Re: Dynamic Chromosome Mapping

in reply to Dynamic Chromosome Mapping

Could you provide a bit more information? For example, what kind of data are you using as input for this problem? Are you planning on using raw sequence data and then simulating a Giemsa stain with based on G+C content and other factors? Or are you correlating images of stained chromosomes with sequence or some other kind of data?
To a me, this is a very cool project, I'd definitely like to hear more about it. No matter what sort of data you're using, I would thinkg about using bioperl, as it's very likely that they have a module for doing at least some of what you're interested in. I highly recommend the GD package for this sort of stuff, and the Tisdale articles mentioned above can be relevant if you're manipulating megabases of nucleotide data.

I wish you luck. :)

Comment on Re: Dynamic Chromosome Mapping

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Re: Re: Dynamic Chromosome Mapping by Itatsumaki (Friar) on Nov 12, 2003 at 03:51 UTC
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!	[reply]

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Re: Re: Dynamic Chromosome Mapping
by Itatsumaki (Friar) on Nov 12, 2003 at 03:51 UTC

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!

[reply]

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