Multiple Experiment Comparison

The "Multiple Experiment Comparison" function collects gene expression profiles from publicly published RNA-seq data in the SRA database, allowing users to query the expression of any gene in all included transcriptome data. In this project, Sapbase have normalized the transcriptomic data using the Transcripts Per Million (TPM) method. TPM is a commonly used metric for gene expression that effectively eliminates the influence of sequencing depth and transcript length, allowing for direct comparisons of expression levels across different samples and genes.

Multiple Experiment ComparisonMode 1: Single gene queryMode 2: Multi-gene searchDownload histogram or heatmap

Mode 1: Single gene query

In mode 1, the user can specify any Sapindaceae species to be queried and enter the corresponding Gene ID to query its expression in all transcriptome data.

Example of Gene ID format:


x
Litchi: LITCHI002021
Longan: Dil.09g019490
Rambutan: Nl01g14020
Yellowhorn: EVM0009016
Acer: Acyan11G0132000
Soapberry: whz_017298-RA

single_expression_search_demo

The search results display the expression of genes in different tissues or treatments in the form of study. For different study, the corresponding topics and abstracts of experimental contents are showed. In addition, two links are provided, which can jump to NCBI to browse the detailed introduction of the research project and the detailed information of each sample. Finally, histogram were used to interactively visualize gene expression in each sample, allowing users to obtain gene expression more intuitively.

Animation display of mode1

search_by_SRP_single

Mode 2: Multi-gene search

In mode 2, users can specify any Sapindaceae species to be queried and input the corresponding gene set, one gene per line, to query the expression of all genes in all transcriptome data.

Example of Gene set format (Note: one gene per line):


xxxxxxxxxx
LITCHI002020
LITCHI002021
LITCHI002022

The search results display the expression of genes in different tissues or treatments in the form of study. For different study, the corresponding topics and abstracts of experimental contents are showed. In addition, two links are provided, which can jump to NCBI to browse the detailed introduction of the research project and the detailed information of each sample. Finally, an interactive heatmap is used to display the expression of the gene set. Mouse over to display specific gene expression values.

Animation display of mode2

search_by_SRP_multiple