Search implementation

Instead of fixed listings for publications containing CGH/aCGH/banding analyses, a search engine for articles has been implemented. Options are:

• Autor names


• words from the title


• techniques


• array parameters for aCGH

Please comment on the features. Future extensions probably will include specific case search based on the pre-selected publications ...

Minor graphics changes

The imbalance histograms have been scaled to increase readability. Also, some broken links have been fixed.

Speed

The active database mining has been sped up (by introducing an indexing system). For registered users, when using:

Tools & Source => Source data selection, download and analysis => Use Progenetix Database

the options for data selection will load almost instantaneously.

Enjoy!

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.