I have copy number data. I'm interested in measuring chromosomal instability of a specific gene computational way. Are there any tools or packages to measure the chromosomal instability? tools and packages are really required for this?
Can anyone help me out how to check the chromosomal instability of a particular gene. thank you in advance.
Can anyone help me out how to check the chromosomal instability of a particular gene.
This statement does not make sense due to the fact that chromosomal instability is a general term that has no defined criteria.
A gene may exhibit deletion or some other copy number or structural variant, which could be reflective of widespread chromosomal instability. In this case, you need to determine the copy number profile across your gene.
Also look up CIN signature genes, which are genes the mutations in which can result in chromosomal instability.
Kevin
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The specific gene I'm interested in is
CENPH. For chromosomal instability Do you think the following way is right? I have the gistic2 thresholded gene level Copy number data.Classifying samples into
CENPHhigh andCENPHlow groups. And then checking the % of genes which are not 0.Do you think this is the right way?
Seems like an interesting gene that is very much involved in chromosomal maintenance during mitosis. I cannot comment on whether your approach is right or wrong - if the results come back interesting, then it is right :)
I have the FPKM expression of that gene with 370 samples. How to classify them into high and low groups?
Use zFPKM package to convert the FPKM values to Z-scores, and then use Z > 3 as
highand Z < -3 aslow. You can deviate slightly from these cut-offs. For example, Z = 2 still equates to p<0.05. Z=1 does not.Edit: Z-score is 'number of standard deviations from the mean'
Yes sure. Thanks a lot. And Z > +/- 1.96 (roughly p=0.05 or 2 SD away)