Question: [clusterprofiler] Transformation from ENSEMBL ID to entrez ID or Symbol got reduced number of genes
0
gravatar for tenger929
3 months ago by
tenger9290
tenger9290 wrote:

Dear, It is convenient to use clusterprofiler in enrichment analysis. However, there is a problem confusing me in ID transformation.

I have a gene list containing 39570 genes with ensembl ID.

1. After transformation with bitr function from Ensembl to entrez ID, the number of genes is 22142, 44.39% of input gene IDs fail     to map.

2. Transformation with bitr function from Ensembl to Symbol,  the number of genes is also 22142, however, it contains duplicates.       After removing duplicates, the number of genes is 22103.

I don't know why it happened. Any help will be greatly appreciated!

Thanks a lot.

clusterprofiler • 142 views
ADD COMMENTlink modified 3 months ago by James W. MacDonald49k • written 3 months ago by tenger9290
Answer: [clusterprofiler] Transformation from ENSEMBL ID to entrez ID or Symbol got redu
0
gravatar for James W. MacDonald
3 months ago by
United States
James W. MacDonald49k wrote:

Converting IDs from one annotation service to another is a fraught process. EBI/EMBL and NCBI use different criteria to say what is and isn't a gene, and it is not uncommon to lose a significant proportion of your annotations when converting from one to the other. The best course of action is to stick with one or the other through the entirety of your analysis.

ADD COMMENTlink written 3 months ago by James W. MacDonald49k

Thanks for your kindly reply.

My RNAseq (mouse species) was obtained from strand specific RNA library,and we got gene list with Ensembl ID by DESeq2. In enrichment analysis by clusterprofiler developed by Prof. Yu.,Entrez ID is prefered. I have no idear why so large proportion of genes are unmapped during ID transformatiom from Ensembl to Entrez.

ADD REPLYlink written 3 months ago by tenger9290
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 206 users visited in the last hour