Question: Using microarray re-annotation to combine array and Chip-Seq data
gravatar for 2323982403
16 months ago by
23239824030 wrote:

I'm using the mouse Clarium D array from affymetrix to compare the differentially expressed mRNAs and lncRNAs. However, the lncRNAs annotated in the array are from different databases, such as ensembl, noncode, vega and But I want to get a consensus annotation, like ensembl, because I want to combine the microarray data with Chip-Seq results. I want to identify the differentially expressed lncRNAs that are also regulated by my target transcription factor.

My problem is, Chip-Seq can provide a common identifier like ensembl, but the lncRNA annotations are from different database, making it impossible to compare the two sets.

I have one solution, that is to re-annotate the probes from the array, by mapping all the probes to the Gencode mouse genome assembly, and then get a common ensembl annotation. Is that feasible for the mouse Clarium D array? Could anybody give any suggestions?

ADD COMMENTlink written 16 months ago by 23239824030

Can anybody give me suggestions?

ADD REPLYlink written 16 months ago by 23239824030
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1101 users visited in the last hour