Gene expression on same Chromosome region possible? - microarray (Sep/02/2006 )
Hi!
I was looking at the expression of a particular gene in 4 independent microarray studies and I wanted to find out what were the genes that had a similar pattern of expression (strong correlation). I got 16 genes that strongly correlated and 10 of them are on the same chromosome locus.
What does this mean? Can it be that this region is amplified or deleted and all the genes in this region are expressed under a same regulation mechanism??
Could someone help me interpret this!?
they could be related in function
this happens often; genes that are related will be 'grouped' and will share transcriptional regulation. consider the redunancy in many systems, inflammatory response is a good example...if exposed to something like endotoxin, you'll get many inflammatory genes upregulated simultaneously, because more than one gene will be involved in the response. do you see? and upregulation at the same time does not always mean by the same mechanism (although it is possible).
is aCGH (array comparative genomic hybridisation) an option for you? - yep, chunks of the chromosome can be duplicated and the genes inside may be upregulated (depending on where the duplicated chunk has inserted)......
- this technique will help you see it.
Alternatively, you could do some FISH with a BAC clone corresponding to your region of interest.
good luck
- this technique will help you see it.
Alternatively, you could do some FISH with a BAC clone corresponding to your region of interest.
I don't think array CGH or BAC FISH work will help here. Upregulation of several specific genes on the same chromosome doesn't necessarily corespond to duplication of that material. If the (10) genes at the same locus (does this mean 10 contiguous genes?) are in no way related then this might suggest a duplication however. BAC FISH on metaphase chromosomes will be difficult to see unless the duplication is at least a few Mb although smaller duplications can be visible in interphase cells. Array CGH will allow higher resolution.