Question: Plotting Exons Of A Transcript Using Bioconductor Genomegraphs
gravatar for Tonig
6.8 years ago by
Tonig420 wrote:

Hi, I was looking the list but there was no response to my questions: How do I plot the exons of a specific transcript of my gene in question using Bioconductor Genographs package?


mart <- useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl")

#getting the gene

gene <- makeGene(id = "ENSG00000171988",type = "ensembl_gene_id", biomart = mart)

I know to plot the gene, but how can i do to plot an specific transcript, let's say ENST00000399262 in order to view the exons?

Thanks in advance

ADD COMMENTlink modified 2.8 years ago by Biostar ♦♦ 20 • written 6.8 years ago by Tonig420
gravatar for Malachi Griffith
6.8 years ago by
Washington University School of Medicine, St. Louis, USA
Malachi Griffith17k wrote:

In addition to the reference manual, the user guide / vignette offers some nice tips. I was curious what the result would look like for the answer provided by @Michael. For anyone else interested, this script (GenomeGraphsExample.R) contains a complete example and creates the images shown below. I generated @Michael's two examples and an additional one with more annotation of a gene locus and its alternative transcripts.

Figure 1. All exons of the gene, followed by a specified transcript

alt text

Figure 2. All exons of the gene, followed by all transcripts

alt text

Figure 3. A different gene. This time the chromosome ideogram is included, the gene region is highlighted in red, the gene and transcript structures are displayed, exon 2 is highlighted, a main title is added, each track is labeled individually, and the transcript IDs are provided. alt text

ADD COMMENTlink written 6.8 years ago by Malachi Griffith17k
gravatar for Michael Dondrup
6.8 years ago by
Bergen, Norway
Michael Dondrup45k wrote:

Have a look at section 2.2 of the manual:

2.2 Adding alternative transcripts To add alternative transcripts you rst have to create a Transcript object. Note that the order of the objects in the list determines the order in the plot.

> transcript <- makeTranscript(id = "ENSG00000095203", type="ensembl_gene_id", biomart = mart)
> gdPlot(list(gene, transcript))

This works with the example gene ids but needs a change with your transcript id. To use your transript id you have to change type to "ensemble_transcript_id" like so:

mart <- useMart("ensembl", dataset="hsapiens_gene_ensembl")
gene <- makeGene(id = "ENSG00000171988",type = "ensembl_gene_id", biomart = mart)
transcript <- makeTranscript(id = "ENST00000399262", type="ensembl_transcript_id", biomart = mart)
gdPlot(list(gene, transcript))
ADD COMMENTlink written 6.8 years ago by Michael Dondrup45k
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