Question: Identifying TFs from a list of genes
0
gravatar for snp87
15 months ago by
snp8740
snp8740 wrote:

Hello! Is there a way I can feed a list of genes generated from a RNAseq experiment and find out which ones are transcription factors? This is in mouse. Any help is much appreciated.

rna-seq gene • 595 views
ADD COMMENTlink modified 15 months ago by svlachavas560 • written 15 months ago by snp8740
0
gravatar for svlachavas
15 months ago by
svlachavas560
Greece
svlachavas560 wrote:

Dear snp87,

for a quick exploration, you cold try the enrichr tool (http://amp.pharm.mssm.edu/Enrichr/) and the Transcription section gene-set libraries.

If you want a more detailed and validated approach, as long as you have normalized counts of your RNA-Seq data, you should definately try the R packages CoRegNet (http://bioconductor.org/packages/release/bioc/vignettes/CoRegNet/inst/doc/CoRegNet.html) and TReNA (http://bioconductor.org/packages/devel/bioc/vignettes/trena/inst/doc/TReNA_Vignette.html).

Best,

Efstathios

ADD COMMENTlink written 15 months ago by svlachavas560
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 2.3.0
Traffic: 1957 users visited in the last hour