2008-04-02

ProgenetiXML format enhancement: Golden Path

I have updated the ProgenetiXML format. The main improvement is the addition of a Golden Path aberration annotation:

<GPANNOTATION>chr7:0-158628139:1::chr8:0-146274826:1::chr10:70300000-135413628:-1::chr12:0-132449811:1::chr13:16000000-114142980:-1</GPANNOTATION>

The GP-annotation represents a transcription of the chromosomal band status. For data derived from aCGH experiments, this may lead to an expansion of imbalances, since originally every band containing a full or partial gain/loss is considered as imbalanced. This may be changed in the future, with direct usage of the original GP array data, where available.

Additional changes:

  • removal of extraneous XML tags, for the cases lacking data in those entries

  • addition of a full data matrix (862 bands status and all annotations) as download option prior to visualization


Enjoy,

Michael.