for root)||14 days after germination||Yoshida's nutrient medium|
|Low phosphate (0 mM NaH2PO4)2||Shoot/Root||O||O||O||O||O (only for root)||14 days after germination||Yoshida's nutrient medium|
|High cadmium (50 µM CdSO4)3||Shoot/Root||O||O||O||O||O||10 days after germination||Yoshida's nutrient medium|
|Low cadmium (1 µM CdSO4)||Shoot/Root||O||O||O||O||10 days after germination||Yoshida's nutrient medium|
|Very low cadmium (0.2 µM CdSO4)||Shoot/Root||O||O||O||O||10 days after germination||Yoshida's nutrient medium|
|Drought ( grown without medium)||Shoot/Root||O||O||O||O||O||O||10 days after germination||Yoshida's nutrient medium|
|Flood (completely submerged in medium)||Shoot/Root||O||O||O||O||O||O||O||10 days after germination||Yoshida's nutrient medium|
|Cold (4ºC)||Shoot/Root||O||O||O||O||O||O||10 days after germination||Yoshida's nutrient medium|
|Osmotic (0.6 M Mannitol)||Shoot/Root||O||O||O||O||O||10 days after germination||Yoshida's nutrient medium|
|ABA (100 µM)||Shoot/Root||O||O||O||O||O||O||10 days after germination||Yoshida's nutrient medium|
|JA (100 µM)||Shoot/Root||O||O||O||O||O||O||10 days after germination||Yoshida's nutrient medium|
|Developmental time (no treatment)||Shoot/Root||O||O||O||O||O||O||O||O||O||O||10 days after germination||Yoshida's nutrient medium|
|Sample||Instrument||Read type||DRA Accession|
|High salinity||Illumina, GAIIx||SE, 36bp||DRA000159|
|High phosphate||Illumina, GAIIx||SE, 51bp||DRA000314|
|Low phosphate||Illumina, GAIIx||SE, 51bp||DRA000314|
|High cadmium||Illumina, GAIIx||SE, 76bp||DRA001092, DRA006674|
|Low cadmium||Illumina, GAIIx||SE, 76bp||DRA000959|
|Very low cadmium||Illumina, GAIIx||SE, 76bp||DRA000959|
|Drought||Illumina, GAIIx||SE, 76bp||DRA000959|
|Flood||Illumina, GAIIx||SE, 76bp||DRA000959|
|Cold||Illumina, GAIIx||SE, 76bp||DRA000959|
|Osmotic||Illumina, GAIIx||SE, 76bp||DRA000959|
|ABA||Illumina, GAIIx||SE, 76bp||DRA000959|
|JA||Illumina, GAIIx||SE, 76bp||DRA000959|
|Developmental time||Illumina, GAIIx||SE, 76bp||DRA000959|
The following three entrances are available to access expression data in TENOR.
This function will return the list of transcript IDs that contain "search words" in their ID or description fields. Responsive expression patterns (fold-change and FDR) for each condition are displayed as well as transcript IDs and descriptions. Each transcript has four links to the following external information.
Users can search transcripts by their responsive expression patterns and thresholds. A list of transcripts whose expression pattern is consistent with specified responsive expression pattern will be shown in the bottom frame as in the keyword search.
PARPNTE can predict both protein-coding and non-coding transcript structures simultaneously with coding sequence (CDS) information based on the alignment of mRNA-Seq reads on the genome and the hidden Markov model (HMM) trained with RAP-DB representative transcripts with FLcDNA evidence.
Sensitivity (Sn) and Specificity (Sp) were compared betwee PARPNTE and Cufflinks2 using cuffcompare.
mRNA-Seq data in TENOR and representative transcripts in RAP-DB were used for the gene prediction by two programs.
PARPNTE: # Query mRNAs : 48366 in 38228 loci (30293 multi-exon transcripts) # (5183 multi-transcript loci, ~1.3 transcripts per locus) # Reference mRNAs : 43466 in 37870 loci (30911 multi-exon) #--------------------| Sn | Sp | fSn | fSp Base level: 51.2 64.1 - - Exon level: 52.4 58.9 54.6 61.3 Intron level: 70.1 80.6 71.8 82.6 Intron chain level: 32.5 33.1 57.3 58.5 Transcript level: 0.0 0.0 0.1 0.1 Locus level: 26.2 25.9 34.1 33.2 Matching intron chains: 10035 Matching loci: 9907 Missed exons: 47549/173117 ( 27.5%) Novel exons: 25775/154037 ( 16.7%) Missed introns: 33323/125962 ( 26.5%) Novel introns: 14557/109525 ( 13.3%) Missed loci: 15352/37870 ( 40.5%) Novel loci: 12423/38228 ( 32.5%) Cufflinks: # Query mRNAs : 45415 in 30617 loci (30249 multi-exon transcripts) # (9625 multi-transcript loci, ~1.5 transcripts per locus) # Reference mRNAs : 43466 in 37870 loci (30911 multi-exon) #--------------------| Sn | Sp | fSn | fSp Base level: 59.0 50.8 - - Exon level: 49.1 54.2 51.4 56.7 Intron level: 69.3 79.5 71.4 81.9 Intron chain level: 31.3 32.0 55.3 56.5 Transcript level: 0.0 0.0 0.0 0.0 Locus level: 25.1 31.0 34.4 40.6 Matching intron chains: 9681 Matching loci: 9513 Missed exons: 44641/173117 ( 25.8%) Novel exons: 20563/156764 ( 13.1%) Missed introns: 34431/125962 ( 27.3%) Novel introns: 15408/109802 ( 14.0%) Missed loci: 13968/37870 ( 36.9%) Novel loci: 5892/30617 ( 19.2%)
Please download from "Data Downloads" page
PARPNTE predicts gene structures and protein-coding regions based on mapping data of mRNA-Seq reads and genome sequence data.
The prediction depends on parameters generated from genome sequnece, splicing junction and depth of mRNA-Seq reads and reference gene annotation data.
This software is released under the MIT License.
Copyright © 2015 National Institute of Agrobiological Sciences
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