A Unified Expression Platform That Makes Tomato Suitable Model For Exploring Plant-Environment Interactions
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The document discusses the Tomexpress pipeline, a unified platform for analyzing tomato RNA-seq data to explore plant-environment interactions, presenting data from 30 projects across 222 conditions. It enables storage, visualization, and comparative analysis of expression data for over 34,000 tomato genes, addressing challenges in data mapping and normalization. The Tomexpress web portal facilitates these processes and allows for in-depth co-expression network studies.
A Unified Expression Platform That Makes Tomato Suitable Model For Exploring Plant-Environment Interactions
- 1. 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
- 2. PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017 Tomato RNA-Seq Data Search SRA 30 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
- 3. 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)
- 4. 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
- 5. 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
- 6. PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017 The web portal
- 7. PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017
- 8. PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017
- 9. PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017 RIN Fruit specific expression : RIN
- 10. PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017
- 11. PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017 In planta expression data vizualisation
- 12. PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017 Solyc05g012020: MADS-box transcription factor RIN
- 13. PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017 Reference genes for Q-PCR Ubi
- 14. PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017 Ubi and Actin expression profiles Actin Ubi
- 15. PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017 Good candidate for Q-PCR in fruit development Solyc04g008380: GAGA-binding transcriptional activator
- 16. PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017
- 17. PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017 Hierarchical clustering heatmap
- 18. PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017
- 19. PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017 Heatmap of correlation values Co-expression networks Co-expressions identification
- 20. PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017 Web site Access http://gbf.toulouse.inra.fr/tomexpress
- 21. 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