Enrichment

Report created with Sequana (v0.16.0)

1 - Summary

In the following sections, you will find the KEGG Pathway enrichment. The input data for those analyis is the output of the RNADiff analysis where adjusted p-values above 0.05 are excluded. Moreover, we removed candidates with log2 fold change below 1. Using these filters, the list of differentially expressed genes is made of 15 up and 38 down genes (total 53)

In the following plots you can find the first KEGG Pathways that are enriched, keeping a maximum of 15 pathways.

The KEGG name used is ebe.

This table gives you (column N) the number of genes used when performing the enrichment on up-regulated genes (up), down-regulated genes, and when we take all up and down regulated genes (all). We also provide the total number of genes that were analysed in the differential analysis (all genes). This number may be lower that the number of genes found in the annotation if a filter was applied. Finally, using those genes, we provide the percentage of those genes that were found in the KEGG database. the Enrichment analysis relies on a background. This background was defined as 4600

category,mapped_percentage,N
down,9.736842E+01,38
up,6.666667E+01,15
all,8.867925E+01,53
category mapped_percentage N

2 - KEGG

Here are the enrichment kegg pathways and the number of up and down genes found in each of them.

2.1 - KEGG pathways enriched in down regulated genes

3 KEGG pathways are found enriched using the down regulated genes



pathway_id,name,size,Overlap,Odds Ratio,Combined Score,P-value,Adjusted P-value,Genes,links
ebe00440,Phosphonate and phosphinate metabolism,8,8/8,1.505738E+02,5.895632E+03,9.895613E-18,4.947807E-17,phnG;phnH;phnI;phnJ;phnL;phnM;phnO;phnP,https://www.genome.jp/dbget-bin/www_bget?path:ebe00440
ebe02010,ABC transporters,14,14/175,1.492407E+01,3.594944E+02,3.456317E-11,8.640792E-11,fhuB;fhuC;fhuD;phnC;phnD;phnE;pstA;pstB;pstC;pstS;ugpA;ugpB;ugpC;ugpE,https://www.genome.jp/dbget-bin/www_bget?path:ebe02010
ebe02020,Two-component system,5,5/163,4.455931E+00,2.041719E+01,1.023414E-02,1.705690E-02,cusF;phoB;phoR;pstS;uhpT,https://www.genome.jp/dbget-bin/www_bget?path:ebe02020
pathway_id name size Overlap Odds Ratio Combined Score P-value Adjusted P-value Genes links

Here below are the pathways with gene colored according to their fold change. Blue colors are for down-regulated genes and Orange are for up-regulated genes. (Note that absolute log2 fold change above 4 are clipped to 4; So a gene with a log2 fold change of 4 or 40 will have the same darkest color.).

2.1 - KEGG pathways enriched in up regulated genes

1 KEGG pathways are found enriched using the up regulated genes



pathway_id,name,size,Overlap,Odds Ratio,Combined Score,P-value,Adjusted P-value,Genes,links
ebe00330,Arginine and proline metabolism,2,2/25,3.322803E+01,1.947121E+02,2.851605E-03,1.710963E-02,astA;astC,https://www.genome.jp/dbget-bin/www_bget?path:ebe00330
pathway_id name size Overlap Odds Ratio Combined Score P-value Adjusted P-value Genes links

Here below are the pathways with gene colored according to their fold change. Blue colors are for down-regulated genes and Orange are for up-regulated genes. (Note that absolute log2 fold change above 4 are clipped to 4; So a gene with a log2 fold change of 4 or 40 will have the same darkest color.).

2.1 - KEGG pathways enriched in all regulated genes

2 KEGG pathways are found enriched using the all regulated genes



pathway_id,name,size,Overlap,Odds Ratio,Combined Score,P-value,Adjusted P-value,Genes,links
ebe00440,Phosphonate and phosphinate metabolism,8,8/8,1.009341E+02,3.659587E+03,1.793472E-16,1.793472E-15,phnG;phnH;phnI;phnJ;phnL;phnM;phnO;phnP,https://www.genome.jp/dbget-bin/www_bget?path:ebe00440
ebe02010,ABC transporters,15,15/175,1.015211E+01,2.175769E+02,4.924152E-10,2.462076E-09,fhuB;fhuC;fhuD;phnC;phnD;phnE;pstA;pstB;pstC;pstS;tauA;ugpA;ugpB;ugpC;ugpE,https://www.genome.jp/dbget-bin/www_bget?path:ebe02010
pathway_id name size Overlap Odds Ratio Combined Score P-value Adjusted P-value Genes links

Here below are the pathways with gene colored according to their fold change. Blue colors are for down-regulated genes and Orange are for up-regulated genes. (Note that absolute log2 fold change above 4 are clipped to 4; So a gene with a log2 fold change of 4 or 40 will have the same darkest color.).

3 - Info