KEGG Pathway

How can I calculate the KEGG pathways and GO P-values. Moreover, I would like to know which site can provide the miRNA - mRNA interaction map?

Kind Regards

micro rna

• 997 views • link

updated 4.5 years ago by rpolicastro

• written 4.5 years ago by b85_assil •

1 answer

The R bioconductor package clusterProfiler (vignette) allows for both KEGG and GO enrichment (and GSEA).

• 0 views • link

written 4.5 years ago by rpolicastro

More posts like this

lncRNA-miRNA interaction
written 2.8 years ago by ziyan •

I want to predict lncRNA-miRNA interaction, so can I use TargetScan which is usually used for predicting mRNA-miRNA interaction, and can I consider full length …
RNA interaction network analysis
written 4.5 years ago by Archit •

Hi. So I have performed differential expression (DE) for mRNA, miRNA, and lncRNA of a control and a cancer cell line. I have one file …
Finding differential subpathways of metabolic networks using RNA-seq data
written 4.7 years ago by Benedek Dankó •

I would like to find a good approach or R/Python package that would help me to find differential subpathways of selected KEGG metabolic pathways. As …
Gene list to Metabolic pathways,
written 8.3 years ago by Leite

I have a gene list with different expression values, I would like to know if there is any method based on a gene list that …
How to extract known pathways from protein protein interaction network?
written 8.7 years ago by jack

Hi, Given physical protein protein interaction like String and KEGG pathway. I would like to know how many of KEGG pathways or signaling pathways exist …
map lipid chemical formula to KEGG pathways
written 9.7 years ago by TriS

I have a list of chemical formulas for lipids that read like: C18H30O2 C18H34O2 C18H36O2 etc... and I would like to map them on KEGG …
miRNA Target Site prediction from unpaired data
written 10.4 years ago by hAjmal •

Hello Everyone, I am a computer scientist and started working with a group of researchers working in bioinformatics.I have little or no background of genomics. …
Integrated miRNA-mRNA expression pipeline
written 11.5 years ago by orzech_mag

Hallo! I would like to get some advice or recommendations from you about the integrated miRNA-mRNA analysis pipeline. Here is what I would like to …
Are Bioconductor Packages Designed For Enrichment Analysis Affected By Kegg Privatization ?
written 15.0 years ago by Radhouane Aniba

<p>Hi,</p> <p>Some bioconductor packages like GSEA or GOStats that additionally to GO are designed to measure gene set enrichment using KEGG pathways, still work and …
Any Experience With Using Or Building Pathways Containing Micrornas?
written 15.4 years ago by Larry_Parnell

<p>I would like to hear of your experiences or suggestions concerning the incorporation of microRNA entities into pathway information. I am not interested in Miranda, …