Question: Differential lncRNA-mRNA co-expression
1
gravatar for hana
3.0 years ago by
hana170
Malaysia
hana170 wrote:

Hi

I have 3 High-throughput RNA-Seq samples from patients with rare disease and 3 samples from healthy subjects. I have identified the differentially expressed lncRNA and coding-genes between patients and control subjects. I would like to predict the function of identified differentially expressed lncRNA based on the expression of coding genes. What is the best method for this goal ?

I found that one way is to calculate the Pearson's correlation coefficient (PCC) between the expression values of each of the lncRNA-mRNA pairs.

I would like to know is this approach valid for my sample size ( 3 patients) ?

Should I just calculate the Pearson correlation confidence base between the expression values of each of the lncRNA-mRNA pairs only across patients samples?

Thanks

rna-seq • 2.4k views
ADD COMMENTlink modified 11 months ago by geek_y9.4k • written 3.0 years ago by hana170

you can do like this

ADD REPLYlink written 3.0 years ago by Yan Li0
1

yan i think you forgot link

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by kanwarjag960

Would you please send the link

ADD REPLYlink written 3.0 years ago by hana170

Hi Hana,could you help me?our works are somehow similiar

ADD REPLYlink written 2.3 years ago by Edalat30

3 samples is just not really enough for the purposes of constructing a network. You would have a difficult time convincing anyone of the results / inferences from the network.

ADD REPLYlink written 11 months ago by Kevin Blighe41k

Could you please you share the link you wanted to post ? Or kind of approach have you undertaken? Thanks

ADD REPLYlink written 11 months ago by IrK20
2
gravatar for geek_y
11 months ago by
geek_y9.4k
Barcelona/CRG/London/Imperial
geek_y9.4k wrote:

Are those LncRNAs are novel and tissue specific ? Its not valid to do a correlation with 3 samples.

If the LncRNAs are not highly tissue specific, you can gather RNA-Seq data from all resources (GEO, GTEx, bodymap etc where the LncRNAs show a minimum of 1 FPKM/RPM expression) and do a pairwise co-expression correlations to find which genes are most correlate with the expression of LncRNA. This will help to prioritize your differentially expressed genes that are regulated by differentially regulated LncRNAs.

P.S: I just realized its very old post :-/ . Still better to leave an answer.

ADD COMMENTlink modified 11 months ago • written 11 months ago by geek_y9.4k

P.S: I just realized its very old post :-/ . Still better to leave an answer.

Caught me out too ;) Upvoted to help others and prevent this question from being 'bumped' again by the Biostars bot.

ADD REPLYlink modified 11 months ago • written 11 months ago by Kevin Blighe41k
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