Question: Identifying TFs from a list of genes
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gravatar for snp87
8 months ago by
snp8730
snp8730 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 • 377 views
ADD COMMENTlink modified 8 months ago by svlachavas450 • written 8 months ago by snp8730
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gravatar for svlachavas
8 months ago by
svlachavas450
Greece
svlachavas450 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 8 months ago by svlachavas450
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