KEGG Pathway Analysis  

KEGG PATHWAY    by KEGG  

• KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway is a database based on the data of molecular interaction and reaction networks pathway regarding metabolism, genetic information processing, environmental information processing, Cellular Processes, Organismal Systems, Human Diseases.
• The result of KEGG viewer is given with the following analysis steps.
1) In KEGG Viewer, genes are selected based on differential expression gene of each RNA-seq / microarray samples. These genes are mapped to according gene of each map.
2) Enrichment map score is calculated using number of genes that are ID mapped to each map and number of genes that are relevant to the map. Enrichment information of each analysis combination can be checked.
3) Each reference pathway map can be checked by selecting part of pathway in the KEGG map enrichment heat map.
4) You can check not only the different level of expression within the samples, but also meaningful expression difference of genome set with color information.

KEGG viewer

1) KEGG viewer provides pathway information by using 'HTML source tag'.
2) Among these pathway information, Global and overview maps of metabolism provide pathway information by using 'ATlas' which is based on web image of the database.
3) DB version used in the KEGG viewer and the current DB version may vary which can delete map of Metabolism or cause disfunction.

KEGG pathway enrichment map test

help

1	· Differential expression gene combinations.
2	· Metabolism, Cellular process, Environmental information processing, Genetic information processing, Organismal system
3	· Categorized pathway map
4	· Pathway map name
5	· KEGG enrichment map score(p-value) heat map     · empty = none mapped gene
6	· Following information are separated with comma and can be checked by putting mouse over.     · Combination information     · Pathway name     · KEGG enrichment map score (p-value)
7	· New Window pops up when Color box is clicked.

- Global and overview maps is not directly drawing the data saved from HTML. It directly shows genes from KEGG homepage.
   This may slow down the loading time.

KEGG pathway map

help

8	· Fold change values of DEG are shown in colors.
9	· You can change to different combination within the current KEGG pathway page. The combination shown in the box is currently shown combination.
10	· Significant pathway module is marked with star (data3 file of DEG result).
11	· The name and fold change value of the gene are shown when mouse is over. (genes are separated with comma).     · If the gene id exists but there is no FC value on the title of module, then the gene does not exist in data2 file.
12	· Green color boxes of pathway map are modules that are not mapped.     · Gene is in the pathway map but the expression is not shown.
13	· White boxes of pathway map are module that are not relevant to the species.