# Which gene I should select from this qqplot [closed]

I have a qqplot of my whole genome sequencing data; A plot is for showing possibly significant driver genes. I tried to read about qqplot though but people only say about the skewedness while I want to know from these two genes which one are more likely to be driver

Given that TP53 is the most significant and is already known to have driver mutations in cancer it would seem to be the logical choice.

• Thank you, does that mean I must ignore MAP1S as a candidate even though it has significant p-value but non-significant q-value? Feb 18 '19 at 14:57
• Nothing I wrote suggests that you must ignore MAP1S, your question indicated you only wanted a single candidate. If you're fine with more then take more. Feb 18 '19 at 14:59

You can't know which is the driver and which is the carrier. At most you can say that a specific gene deviate more of the expected underlying hypothesis. See also other resources online.

You also seem to ignore other genes that deviate more of your null hypothesis. I recommend to plot the histogram of the p-values to see if the distribution is uniform

• I think it's pretty clear from the QQ-plot that these p-values are uniformly distributed (except for the twenty or so in the tail of the distribution)? Feb 20 '19 at 15:34
• @winni2k Usually the QQ-plot is centered around 0 (if using qqnorm), in this plot it is not centred, also a expected and observed pvalue above 1 indicates that this is not a normal QQ-plot. That's why I recommended the histogram.
– llrs
Feb 20 '19 at 16:01
• Ah! I see. I think the x and y-axes must be -log10(p-value) as shown for example here, and not quantiles as would be reported by qqnorm. #missingaxislabels Feb 20 '19 at 16:57

This looks to be a pretty good Q-Q plot. My recollection of doing Q-Q plots is that a good Q-Q requires a "more or less" linear relationship for the model to be considered okay. Again this model looks good, its 1:1, albeit it does deviate a little (for the gene of interest). TP15 falls outside the 1:1.

@Devon Ryan states TP15 has good biological credentials, which is clearly important. It maybe worth checking MAP15 because this is "more or less" within your model (for my Q-Q plots definitely within the model :-) ).

In summary, its just my opinion - that on the basis of the Q-Q plot the driver is the not the expected candidate.