Gene-level annotation track (Gene CNVs)
If you have specified a gene track in the input parameters, you will get a gene-level CNV track as well. The gene-level CNV track is an annotation track, which is obtained by intersecting the region-level CNV track with the gene track in the input (ignoring any genes that do not overlap with the targets). Note that a single CNV may be reported several times in different genes, and a single gene may also be reported several times, if it is affected by more than one CNV. In addition to the annotations on the gene track supplied in the input parameters, the gene-level CNV track contains the following annotation columns:- Region length:
- The length of the actual annotation. That is, the length of the CNV region intersected with the gene.
- CNV region:
- The entire CNV region affecting this gene (and possibly other genes).
- CNV region length:
- The length of the entire CNV region affecting this gene (and possibly other genes).
- Consequence:
- The consequence classifies statistically significant CNVs as "Gain" or "Loss".
- Fold-change (adjusted):
- The adjusted fold-change of the entire CNV region affecting this gene (and possibly other genes).
- P-value:
- The p-value of the entire CNV region affecting this gene (and possibly other genes).
- Number of targets:
- The total number of targets forming the entire CNV region affecting this gene (and possibly other genes).
- Comments:
- If the CNV region affecting this gene had any comments (as described in section 19.11.2), this will be present in the gene-level results as well.
- Targets:
- A list of the names of the targets forming the (minimal) CNV region forming the entire CNV region affecting this gene (and possibly other genes). Note however that the list is truncated to 100 characters. If you want to know the full list of targets inside the CNV region, you can use the target-level output track.