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Before logging in to the caArray application, please download the sample array design file Image_Hu6800.zip, and the sample experiment data file Image_caArrayCaArray_golub-00095_files.zip, if you have not already done so. You may unzip the design file to get Hu6800.cdf, but do not extract the sample data file caArray_golub-00095_files.zip.

Step 1: Design File Upload

Step 1.1.

Log into the caArray Application. Click on the "MANAGE ARRAY DESIGNS" button under "CURATION" on the right left side of the Welcome page.

A new windowpage, "Manage Array Designs", opens. Before uploading the design file, check if your application already has a copy of the design file by the same name. If yes, skip the design file upload and proceed to #Step 2 Experiment Data File Upload. You can use this design file for your experiment. If not, follow Step 1.2 to upload a new design file.

caArray Data Portal Welcome Page
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Manage Array Designs Page
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Steps 1.2

On the "Manage Array Designs" page, Click click the "Import a New Array Design" button, see Fig.1.1. Another page, "New Array Design (Step 1)", opens, see Fig. 1.3. Fill out the "New Array Design" form with the information shown in Fig.1.3Description (Affymetrix Hu6800 Sample Arrya Design in the example); Selected Assay Type (Gene Expression is selected in the example); Provider (here Affymetrix); Version number (here 1.0); Feature Type (in_situ_oligo_features (MO) in the example); and Organism (Homo sapiens (ncbitax) in the example). Then click "Next".

Manage Array Designs Page with Import a New Array Design Button
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New Array Design (Step 1) Page with Form Completed
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Step 1.3

The page "New Array Design (Step 2)" opens. Click the "Browse" button. Browse to the location where the sample array design file (Hu6800.cdf) was unzipped. Then click "Save". See Fig 1.4 and Fig 1.5.Image Removed - 4
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New Array Design (Step 2) Page with Browse Button
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New Array Design (Step 2) Page with Save Button
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Step 1.4

On clicking the "Save" button, the screen shown in Fig 1.6 openswindow opens with a message to confirm the file has been uploaded. Click "Close window and go to Manage Array Designs". The "Manage Array Designs" re-opens, as shown in Fig 1.1b (c)listing the newly uploaded file. (Please note that for large array design files, the importing process might take a while. An array design can only be used when it is fully imported.)Image Removed - 6
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Window with Message Confirming Upload of Hu8800 File
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Manage Array Designs Page Listing the Uploaded Hu8800 File
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Step 2

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Experiment Data File Upload for Creating an Experiment Automatically

Step 2.1

Click the "CREATE/PROPOSE EXPERIMENT" button under "EXPERIMENT MANAGEMENT" on the left side menu bar of the Welcome page. The "Overall Experiment Characteristics" screen opens. See Fig 2.2.Image Removed - 1
!800px-Fig2.2.png|alt="screenshot representing the step"1 - 2window of the Experiment Details page opens.

Welcome Page with CREATE/PROPOSE EXPERIMENT Button Selected
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Overall Experiment Characteristics Window with Completed Form
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Step 2.2

Fill out the form with the information shown in Fig 2.2the Experiment Type (Diffuse large B-cell lymphoma outcome prediction in the example); Experiment Description; Selected Assay Type (here Gene Expression selected); Provider (here Affymetrix); Array Designs (here Hu8800 selected in the example); and Organisim (Homo Sapiens ncibtax in the example). You can use your own description or use the sample text displayed below. Make sure the "Array Designs" field is selected with the right platform (here Hu8800, highlighted in blue). Click the "Save" button.

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Description: Diffuse large B-cell lymphoma (DLBCL), the most common lymphoid malignancy in adults, is curable in less than 50% of patients. Prognostic models based on pre-treatment characteristics, such as the International Prognostic Index (IPI), are currently used to predict outcome in DLBCL. However, clinical outcome models identify neither the molecular basis of clinical heterogeneity, nor specific therapeutic targets. We analyzed the expression of 6,817 genes in diagnostic tumor specimens from DLBCL patients who received cyclophosphamide, adriamycin, vincristine and prednisone (CHOP)-based chemotherapy, and applied a supervised learning prediction method to identify cured versus fatal or refractory disease. The algorithm classified two categories of patients with very different five-year overall survival rates (70% versus 12%). The model also effectively delineated patients within specific IPI risk categories who were likely to be cured or to die of their disease. Genes implicated in DLBCL outcome included some that regulate responses to B-cell-receptor signaling, critical serine/threonine phosphorylation pathways and apoptosis. Our data indicate that supervised learning classification techniques can predict outcome in DLBCL and identify rational targets for intervention. **NOTE: Migrated from caArray 1.x, identifier='gov.nih.nci.ncicb.caarray:Experiment:1015897558868337:1'.

Step 2.3

The screen shown in Fig 2.3 Experiment Details page opens. Check for the "Experiment has been successfully saved" message. Click the "Contacts" tab. Fill the form with your information. You can also edit the contact information from the screen shown in Fig 2.4.!800px-Fig2.3.png|alt="screenshot representing the step"
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Experiment Details Page with Message Confirming the Experiment has been Saved
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Experiment Details Page Showing Contact Information and Buttons to Add or Edit
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Step 2.4

Click the "Data" tab. Then Click the "Upload New File(s)" button, see Fig 2.5. A new popup window, . The "Experiment Data Upload" window opens, see Fig 2.6.!800px-Fig2.5.png|alt="screenshot representing the step" - 5
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Experiment Details Page Data Tab with Upload New File(s) Button Selected
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Experiment Data Upload Window with Browse and Upload Buttons
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Step 2.5

Browse In the Experiment Data Upload Window, browse to the location where the sample experiment Data file (caArray_golub-00095_files.zip) was saved and click on the "Upload" button, see Fig 2.6.*

Step 2.6

Wait until the window message "Your file upload is complete" is displayed. Click "OK" (Fig 2.7). Then click the "Close Window and go to Experiment Data" button as shown in Fig 2.7.!Fig2.7.png|alt="screenshot representing the step" - 7.

Message Showing the File Upload is Complete with Close Window Button Selected
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Step 2.7

On the main window shown below (Fig2.8)Data tab of the Experiment window, make sure the column "STATUS" displays the word "Uploaded" for each file. Select the check boxes for all experiment data sets and then click on the "Import" button. A new window "Import Options" opens (Fig2. 9). Select the first option, "Autocreate annotation sets...", ; then click on the "Import" button.!630px-Fig2.8.png|alt="screenshot representing the step" - 8
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Data Tab of Experiment Window with Status Displaying "Uploaded" and Files Selected for Import
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Import Options Window with First Option and Import Button Selected
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Step 2.8

Depending on the speed of the machine and the size of the data, it may take a few minutes for the sample data to be imported. Check the status of the import by Clicking on clicking the "Refresh Status" button (Fig2. 10). The initial status will be is shown as "In queue" (Fig2. 10). When the import is complete, no data will be displayed under the "Manage Data" tab (Fig2.11). Click on the "Imported Data" tab to view imported data file (Fig2.12). If you have completed all these steps, Congratulations! You have just successfully created an experiment and deposited your microarray experiment data into the caArray.

Data Tab of Experiment Window with Refresh Status Button
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Manage Data Tab Showing No Data to Display
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Imported Data Tab Showing the Imported Data File
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Step 2.9

;<font size="3" >'''Step2.9. </font> To make the experiment data public so people other than you others can view your data, click on the "My Experiment Workspace" button (Fig2.13). Locate the experiment of interest on the "My experiment Workspace" page. Click on the "Permissions" icon (Fig2.13), the . The "Experiment Permissions" page will appear (Fig2.14)opens. Click on the "Edit Access Control" button in the left panel. <gallery widths=450px heights=150px perrow=2">
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Fig2.13.png| Fig. 2.13 Click on the picture to enlarge
Image:Fig2.16.png| Fig. 2.14 Click on the picture to enlarge
</gallery>
 

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My Experiment Workspace Page with Permissions Button
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Experiment Permissions Page with Edit Access Control Button Selected
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Step 2.10

In the access control window, select "Read" from the drop down list

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. Then click the "Save" button

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Your experiment is now set to be

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accessible by the pubic

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Access Control Window with Read Selected and Save Button
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Experiment Permissions Window Showing the Public has Read Access
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Step 3

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<font size="4" ><div align="Left">*Step 3

Verification of Data Sharing on caGrid

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For those Institutions that register their caArray instance on caGrid, the public data is available to other integrated tools that use the caGrid service. To verify whether your caArray data is shared on caGrid, go to CaArray071 and follow the instructions.</html>

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