Question: How To Plot Splicing Map
3
gravatar for Curiosity
9.0 years ago by
Curiosity120
Curiosity120 wrote:

I'm aware of density plots around TSS. These are very straight forward. However I am trying to to do the same, by using alternative exons instead of TSS/promoters. It seems very tricky, especially because of variable length of exons. Does any one know how to plot these profiles ?

Ex: http://www.nature.com/nsmb/journal/v17/n7/images_article/nsmb.1838-F4.jpg

• 1.8k views
ADD COMMENTlink written 9.0 years ago by Curiosity120
0
gravatar for seidel
9.0 years ago by
seidel7.1k
United States
seidel7.1k wrote:

Isn't it just like average gene analysis, where the length of the feature doesn't matter because you divide each feature into the same number of bins so that data across a large number of features can be displayed as an average conglomerate? It's like taking column averages of a large table representing the bins of the features (assuming all features have been divided into say 20 bins, regardless of feature size), and plotting that. Have you read the materials and methods of the referenced paper? Don't they say there? (you might mention the author of the paper, or a better way to look it up instead of a deep link to one figure).

ADD COMMENTlink written 9.0 years ago by seidel7.1k

I think it is not like "average gene analysis". Because the intron length is constant but not the exon. Yes there is a brief description available regarding this plotting, i.e. "normalized complexity" which will highlight common features shared by multiple transcripts.

ADD REPLYlink written 9.0 years ago by Curiosity120
0
gravatar for Larry_Parnell
9.0 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

My understanding of such graphs and really the data behind them is the different exon lengths are standardized to a common value while the intronic features are displayed as measured from the respective end of the exon. In other words, all exons (length = n) treated as equal in size and the measures taken within the exon are measured in actual base pairs from either the 5' or 3' end of the respective exon.

So, make all exons oriented from left to right, 5' to 3'[?] All features to the left are measured from base 1 of the 5'end[?] All features to the right are measured from base n of the 3' end[?] Thus, an "upstream" feature is never measured relative to the 3' end and vice versa.

ADD COMMENTlink modified 9.0 years ago • written 9.0 years ago by Larry_Parnell16k

Totally agree. .

ADD REPLYlink written 9.0 years ago by Curiosity120
0
gravatar for polarise
8.2 years ago by
polarise380
Galway, Ireland
polarise380 wrote:

What paper is that? I'm studying AS and that seems to be relevant to my work. Please give me the DOI or reference.

Thanks in advance.

PK

ADD COMMENTlink written 8.2 years ago by polarise380
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1780 users visited in the last hour