PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017
An unified expression platform that makes tomato a suitable model for exploring plant-environment interactions
Mohamed Zouine (GBF, UMR990 INRA/INPT)
Toulouse, France
PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017
Tomato RNA-Seq Data Search
SRA30 projects, 222 conditions, 755 samples (.fastq sequence files)
Plant and fruit Development, Tomato mutants, Hormones treatments , Biotic interactions…
Issues:✓ Different software and parameters for RNA sequences
mapping ✓ Different statistical methods for data normalization
Need for an unified pipeline
PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017
TomExpress pipeline
Fastq(FTP)
Public data
(ENA)
Projects/Samples (Annotation download)
Quality Control(fastQC)
Projects/Samples (Manual curation)
Alignment(TopHat/Bowtie)
Counting(HTSeq-count)
Normalization
Database integration(SQL)
Private data
(Apache, HTML, perl, PHP, R)
PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017
Depth and mapping statistics
Million of reads
755 illumina RNA-seq sequence files (.fastq)
~ 90% mapped on the reference genome~ 80% mapped on the iTAG gene models
16
PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017
TomExpress, a unified ressource to:
• Store the Normalized expression data of the 34,727 tomato genes in 222 conditions.
• Visualize expression profile of a gene in chosen conditions
• Compare expressions between genes
• Create Heat maps of Hierarchical clustering of expression values
• Identify Co-expressions for correlation networks study
TomExpress web portal
PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017
The web portal
PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017
PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017
PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017
RIN
Fruit specific expression : RIN
PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017
PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017
In planta expression data vizualisation
PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017
Solyc05g012020: MADS-box transcription factor RIN
PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017
Reference genes for Q-PCR
Ubi
PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017
Ubi and Actin expression profiles
Actin
Ubi
PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017
Good candidate for Q-PCR in fruit development
Solyc04g008380: GAGA-binding transcriptional activator
PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017
PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017
Hierarchical clustering heatmap
PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017
PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017
Heatmap of correlation values
Co-expression networks
Co-expressions identification
PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017
Web site Access
http://gbf.toulouse.inra.fr/tomexpress
PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017
Acknowledgments
GBF, INRA/INPT, Toulouse France:
• Elie Maza
• Anis Djar
• Pierre Frasse
• Mondher Bouzayen
• Mohamed Zouine