Plant & Animal Genome Conference XXIV
Computer Demo 1 (C05) January 09, 2016

TENOR
Database for ComprehensivemRNA-Seq Experiments in Rice
Yoshihiro Kawahara1, Youko Oono1, Hironobu Wakimoto1,2,Jun Ogata1, Hiroyuki Kanamori1, Harumi Sasaki1, Satomi Mori1,Takashi Matsumoto1 and Takeshi Itoh1
1Agrogenomics Research Center, National Institute of Agrobiological Sciences, Japan

2BITS. Co., Ltd.

TENOR development teamSample & library preparation• Youko Oono
• Jun Ogata• Takashi Matsumoto

DB & software development• Yoshihiro Kawahara• Hironobu Wakimoto• Takeshi ItohmRNA-Seq sequencing• Harumi Sasaki• Satomi Mori
• Hiroyuki KanamoriFunding
This work was supported by a grant from the Ministry of Agriculture,Forestry and Fisheries of Japan (Genomics for AgriculturalInnovation, RTR1001).

What is TENOR?
A database that contains large-scale mRNA sequencing(mRNA-Seq) data obtained from rice under a wide
variety of conditions.
URL
http://tenor.dna.affrc.go.jp

Publication
Kawahara Y. et al.
Plant Cell Physiol. 2015 Nov 16
doi: 10.1093/pcp/pcv179

TENOR provides rice transcriptome information
under 10 abiotic stress and 2 plant hormone

treatment conditions (+ no treatment)of Shoot and Root tissues(seedlings 14 days after germination)

at Multiple timepoints(0h, 1h, 3h, 6h, 12h, 1d, 3d, 4d, 5d, 10d after treatments)

Total 140 conditions (250 billion bp from 3.5 billion reads)

10 abiotic stress and 2 plant hormone
treatment conditions (+ no treatment)
Salinity a

Low Pi b High Pi b

Very-low Cd

ABADrought

JA

High Cd c

Flood

Low CdOsmotic

No treatment

aMizuno H, Kawahara Y et al. (2010) BMC Genomics
bOono Y, Kawahara Y et al. (2011) RicecOono Y, Yazawa T, Kawahara Y et al. (2014) PLoS One

All experiments were performed
at a single laboratory
under standardized conditions
using a single analysis platform (mRNA-Seq)- a highly reliable resource- a standard data set
for comprehensive understanding of genome-wide
gene expression under the various conditions

Use of mRNA-Seq technique provides- transcriptional activity at single nucleotide
resolution- expression profile of unannotated transcripts

a RAP-DB transcript
might be truncatedDistribution ofmRNA-Seq reads

Use of mRNA-Seq technique provides- transcriptional activity at single nucleotide
resolution- expression profile of unannotated transcripts
No transcripts
in RAP-DB
RNA-Seq based
predicted transcripts(Cufflinks & PARPNTE)
Low P, 5d, RootDistribution of
RNA-Seq reads

Cold, 1d, Root

Drought, 1d, Root

Functions in TENOR

Three entrances on the top pageby Keywords

by genomic
coordinates

by responsive
expression profiles

Search by Keywords

Enter keywords (Transcript ID or description)

Search!!

Search results in a table
FC: fold-changes relative to the control samples
FDR: statistical significances of differential expressionsSearch by Responsive expression profile
Set search parameters

Search!!

Specify responsiveexpression pattern

Search results in a tableLinks to other viewers and database
Links to- Genome Browser (GB: GBrowse)- Expression profile view (EPV)- Functional annotation (RAP-DB)- Microarray data (XPro: RiceXPro)- Co-expression gene list (CoExp)

RAP-DB:

RiceXPro:

Functional annotation

Expression data by Microarray

Quick overview of expression profiles

By hovering the mouse cursor over,
You can quickly overview expression profiles

Quick overview of expression profiles

By clicking
or the thumbnail image,
You can get the details of the expression profile
in expression profile view (EPV)Expression profile view (EPV)

Sample condition and expression level are appeared,
when hovering the mouse cursor over each bar

Functions in Expression profile view

You can select sample conditions
to be displayed in the bar plot

Functions in Expression profile view

A list of co-expressed transcripts

By clicking, you can get
the list of co-expressed transcripts

PCC: Pearson’s correlation of coefficientA list of co-expressed transcripts

Genome Browser (GBrowse)
Annotated transcripts in RAP-DBand unannotated transcripts
predicted by RNA-Seq datacis-regulatory elements
within the 1kb promoter regions

Transcriptional activity atsingle nucleotide resolution
under the 140 conditions

GBrowseGenome Browser (GBrowse)
By hovering the mouse cursor over the transcript structures,
you can quickly overview expression profiles along the chromosome.

cis-regulatory elements within 1kb promoter regions

Download data Expression profile data (tab-delimited text file)
Normalized RPK values for annotated and unannotated transcripts
under various conditions.

mRNA-Seq based unannotated transcripts (GFF, GTFand FASTA files)
Exon-Intron structures and sequences of Cufflinks and PARPNTE
predicted transcript that are not annotated in RAP-DB.

 cis-regulatory elements (GFF file)
PLACE cis-regulatory elements in 1-kb promoter regions of eachtranscript.

 Gene prediction program PARPNTE (JAR file)mRNA-Seq and HMM based gene prediction program written in Java

Poster@PAG

URL http://tenor.dna.affrc.go.jp

MONDAY, JANUARY 11
10:00 AM - 11:30 AM

P0320

Kawahara Y. et al.
PaperPlant Cell Physiol. 2015