End of progenetix@googlegroups

We have closed down progenetix.googlegroups.com due to spamming/maintenance issues. The site has now a locally hosted WiKi which currently only allows posts by administrators; so please email me directly with issues.

One FISH, two FISH, red FISH, blue FISH ...

... is:

A) the title of one of the "Dr. Seuss" books (you would know if you have lived with children in pre-school age in the U.S.)
B) an editorial aricle by Michelle LeBeau

To not stick too much to the green=gain | red=loss color scheme (compared to the strange but widely used red=high expression etc. scheme of the expression array community), today two radical changes took place:

1. yellow is the new green, blue is the new red (therefore accommodating people with color recognition problems, though we already did refrain from pure red/green ...)
2. ideograms are plotted by new routines, implemented in R: larger chromosomes, better level lines, PNG + PDF vector graphics (after the links); however, no single band links to USCC anymore (you either know how to get there, or you want a data analysis collaboration).

Enjoy,

Michael.

The end of our metaphase banding data ...

Today we have published an update to the Progenetix database, which does not contain any data from metaphase analyses. However, we will keep the publication data online (e.g. mostly Mitelman references, with some updates/addtl. information). Users interested in mining data from banding analyses may contact me directly.

Overall, this reduces the total number of cases slightly, to now 21436 (18291 CGH, 3217 aCGH) from 763 chromosomal and array CGH publications.

Article access

For all people with database registration, access to all the PDFs (>1500) has been enabled. Authentication is required, and this is considered as personal information sharing among collaborators ...

GEO data sets

We have started to re-evaluate public aCGH data sets, available as raw or Log2 data from NCBI's GEO. Since the data there exists in a heterogeneous (MIAME-compatible) mess of data formats, GEO data will be made accessible either as locus-mapped (normalized) probe data, or as segmentation output files. For a start, we have posted some data sets from Affymetrix genome array experiments, for which the raw data was re-analyzed using the aroma.affymetrix package with custom plotting routines. Please browse the aCGH publications for the corresponding icon.

Progenetix@GoogleGroups

I have created a group site at GoogleGroups:

http://groups.google.com/group/progenetix/

Comments, site updates etc. will now be discussed there; please subscribe!

And the current tally is:

• 21256 cases from 777 publications


• 17409 CGH


• 2674 array CGH

Mitelman database publication update

As reference for tumor karyotype analyses using traditional cytogenetic techniques, the literature database has been updated with the current content of the Mitelman database. The listing references now to 3207 publications from that source, representing 58197 cases. The vast majority of these cases are not included in the Progenetix database, but can be visualized through the article links.

Change in ProgenetiXML format

For more flexible analysis options, the ProgenetiXML format now has separate fields for the Golden Path mapped status information for CGH, aCGH and banding data.

> 20,000 individual oncogenomic profiles

By incorporation of some large aCGH studies, today the Progenetix database jumped the 20k mark and contains now 20122 cases from 682 publications:

• 17154 of 31614 found CGH experiments


• 1926 of 10814 found aCGH experiments


• 1787 metaphase banding data sets

Again, above numbers include some overlaps.

19013 cases ...

The database has reached >19000 cases today:

• 16542 CGH


• 1503 aCGH


• 1757 banding/MFISH/SKY (mostly cell lines)

Also, the website tools (e.g. aCGH to ProgenetiXML) have seen some overhaul, making them more robust and introducing new features (high-resolution ideograms, segments file input etc.).

Enjoy!

Improved search options

Search options have been improved, with free text search now used in "Search Entities, Loci and Analysis Groups". As example:

lymphoma, NHL, lymph node, leukemia, hemato

will return all ICD entities, ICD loci and analysis groups with one of the comma-separated values in the title. From here, you can display each single subset by clicking on the ideogram button, or select several of the subsets for further filtering & analysis (registered users only).

Jumping 18k

Thanks to some data submissions, and notably today's articles from Itziar Salaverria Frigola (lab of Elias Campo), Progenetix has finally jumped the 18000 cases mark. The lack of ost of the array CGH data is still somewhat puzzling; either case specific data is not shown at all, or "raw data" is dumped in GEO | ArrayExpress | SMD - where nobody but groups with dedicated bioinformaticians will get it out. Probably, I will have to work on that ...

Enjoy the data, especially the expanded new B-NHL content!

Search update

The future is here (according to last post): For registered users, the pre selected publications can now be used to further limit the selection & analyze the cases ...

Feedback, please.

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.

improved color scheme

since pure red-green works bad for some people, the histo and ideogram colors have been slightly changed (yellowish red, blueish green). i am happy about further suggestions!

new server

sometime late january, the site has been moved to a new server (Mac Pro, Dual 2.8GHz, 8GB RAM). this should make the site more user-friendly ...

but: do not use deep links or bookmarks - stick to www.progenetix.net!

and, please, do report problems.

ISCN parser modifications

Thanks to a review of selected cases by Turid Knutsen, a number of changes have been implemented in the karyotype parser portion of the ISCN2matrix engine. This concerns mostly the handling of ambiguous annotations, but also some previous omissions of specific patterns.

The changes are active in the online parser, and will be propagated to the data set soon.