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xGSEAdotplot





choosefile   example


choosefile   example





1. Function: According to the analysis result of the GSEA enrichment tool on the OmicShare platform as the input of the xGSEAdotplot tool, select significant gene sets to draw xGSEAdotplot.

Note: This tool is used in conjunction with the platform GSEA enrichment analysis tool. If you want to use this tool, you need to use the GSEA enrichment tool for enrichment analysis.

 

GSEA enrichment tool link: (click the blue text to jump)

GSEA          report_gsea

2. Input file:

File format: The input file must be a tab-delimited .txt format file with a header. The table name is composed of letters, numbers, and underscores, and the hyphen "-" cannot be used.

 

(1) Summary table after GSEA analysis:

The red dashed box is the total table after GSEA analysis. You can select which gene set in the database you want to draw. Note that the xls format file should be saved as a txt format separated by tabs.

 

The file format after opening the summary table is as follows:

 

id

name

SIZE

ES

NES

NOM p-val

FDR q-val

Genes

 

 

 

 

 

 

 

 

 

For example:

 

(2) Open the next level folder after GSEA analysis, select the significantly enriched gene set file, and use it as input.

Open the next level folder after GSEA analysis enclosed by the red dotted frame.

 

The content of the opened file: (The red box is the details of each database. For example, if you want to draw CHR1P13, you can use this file as the second data file of the OS tool.)

 

Find the file you want to draw, the format is as follows:

NAME

PROBE

DESCRIPTION
(from dataset)

GENE SYMBOL

GENE_TITLE

RANK IN GENE LIST

RANK METRIC SCORE

RUNNING ES

CORE ENRICHMENT

 

 

 

 

 

 

 

 

 

 

For example:

 

3. Output file:

Click "Download" in "My Tasks" to get the graphics.

 

The following figure is the output file, the most important .pdf and .png are the output results. (Others are program running information and can be ignored)

 

 

Result graphics:

 

4. Interpretation of results:

 

The peak in the figure divides the curve into two sides.

 

The first side is called leading edge, and the genes on this side are called leading targets. These genes are also genes worth exploring.

 

The graphic title has 3 lines, the first line is the name of the data set; the second line describes the leading edge analysis information; the third line describes the enrichment score ES information.

 

The abscissa is Target ranks, which represents the ranking of Targets.

 

The ordinate is the enrichment score.

 

 

 

For more detailed case application interpretation, please click the forum article: Comprehensive and detailed GSEA enrichment analysis graphic interpretation and case application

 

Note: First use the output of the GSEA enrichment analysis tool on the OmicShare platform as the input of the xGSEAdotplot tool.

 

1. Input file:

 

 

File format: The input file must be a tab-delimited .txt format file with a header. The table name is composed of letters, numbers, and underscores, and the hyphen "-" cannot be used.

(1) The summary table after GSEA analysis: (use the enrichment results of KEGG for display) Sample file one

 

 

The format of the sample file after opening is as follows:

 

The gene sets with |NES|> 1, NOM p-val <0.05, and FDR q-val <0.25 were screened from the GSEA enrichment analysis summary table as significant gene sets.

Therefore, the output demonstration file of GSEA_term of this tool uses the first path (KEGG_SPLICEOSOME in the dashed box in the figure).

 

 

(2) Open the next level folder after GSEA analysis, select the significantly enriched gene set file, and use it as input. Sample file two

 

2. Output:

Click "Download" in "My Tasks" to get the graphics.

The following figure is the output file, the most important .pdf and .png are the output results. (Others are program running information and can be ignored)

 

 

Result graphics:

 

Graphic interpretation:

 

The peak in the figure divides the curve into two sides, and the peak position is at rnk=6828.

 

The first side is called leading edge, and the genes on this side are called leading targets. These genes are also worth exploring. For example, there are 18 significant genes such as U2AF2, PPIE, and 48 genes that are not significant. In total, they are enriched on this pathway. 18+48=68 genes.

 

The graphic title has 3 lines, the first line is the name of the data set or pathway; the second line describes the leading edge analysis information, indicating that the pathway is significant; the third line describes the information of the enrichment score ES, which describes the peak position and the significant gene Number, the number of insignificant genes.

 

The abscissa is Target ranks, which represents the ranking of Targets.

 

The ordinate is the enrichment score.