How to make circos plot in R for miRNA and target genes retrieved from targetscan?

Question

[Björn]

How to make circos plot in R for miRNA and target genes retrieved from targetscan ?

Out of many genes, is there a way to filter out only significant target genes. I believe there must be a scientific reasoning for it.

Any hands-on tutorial documents or reference would be appreciated.

[Sej Modha]

Circlize would be suitable for this, extensive documentation available on https://jokergoo.github.io/circlize_book/book/introduction.html#principle-of-design

[Björn]

Hi Sej, Thanks for your comment. Can you suggest me the input data to create such plots Thanks in advance

[Sej Modha]

I would like to prepare a plot similar to Figure 2-Circos plot between the three predicted miRNAs and their targets. of this paper doi: 10.1016/j.gdata.2015.09.005 paper I have 10 miRNAs and respective predictive genes from TargetScan. What are the input data to create circos plots. e.g. hsa-miR-27b-5p, and hsa-let-7f-5p Thanks

I think you should try to recreate the figure 2 using Circlize package. It is often the best way to get started and familiarise yourself with a new package.

[Bastien Hervé]

I know RCircos package, which works pretty well. I use it to display double stranded breaks events. Could you develop what you want to achieve and what are your data please ?

[Björn]

I would like to prepare a plot similar to Figure 2-Circos plot between the three predicted miRNAs and their targets. of this paper doi: 10.1016/j.gdata.2015.09.005 paper I have 10 miRNAs and respective predictive genes from TargetScan. What are the input data to create circos plots. e.g. hsa-miR-27b-5p, and hsa-let-7f-5p Thanks

Answer 1

[Bastien Hervé]

You'll have to create a custom circos plot background (in my example GRCm38.cyto) using the length of the miRNAs and predictive genes. Then create a matrix with name_miRNA/start_miRNA/end_miRNA/name_gene/start_gene/end_gene (in my example my_data).

I let you an example with my_data:

Rname   Rstart  Rend    B_Rname B_Rstart    B_Rend
chr12   117525571   117525854   chr6    70844502    70844520
chr6    70769437    70769572    chr6    70844502    70844517
chr6    73225769    73226060    chr6    70844502    70844536
chr7    87284448    87284477    chr6    70844502    70844563

---

library(RCircos)
data(UCSC.Mouse.GRCm38.CytoBandIdeogram)
GRCm38.cyto <- UCSC.Mouse.GRCm38.CytoBandIdeogram
RCircos.Set.Core.Componentscyto.info=GRCm38.cyto, chr.exclude=NULL, tracks.inside=3, tracks.outside=0)
RCircos.Set.Plot.Area()
RCircos.Chromosome.Ideogram.Plot();
RCircos.Link.Plot(link.data=my_data, track.num=2, by.chromosome=TRUE);

Answer 2

[Tm]

You can use expectation value <=3 to obtain significant miRNA/target pair from psRNAtarget result.

Here, Maximum expectation as explained in psRNAtarget help is as follows:

Expectation value is the penalty for the mismatches between mature small RNA and the target sequence. A higher value indicates less similarity (and possibility) between small RNA and the target candidate. The default penalty rule is set up by the scoring schema. Maximum expectation is the cutoff; any small RNA-target pair with an expectation less than the cutoff will be discarded in the final result. The recommended values are 3.0-5.0 depending on the scoring schema.

And why you are not using Circos tool for representing miRNA and its target? The publication which you have referred, there also they have used circos tool for its representation.

[Björn]

@toralmanvar, My question was about input data required for such Circos graph. I have lists of miRNAs and target genes from target scan. Now, what additional data do I need before I proceed. Thanks