Winberige

Bioinformatics for grape genus (Vitis L.)

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RNA

RNA-seq processor:
Based on NCBI SRA database.
Aim to explore gene expression and intron splicing.

-seq  processor:



The genome and annotation files of V2.4 in EnsemblPlants were used.
Keyword mode:
Grape V2.4 gene ID, get expression and splicing summary. e.g. Vitvi15g01539 (All = 34965)
Project, get basic Information. e.g. PRJNA638227 (All = 283)
NCBI SRA Run, get basic Information. e.g. SRR11963070 (All = 8345)
Treatment vs control ID defined by this website. e.g. pair940 (All = 1366)
Treatment description, similar to selection mode in this page. e.g. Cold, Amurensis, Merlot, Bud, Acclimation
Input:
Selection mode:
Abiotic stress and simple environment (966 samples, 249 comparisons)
Light   Temperature   Water   Osmotic   pH   Air  
Biotic stress, disease, disorder and wounding (1119 samples, 214 comparisons)
Bacterium   Disorder   Fungus   Insect   Oomycetes   Phytoplasma  
Virus   Wounding   Yeast  
Hormones or chemicals (573 samples, 139 comparisons)
1-MCP   4-HBA   5-AZA   ABA   Acibenzolar-S-methyl   BR   BRZ   CaCl2   CPPU  
Cyanamide   DIECA   ETH   Fosetyl-aluminum   GA   Heavy metal   IPT   JA  
K3PO4   Melatonin   Metiram   Nitrogen   NAA   NaN3   NBD   NDGA   SA  
STE   Sucrose   Vitamin   Zebularine  
Agricultural measures and complex environment (575 samples, 114 comparisons)
Biocontrol products   Cluster bagging   Deficit irrigation   Double Cropping   Leaf moving  
Leaf removal   Nitrogen supply   Root restriction   Rootstock   Shade  
Growth and development (Normal) (2370 samples, 600 comparisons)
Berry development   Berry flesh development   Berry seed development  
Berry skin and flesh development   Berry skin development   Bud/stem development  
Flower/inflorescence development   Leaf development  
Growth and development (Special) (208 samples, 39 comparisons)
Berry flesh color   Berry skin color   Bioclock   Cluster shape   Fruit shape  
Leaf shape   Parthenocarp   Polyploidy   Regenerative ability   Seedeed and seedless  
Overexpression  
Sample source (5870 samples, 1366 comparisons)
berry & seed   bud & stem   callus & suspension cell   flower & inflorescence  
leaf & petiole   root & root border cell   whole organism  
Calculation mode:
Only SRA runs from published RNA-seq data were supported.
Control SRA Runs
Treatment SRA Runs