OmicShare Tools - 基迪奥生信云工具

Instructions
Example

Pathway enrichment analysis tool to use and interpret detailed tutorial

function：
KEGG pathway enrichment analysis provides not only pathway functional annotations of given gene set, but also pathway enrichment analysis. First, Gene numbers of each pathway in a given gene set is calculated. Then significantly enriched pathways in the given gene set comparing to the genome background are defined by hypergeometric test. The calculating formula of P-value is:

Here N is the number of all genes with KEGG pathway annotation; n is the gene number of given genes set in N; M is the number of all genes that are annotated to the certain pathway; m is the gene number in the given gene set that are annotated to the certain pathways. The calculated p-value is gone through FDR Correction, taking FDR ≤ 0.05 as a threshold. Pathways meeting this condition are defined as significantly enriched pathways in the given genes set.

Scope of application:

The gene sets of 18 common species can be enriched and analyzed, including bovine, zebrafish, human, macaque, mouse, rat, pig, elegans, drosophila, Arabidopsis, rice, tomato, wheat, corn, yeast, goat, chicken and indica rice, and 2 genomic versions are provided.

The background genes of the species can also be prepared by themselves for enrichment analysis.

Input：

①File format: a tab delimited text file. If your data is not TAB delimited, you can use Excel to convert it.

②Gene set: genes need enrichment analysis. Gene IDs must be separated by new lines and included in the background set. Notice that the file contains only true Gend ids, please check it on the example file.

③Background set: The gene list of background set, usually it's all genes of a genome. The first column is gene id, the second column is gene annotation id. There are three kinds of ID type available: keggid, ncibi-geneid, KO id.

④Gene expression fold change file: the first column is gene names, and the second column is log2 Fold Change value.

1.总览

2.Results statistics

3.statistical graph

4.Senior Bar graph

5.Senior Bubble plot

Results statistics
Function	Display the results of gene enrichment and provide screening
Operating Instructions	1. You can search by Pathway、Pathway ID、KEGG B class 、KEGG C class、Gene ID. 2.You can filter by Pvalue and FDR value. 3. The selected results can create gene sets;In addition, each row in the table can be selected in the first column to create the gene set. 4. Click the name of Pathway in the "Pathway" column in the table to connect to the corresponding Pathway page in the KEGG website.A download button is provided next to the pathname in the table to download the map.

Results statistics

Function

Display the results of gene enrichment and provide screening

Operating Instructions

1. You can search by Pathway、Pathway ID、KEGG B class 、KEGG C class、Gene ID.
2.You can filter by Pvalue and FDR value.
3. The selected results can create gene sets;In addition, each row in the table can be selected in the first column to create the gene set.
4. Click the name of Pathway in the "Pathway" column in the table to connect to the corresponding Pathway page in the KEGG website.A download button is provided next to the pathname in the table to download the map.

statistical graph
Function	The number of genes exhibited in KEGG pathway
Operating Instructions	1.Figure interpretation: the black font in the ordinate indicates KEGG A class,the colored font in the ordinate indicates KEGG B class, and the abscissa is the number of genes on the corresponding B class. 2.The corresponding statistical tables can be downloaded 3.You can select the pathway to draw by checking the box in the table below

statistical graph

Function

The number of genes exhibited in KEGG pathway

Operating Instructions

1.Figure interpretation: the black font in the ordinate indicates KEGG A class,the colored font in the ordinate indicates KEGG B class, and the abscissa is the number of genes on the corresponding B class.
2.The corresponding statistical tables can be downloaded
3.You can select the pathway to draw by checking the box in the table below

Senior Bar graph
Function	The figure was used to show the pathway of significant enrichment
Operating Instructions	1. Figure interpretation: the x-coordinate is pathway, and the y- coordinate is -log10 (Pvalue) 2. You can use the P value or Q value to filter and then draw the graph 3. You can selecte the top N terms to draw the graph 4. You can select the pathway to draw by checking the box in the table below

Senior Bar graph

Function

The figure was used to show the pathway of significant enrichment

Operating Instructions

1. Figure interpretation: the x-coordinate is pathway, and the y- coordinate is -log10 (Pvalue)
2. You can use the P value or Q value to filter and then draw the graph
3. You can selecte the top N terms to draw the graph
4. You can select the pathway to draw by checking the box in the table below

Senior Bubble plot
Function	A bubble plot was used to show the pathway of significant enrichment
Operating Instructions	1. You can use the P value or Q value to filter and then draw the graph 2. You can selecte the top N terms to draw the graph 3. You can select the pathway to draw by checking the box in the table below

Senior Bubble plot

Function

A bubble plot was used to show the pathway of significant enrichment

Operating Instructions

1. You can use the P value or Q value to filter and then draw the graph
2. You can selecte the top N terms to draw the graph
3. You can select the pathway to draw by checking the box in the table below