The 57th Annual Meeting of the Japanese Society of Plant Physiologists
＠Iwate University, Morioka, JapanThe 12th Database Workshop (March 19, 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, Takeshi Itoh1(1 Agrogenomics Res. Center, NIAS, 2 BITS. Co., Ltd.)What is TENOR?
TENOR (Transcriptome ENcyclopedia Of Rice)
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. 2016 57 (1):doi: 10.1093/pcp/pcv179

Funding
This work was supported by a grant from the Ministry of Agriculture, Forestryand Fisheries of Japan (Genomics for Agricultural Innovation, RTR1001).

2 / 36TENOR provides rice transcriptome data
under 10 abiotic stress and 2 plant hormone
treatment conditions (+ no treatment)

Shoot and Root tissues of Oryza sativa L. ssp. japonica
cv. Nipponbare (seedlings 10 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)
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10 abiotic stresses and 2 plant hormones
Salinity a

Low CdOsmotic

Low Pi b

Very-low Cd

JAHigh Pi b

Drought

ABA

High Cd cFloodCold

No treatment

Previous studies published from our groupa. Mizuno H, Kawahara Y et al. (2010) BMC Genomics
b. Oono Y, Kawahara Y et al. (2011) Ricec. Oono Y, Yazawa T, Kawahara Y et al. (2014) PLoS OneHydroponic cultivation in growth chamber(at 28ºC temperatures, 16h-light/8h-dark cyclewith the light period from 6:00 A.M. to 10:00 P.M.,
and 70-80% relative humidity)

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Features of transcriptome data in TENORAll experiments were performed
at a single laboratory
under standardized conditions
using a single analysis platform (mRNA-Seq)••a highly reliable resourcea standard data set

for comprehensive understanding of genome-wide gene
expression under the various conditions
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The TENOR development teamSample & library preparation•••

Youko Oono
Jun Ogata
Takashi MatsumotomRNA-Seq sequencing•••

Harumi Sasaki
Satomi Mori
Hiroyuki Kanamori

DB & software development•••

Yoshihiro Kawahara
Hironobu WakimotoTakeshi Itoh

National Institute of Agrobiological Sciences (NIAS)
Agrogenomics Research Center6 / 36

Features of transcriptome data in TENORUse of mRNA-Seq technique provides- transcriptional activity at single nucleotide resolution- expression profile of unannotated transcripts

This transcript might
be truncatedDistribution of mRNA-Seq reads
on Genome browser
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Features of transcriptome data in TENORUse of mRNA-Seq technique provides- transcriptional activity at single nucleotide resolution- expression profile of unannotated transcripts

No RAP-DB
transcript

mRNA-Seq-based
predicted transcripts

Low P, 5d, RootDistribution ofmRNA-Seq reads

Cold, 1d, Root

Drought, 1d, Root
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What is PARPNTEPARPNTE (Training)

PARPNTE, which is our in-house gene
prediction program, integrates alignmentsof mRNA-Seq reads (depth of coverage andsplice junction) and a HMM-based algorithm
for prediction of transcript structures andcoding sequences.

PARPNTE (Prediction)

Program

Transcripts

LociMulti-exon
transcripts

BaseSn Sp

ExonSn Sp

IntronSn Sp

PARPNTE

48,366 38,228

30,293

51.2

64.1

52.4

58.9

70.1

80.6

Cufflinks

45,415 30,617

30,249

59.0

50.8

49.1

54.2

69.3

79.5
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Statistics of annotated and unannotated genes

No. of loci

Mean transcript
length (bp)

Mean no. ofexons

Mean exp. level(RPK)- with mRNA evidence

35,4691,580.0

912.0

4.3

327.9

- ab initio pred. with EST

2,400

1,067.0

1,067.1

3.0

59.2

RAP-DB predicted genes

8,121

541.3

541.3

1.6

4.7

742

2,069.1

552.8

2.3

40.1

- PARPNTE non-coding

2,274

1,281.2

–2.0

48.5

- Cufflinks genes

1,263943.4

–

1.8

22.5

Category

Mean CDS
length (bp)

RAP-DB representative genes

Unannotated genes- PARPNTE protein-coding

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Functions in TENORGoogle search for TENOR

URL

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

12 / 36Three entrances on the top pageby Keywords

by Genomic
coordinates

by Responsive
expression
profiles13 / 36

Search by Keywords
SPX genes play importantroles in phosphorus
signaling network
regulating root growth andphosphorus homeostasis

Enter keywords(transcript ID/description)

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Search results
Conditions

FC: fold-changes relative FDR: statistical significances
to the control samples

of differential expressions 15/ 36

Three entrances on the top page

by Responsive
expression
profiles16 / 36

Search by responsive expression profile
Set searchparameters

Specify responsive
expression patterns

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Phosphate starvation induced genes

Pi transporters

SPX genes

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Links to other DB & viewer

GB: Genome Browser
EPV: Expression Profile Viewer
RAPDB: Rice Annotation Project DB (RAP-DB)
XPro: RiceXPro
CoExp: List of co-expressed genes19 / 36

Expression Profile Viewer (EPV)

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

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Expression Profile Viewer (EPV)

Output: PNG, Table View and CSV
Change scale: logarithmic/arithmetic

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Genome Browser (GBrowse)

Transcripts
cis-regulatory elements

distribution ofmRNA-Seq reads

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Genome Browser (GBrowse)

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Genome Browser (GBrowse)

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Genome Browser (GBrowse)

Link to GBrowse: http://tenor.dna.affrc.go.jp/gb2/gbrowse/rnaseq_db/?chr06:12,679,000..12,713,999

25 / 36cis-regulatory elements in 1kb upstream regions

26 / 36cis-regulatory elements in 1kb upstream regions

27 / 36cis-regulatory elements in 1kb upstream regions

28 / 36cis-regulatory elements in 1kb upstream regions
Link to PLACE data

29 / 36co-expressed genes

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

30 / 36co-expressed genes

PCC: Pearson’s correlation of coefficient

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Links to external databases

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Link to TENOR in RAP-DB

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Downloadable data files

mRNA-Seq-based predicted transcripts(GFF/GTF/FASTA)

cis-regulatory elements (GFF)

normalized expression profiles (tab-delimited txt)
34 / 36TENOR paper

enriched GO

Similarity of responsive
transcriptome

enriched cis-elements

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Summary

Search by Keywords/responsive
expression profiles

Transcriptional activity atsingle nucleotide resolution
under the 140 conditions
Expression profiles &co-expression information

cis-regulatory element

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