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Introduction Version

Kegg Visualisation

TASK
Typing name :  TASK.gws_gena.KEGGVisualisation Brick :  gws_gena v

Generate KEGG pathway from a list of genes.

Generates a KEGG pathway using the genes specified in the input.

Please provide a list of genes such as: ,FoldChange Gene1,value Gene2,value

If you don't have gene expression, just provide the gene names with a header. If you want to compare more than one fold change, add the other fold change in the following columns. In the output, each box of the pathway will be separated depending on the number of fold changes. So the colours may be different depending on the condition.

For the specie, you need to provide the kegg.code. You can find the list of allowed values attached to this story: https://constellab.community/stories/e330483b-5b9e-452c-b5a4-f6b62506c9ad/how-to-visualise-a-kegg-pathway-using-constellab#introduction

Organism names are constructed by concatenating the first letter of the name and the family name. Example: human - 'hsapiens', mouse - 'mmusculus'. You can find the complete list here: https://biit.cs.ut.ee/gprofiler/page/organism-list

Be aware that this task can take some time, especially the first time, as a virtual environment has to be installed, and also depending on the length of the genes provided, it can take more time.

In the output you will also get a Table with the pathways where genes are mapped, but these pathways can't be shown with the pathview package.

KEGG is a database resource for understanding high-level functions and utilities of the biological system. Kanehisa Laboratories owns and controls the rights to KEGG. Although the KEGG database is made freely available for academic use via the website, it is not in the public domain. All commercial use of KEGG requires a license. Please ensure that you have licence to use KEGG database.

Input

Genes List
The file or the Table with genes and fold changes.

Output

Pathways KEGG
Pathways KEGG colored.
list_pathway_error
List of pathways in error.

Configuration

genes_database

Optional

The database of the genes.

Type : stringAllowed values : entrez  ensembl  Default value : entrez

organism

Optional

If genes are ensembl genes, please provide the organism studied (see documentation)

Type : string

specie

The specie studied.

Type : string

email

Optional

Your email to use NCBI.

Type : stringDefault value : your email here

fold_change

Optional

Does the file contain the fold change of gene expression?

Type : stringAllowed values : No  Yes  Default value : No