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Pathway Enrichment Analysis Advanced

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Pathway Enrichment Analysis使用教程

To understand the principle and detailed analysis of the tool, please click >>

 

Principle:

 

In organisms, different genes coordinate with each other to perform their biological functions. Pathway-based analysis helps to further understand the biological functions of genes. KEGG is the main public database about Pathway. Pathway significant enrichment analysis takes KEGG Pathway as the unit, and applies hypergeometric test to find pathways that are significantly enriched in differentially expressed genes compared with the background of the entire genome.

Calculation formula of P:

Among them, N is the number of all genes (background genes), n is the number of differential genes (target genes), M is the number of this pathway in all genes, i is the number of differential genes annotated to the pathway, calculated pvalue After the FDR is corrected, the corrected-pvalue≤0.05 is used as the threshold. The pathway that meets this condition is defined as the pathway that is significantly enriched in the differentially expressed genes.

 

Function:

 

Input gene set or differential analysis gene set, through preset parameters, perform KEGG enrichment analysis and visualize the analysis results with exquisite graphics. The output graphics include enrichment classification bar chart, enrichment bubble chart, enrichment bar chart, Enrichment circle graph, z-score bubble graph, kegg network graph.

 

Input:

 

① The input form file must be in txt format. You can choose to open the data in excel and save it as a "text file (tab delimited) (*.txt)".

 

② The enriched target gene list, that is, the gene list that you want to study, the first column of each row is the gene id, which should be included in the background gene table. Note that this file does not need to add a row name. Note that the first line of this file is not the line name of the text description, it is directly the specific gene ID number. Please check the example file format.

 

③ Background gene summary table, that is, a list of all genes. The first column is the gene id, and the second column is an id used to obtain the pathway. There are 3 types:

Type 1: kegid, such as mmu:18053, which is the id on KEGG official website, which can be obtained through KEGG annotation or KEGG official website.

Type 2: ncbi-geneid, such as 18053, which is the geneid obtained on ncbi, composed of a series of numbers.

Type 3: KO number, such as K10942. The same KO number between different species will correspond to different pathways. For details, please check the KEGG official website. Obtaining the pathway directly through the KO number will be inaccurate. It is recommended to obtain through the first two types.

Type 4: Type 4, kopath, the type file provided by the company, the first column is the gene id, the second column is the KO number, the third column is the pathway number, separated by ",", and the fourth column is the kegid.

 

④ (Optional) Gene differential expression multiple table: the first column is the gene ID, and the second column is the differential expression multiple log2 (FC).

 

Tip: If you do not enter the gene differential expression multiple table, the enriched differential z-score bubble chart will not be output.

 

Parameter:

 

① There are 3 types of background gene tables, namely: KO, ncbi-geneid, and KEGGid.

② Database: When the background gene table type is keggid and ncbi-geneid, both the corresponding species library and the full library can be selected, but selecting the corresponding species library can shorten the running time; when the background gene table type is KO type, it is recommended to select the corresponding species Annotate the library.

③ Optional parameters: add a table of differential gene expression differences.

 

Output:

 

① out.path.xls: The enrichment statistics table of the target gene relative to the background gene.

② out_map: The result map of the target gene in each pathway map.

③ out.path.png/svg: B-class statistical diagram of each pathway (png/svg format).

④ out.barplot/gradient.png/pdf: bar graphs and bubble graphs of the first 20 significant enrichment pathways (png/pdf format).

⑤ out.bubble/bubble_sp.png/pdf: z-score bubble chart of the first 20 significantly enriched differential pathways (png/pdf format).

⑥ out.circular.png/svg: Circle diagram of the first 20 significantly enriched differential pathways (png/svg format).

⑦ out.bar_Gradient.xls: Draw the enrichment circle map file, which can be used for personalized modification in the dynamic enrichment circle map tool.

⑧ out.edge.txt and out.node.txt: Use these two files to draw kegg network diagram in Cytoscape tool. (Including supplementary connection pathways and supplementary adjacent pathways) (see kegg network diagram for details)

⑨ Click "Preview" in my running window, you can make personalized modification to the kegg network diagram. (Users who don't know this function can refer to the kegg network diagram) (Note: This function is not in the output file, you need to adjust it yourself to output graphics in png/svg format)

⑩ out.htm: webpage format result.

 

To interpret and apply the enrichment analysis graphics, please click the link to view the details:

Come and receive a full set of enrichment analysis related graphics details! (Part 1)                                                                                                                                                         

Come and receive a full set of detailed enrichment analysis related graphics! (Part 2)

 

 

Sample file:

                Enriched target gene list(not include differential gene multiple list)

                Enriched target gene list(include differential gene multiple list)

                 Background gene list     

     

 

 

Output:

 

① out_map: The result map of the target gene in each pathway map

 

 

② out.bubble/bubble_sp.png/pdf: z-score bubble chart of the first 20 significantly enriched differential pathways

 

 

③ out.circular.png/svg: circle diagram of the first 20 significantly enriched differential pathways

 

 

④ kegg network diagram (this diagram needs to click "Preview" on the task running result page, and customize the path to be displayed to draw the kegg network diagram)

 

 

⑤ out.barplot/gradient.png/pdf: bar chart and bubble chart of the first 20 significant enrichment pathways

 

 

⑥ out.path.png/svg: B-class statistical diagram of each pathway

 

 

⑦ out.htm: The webpage format result is divided into two parts, the above is the enrichment information of the pathway (Figure 1), including the pathway name, gene number, background gene number, P value, Q value, pathwayID, and the following is the specific information of each pathway Gene (Figure 2), click on the pathway name to view the information of the gene in the pathway (Ie ① out_map)

 

                                                                                       Figure 1

 

                                                                                           Figure 2