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When you zoom into the map as far as possible, each horizontal pixel represents 25 base pairs

A vertical line on the map means that at least one Exon probe hits the genome within that 25 base region. If the line is coloured green, then at least one of those probes hits no where else on the entire genome (ie: it is unique to this location)

The annmap website has been tested on the following browsers/systems and found to work:

• Linux (RedHat) / Firefox 3+
• Linux (RedHat) / Opera 9

• Windows 2000 / Internet Explorer 6
• Windows XP / Firefox 2.0
• Windows XP / Internet Explorer 6
• Windows XP / Internet Explorer 7
• Windows XP / Internet Explorer 8

• Mac OSX 10.5 / Firefox 3+
• Mac OSX 10.5 / Safari 4+
• Mac OSX 10.4 / Opera 9

The following browsers do not work

• Linux / Konqueror 3.3

We hope to have a system in place to test more browser/OS combinations in the not too distant future. If you have a different system, and find that the site works (or doesn't), please email Tim Yates (tyates at picr dot man dot ac dot uk) and we will get it added to the list.

If all of the probes of a probeset hit the genome a single time, and each of those hits aligns with an exon, then a probeset is marked as being Exonic

If one or more of those probes misses an exon, and hits an intronic region, the whole set is marked as Intronic

Or, if one or more of those probes hits an intergenic region, then the whole set is marked as Intergenic

Probesets where one or more probes hit multiple locations, or one or more probes miss mapping to the genome at all, are marked as Unreliable

Symbol refers to the main name given to a gene by the specified external database.

You can append parameters to the URL to set where the view starts at (It defaults to human at the maximum zoom level of 16). Here are a couple of examples to get you going:

http://annmap.picr.man.ac.uk/?s=mus_musculus&z=15
Link to start on the mouse genome at zoom level 15 (once zoomed out from the maximum)

http://annmap.picr.man.ac.uk/?s=homo_sapiens&q=tp53
Link to start on the human genome and perform a search for TP53

If you get the browser to a position you want to show someone else, then clicking on the "link to this page" link at the top of the screen will give you a URL to copy and paste

Here is a list of all the icons, and what they mean:

A Gene,	A Transcript,	An Exon,
An Affymetrix™ Probeset,	A Probe,	A Probe-Hit location,
A Protein,	A Domain,
An EST Gene,	An EST Transcript,	An EST Exon,
A Prediction Transcript,	A Prediction Exon,
An Exonic Probeset,	An Intronic Probeset,	An Intergenic Probeset,
An "unreliable" Probeset,	← / →   These show directionality

This is, unfortunately, currently true. I am working on a solution, but it is not a simple matter due to the complex nature of the site...

• All Transcript probesets is simply a list of all of the probesets that hit within the genomic range of the transcript.
• Transcript sequence probesets are those probesets which hit the CDNA (or ncRNA) sequence for the probeset. This will therefore include probes which for example hit exon boundary locations.

This site relies heavily on javascript to fetch the data from the server. When the site gets an update with new functionality, your browser (or in some examples, a proxy in your IT department) can cache this javascript so that it will fail to work correctly.

This can often be corrected by clearing your browser's cache (holding SHIFT while clicking reload is a quick way of doing this).

Unfortunately, yes. This server doesn't have the power we think would be required to serve the world's exonmap needs, in the future this may change, but for now you will need to install a local copy of Ensembl and the matching annmap data if you wish to use the exonmap package.

These are the UTRs

Yes. On the Exon arrays, some probesets do have probes with the exact same sequence as is in a different probeset. In every example we have looked at, these probes are at a different location on the chip, but they just have the same sequence. Why this is, we are not sure...

Unfortunately due to the amount of resources it takes to build annmap, we are currently only producing mappings for the odd numbered* versions of Ensembl (* due to issues with v49 of the database, we have -- since v50 switched to the even releases). Usually it takes a couple of weeks from the Ensembl release date for us to get our data and images generated, and all our systems updated to the new version. We always update the News page (and the RSS feed on that page) when a new release is out

Due to the complexities of the chemistry involved in Exon arrays, and the differences to this chemistry from the older Expression Arrays, the probe sequences will differ between annmap and NetAffx. NetAffx shows probe sequences as if all arrays used the Expression Array chemistry. Annmap shows the sequence that a probe is targetting. Neither annmap or NetAffx show the actual physical sequence for the probe on the physical Array. If this is required, it can be found in the relevant probe definition file, downloadable from Affymetrix

Firstly, sorry. It's hard to think of all the questions people may have beforehand. If you send an email to Tim Yates (tyates at picr dot man dot ac dot uk), we'll try to get an answer back to you as soon as we can.