Here, you will find help relating to the annmap website, and some areas of the tools which work directly with it
If your issue is with a local install of the database, or the various R packages, and the documentation supplied with them does not help (usually found in a README.TXT file that came with the download), please consider using the Bioconductor mailing lists, where you should get help with a fairly fast turnaround.
Frequently Asked Questions
- What resolution is the map in?
- What do the vertical lines represent on the map?
- What browsers does this work on?
- What is meant by "exonic", "intronic", "intergenic", and "unreliable"?
- What do you mean by "Symbol"?
- How do I link to a particular location?
- What does this icon mean?
- The BACK button on my browser doesn't work!
- What is the difference between "All Transcript probesets" and "Transcript sequence probesets"?
- Do I have to install a local copy of the database to run the exonmap package?
- Why do some of the exons have white or unfilled regions?
- Some probesets seem to have identical Probes. Is this right?
- Where is Version X of Ensembl?
- Why are the probe sequences different from NetAffx?
- This doesn't answer my question!
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:
Link to start on the mouse genome at zoom level 15 (once zoomed out from the maximum)
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 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.