- Get started!
- Why would I register ?
- Why would I get FireFox today ?
- How can I build my own Series ?
- Is there a way to find a Sample if I don't know the chip name or experiment ?
- What to do with a List ?
- Why is there so many color on my histograms ?
- Can I change my Default Series of Samples ?
- Can I change my Customized Series of Samples ?
|You can use Amazonia! to visualize the expression of thousands of genes in many different human samples collection. |
These expression data have been obtained by microarrays (go here to have more informations on microarrays) and have been put public.
How to start? Easy! Give a keyword (gene name or abbreviation) in the Search a Gene box in the margin . You can also search by probe number, Entrez Gene number or Unigene number by clicking on Advanced Search.
For example, type in GFAP, the abbreviation of Glial fibrillary acidic protein. Press Enter.
|The result page shows you the genes that fit you query. In our example, the gene GFAP was the only match. Note that Amazonia! also looks for aliases.
Click on the gene to see its expression .
|The resulting page comprises:|
A box describing the gene displayed on the page : Aliases are indicated if available. And some links are provided so that you can get more information on this gene: for example links to the Entrez Gene website, the GeneCard website or the iHOP website .
The expression of this gene for all the probes in all the Series of Samples available on the current Thematic Page.
At the time this example was printed, the GFAP gene in this Thematic Page (the General Thematic Page) had two probes (203540_at and 40185_at) in three Series of Samples (Embryonic and adult normal tissues (U133A), ALL and normal hematopoiesis (U133A) and GeneNotes: normal adult tissues (U95Av2)).
For some examples there may be more than ten probes in many Series of Samples.
The expression of GFAP is displayed as an histogram. Click on the histogram to enlarge it . Below the histogram are listed the authors and publication related to the data displayed. Click on the icon to get the color legend . Click here to have more information regarding the colors. And if you click on the icon , you will have the expression values used in the histogram.
You can bookmark any probe by clicking on the icon . Click here to have more information on the bookmarks.
And by clicking on the icon , you will be able to annotate this gene.
|An important feature of Amazonia! is the Thematic Page.
According to your specific interest, you may want to see the expression of you favorite gene in lung cancer samples or stem cell samples.
You can change at will your current thematic page by clicking on Thematic Page on the main bar . The same gene will then be displayed in the Series of Samples corresponding to the Thematic Page.
For example, here is printed a screenshot of GFAP in the Glioma Thematic Page.
Note that a different background color is associated with each Thematic Page.
Note also that the Series of Samples Embryonic and adult normal tissues (U133A) is included on all Thematic Pages and provide a universal virtual northern blot in more than 100 different non malignant samples.
Registering is free and gives you access to customized series of samples, personal gene lists, personal gene annotations and to statistical modules. We will not make any use of the information that is collected apart from building general statistics regarding the use of this web site.
Because many features are only available using FireFox or Others "fully W3C's recommandations compliant" browsers.
And also because FireFox is far more secured than Microsoft Internet Explorer and supports web standards.
Amazonia! has been developped and tested using Open Source softwares and FireFox is one of those projects. Using FireFox you'll be able to use every amazing Amazonia! tools.
So take a look at Amazonia! through FireFox's eyes ... and think about what's best for your computer.
In the menu «Amazonia! tools», go to «My Amazonia!» and then to «My series of samples» (or click directly here). In the section «Customized Series of Samples» in the lower part of the web page, click on «Add a series». You must then select, in the following order:
- an array type, then click «Find Data for this Array»
- an experiment category, then click «Find Data for this Experiment Category»
- an experiment, then click «Find data for these Experiments»
- samples : you can tick any box and/or click on All +/All - .
- type in a name for your customized series of samples
- then click on Remind Selection (BEWARE, AT THIS STEP NEVER PRESS ON THE ENTER BUTTON OF YOUR KEYBOARD: USE YOUR MOUSE INSTEAD).
This series of samples will appear on all your queries.
If you want to build a series of samples that includes your favorite sample, you have to know on what array it was processed and in what experiment category it belongs.
To find this information, you will need a specific query tool located on the page «Amazonia! tools» >> «My Amazonia!» >> «My series of samples» : click on Add a Series and then click on the link Search a Sample (click here to find this page). Type a keyword and you will find the following information: array, protocol, experiment name, sample name for all the samples corresponding to this keyword. This data will help you in the selection process while building your own Series of Samples.
You can find your lists by clicking in the margin in the List box on Show lists.
When you display your lists, you can click on one list name. This gives you four columns:
- the items that made the list (probe name or Entrez Gene number or Unigene number)
- the corresponding probe
- the gene abbreviation
- the gene name
By clicking on the probe you will display the expression of this probe across the Series of Samples of your current Thematic Page. By clicking on the gene abbreviation you will display the expression of this gene for all its probes in all the Series of Samples of your current Thematic Page.
A color code has been assigned to each sample category. For instance, all leukemia samples are reddish, all normal nervous system samples are green, etc. Usually, nonmalignant and malignant samples from a same tissue have a close, but not identical, color. White stands for Not Detected and is only available for Affymetrix arrays. You can find the legend for the color code by clicking on the icon found under each expression histogram.
Each Thematic Page of Amazonia! comes with a list of default Series of Samples. You can change the choice of Series of Samples on the page «Amazonia! tools» >> «My Amazonia!» >> «My series of samples». Tick any box you are interested in, either in the Default Series of Samples or in the Customized Series of Samples, then click on Save this Selection. Beware, if you change your thematic page, this selection will be replaced by the default selection of the thematic page you chose.
You can change the choice of Series of Samples on the page «Amazonia! tools» >> «My Amazonia!» >> «My series of samples». Tick any box you are interested in, either in the Default Series of Samples or in the Customized Series of Samples, then click on Save this Selection. You can add a new Series of Sample by clicking on Add a Series. Click here how to do that.