Beefy Boxes and Bandwidth Generously Provided by pair Networks
XP is just a number
 
PerlMonks  

comment on

( #3333=superdoc: print w/replies, xml ) Need Help??

Sure, here's some more info on it. A variety of different factors have been shown to display chromosomal dependencies in the last few years. For instance, there is a profound chromosomal dependence of gene-expression, a strong tendency towards co-expression of neighbouring genes, chromosome-wide patterns in mutation rates (SNPs), and of course in GC content (e.g. isochores).

There are a variety of different ways to slice these things up statistically and experimentally, but it seems to me that the most evident display technique for any of these is just to show a chromosome, along with some colour coding to indicates regions where this phenomenon occur together, or... don't. You can imagine a figure showing the 20+ chromosomes with their particular data sets....

So, the underlying colour coding will be variable. My first pass attempt is just to colour according to cytogenic bands. So, just as that link I gave showed a physical chromosome (that's Rat-1, I think), I would show that. Then, as a first attempt I would colour different bands differently according to, say, how many SNPs they had in them.

It would be a highly intuitive display technique for all biologists, and if I can code it reasonably well, it should be flexible enough to be extended easily to any data set.

I don't believe there is anything in BioPerl to deal with chromosomes, but I'll post to that list and see what they say.

Thanks for the interest!


In reply to Re: Re: Dynamic Chromosome Mapping by Itatsumaki
in thread Dynamic Chromosome Mapping by Itatsumaki

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post; it's "PerlMonks-approved HTML":



  • Are you posting in the right place? Check out Where do I post X? to know for sure.
  • Posts may use any of the Perl Monks Approved HTML tags. Currently these include the following:
    <code> <a> <b> <big> <blockquote> <br /> <dd> <dl> <dt> <em> <font> <h1> <h2> <h3> <h4> <h5> <h6> <hr /> <i> <li> <nbsp> <ol> <p> <small> <strike> <strong> <sub> <sup> <table> <td> <th> <tr> <tt> <u> <ul>
  • Snippets of code should be wrapped in <code> tags not <pre> tags. In fact, <pre> tags should generally be avoided. If they must be used, extreme care should be taken to ensure that their contents do not have long lines (<70 chars), in order to prevent horizontal scrolling (and possible janitor intervention).
  • Want more info? How to link or How to display code and escape characters are good places to start.
Log In?
Username:
Password:

What's my password?
Create A New User
Domain Nodelet?
Chatterbox?
and the web crawler heard nothing...

How do I use this? | Other CB clients
Other Users?
Others making s'mores by the fire in the courtyard of the Monastery: (5)
As of 2023-02-08 04:24 GMT
Sections?
Information?
Find Nodes?
Leftovers?
    Voting Booth?
    I prefer not to run the latest version of Perl because:







    Results (40 votes). Check out past polls.

    Notices?