Hello everyone,
In all theses methods like 3C, 4C, 5C, (Hi-C) what are the relative difference of contact frequency between intra chromosomal interaction and inter chromosomal interaction. Can we put same cutoff for both inter and intra to identify as true interaction between locus i and j.
Suppose my Hi-C data is normalized then what cutoff should we put to consider as genuine interaction between locus i and j.
When should we consider two locus are in the interaction or two locus are making a loop. Both have the same meaning or its different?
Intrachromosomal asymmetry, one of the two aspects of karyotype asymmetry, increases because of shifts of the centromere position from the median/submedian to terminal or subterminal. Conventional measures of asymmetry use comparisons with the most symmetrical karyotype and thus are an absolute measure of variation in the centromeric index. The MCA (Mean Centromeric Asymmetry) value is perfectly suited for the measure of intrachromosomal asymmetry (Peruzzi and Eroğlu 2013).
Concerning the measure of interchromosomal asymmetry,
the main point is to measure how much the chromosome lengths of a complement are different each other, and CVCL (Paszko 2006) is perfectly suited for it.
Thanks for your answer. You have given the answer in terms of karyotyping. I wanted to know in terms of contact frequency between the loci of intra and inter chromosome.
You shall find lot of information online. It is difficult to explain in few sentence here.
Genetics. 2008 Jan; 178(1): 99–112
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