Question: FANTOM gene expression data
0
gravatar for Pappu
11 weeks ago by
Pappu1.8k
Pappu1.8k wrote:

I am looking for FANTOM gene expression data. But I could only find transcript expression in this website: http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_latest/extra/CAGE_peaks_expression/

rna-seq • 177 views
ADD COMMENTlink modified 11 weeks ago by Kevin Blighe9.3k • written 11 weeks ago by Pappu1.8k
1
gravatar for Kevin Blighe
11 weeks ago by
Kevin Blighe9.3k
London
Kevin Blighe9.3k wrote:

I previously downloaded from here http://fantom.gsc.riken.jp/5/datafiles/latest/extra/CAGE_peaks/, as recently as just a few months ago, and they have expression data over genes.

The FANTOM5 data has different promoter expression levels for each gene (CAGE, used by FANTOM, doesn't measure mRNA levels as per RNA-seq and instead measures the 5' cap mRNA, i.e. promoter activity and the transcription start site), generally going from p1-p4. p1 is the peak with the strongest signal and it is recommended to take that. It is a risky idea to average over the promoter expression levels because many genes will have 0 expression at p2-p4 (hint: you could try averaging over only those peaks that have non-zero expression).

ADD COMMENTlink modified 11 weeks ago • written 11 weeks ago by Kevin Blighe9.3k
1

Yes averaging gives weird result as many transcript expression is zero. I just took a sum of transcripts expression for each gene.

ADD REPLYlink written 11 weeks ago by Pappu1.8k
1

Summing is a good option too!

ADD REPLYlink written 11 weeks ago by Kevin Blighe9.3k
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